Michael Greicius, MD, MPH

All Publications

• Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer's disease. Nature genetics Western, D., Timsina, J., Wang, L., Wang, C., Yang, C., Phillips, B., Wang, Y., Liu, M., Ali, M., Beric, A., Gorijala, P., Kohlfeld, P., Budde, J., Levey, A. I., Morris, J. C., Perrin, R. J., Ruiz, A., Marquié, M., Boada, M., de Rojas, I., Rutledge, J., Oh, H., Wilson, E. N., Le Guen, Y., Reus, L. M., Tijms, B., Visser, P. J., van der Lee, S. J., Pijnenburg, Y. A., Teunissen, C. E., Del Campo Milan, M., Alvarez, I., Aguilar, M., Greicius, M. D., Pastor, P., Pulford, D. J., Ibanez, L., Wyss-Coray, T., Sung, Y. J., Cruchaga, C. 2024

  Abstract

  The integration of quantitative trait loci (QTLs) with disease genome-wide association studies (GWASs) has proven successful in prioritizing candidate genes at disease-associated loci. QTL mapping has been focused on multi-tissue expression QTLs or plasma protein QTLs (pQTLs). We generated a cerebrospinal fluid (CSF) pQTL atlas by measuring 6,361 proteins in 3,506 samples. We identified 3,885 associations for 1,883 proteins, including 2,885 new pQTLs, demonstrating unique genetic regulation in CSF. We identified CSF-enriched pleiotropic regions on chromosome (chr)3q28 near OSTN and chr19q13.32 near APOE that were enriched for neuron specificity and neurological development. We integrated our associations with Alzheimer's disease (AD) through proteome-wide association study (PWAS), colocalization and Mendelian randomization and identified 38 putative causal proteins, 15 of which have drugs available. Finally, we developed a proteomics-based AD prediction model that outperforms genetics-based models. These findings will be instrumental to further understand the biology and identify causal and druggable proteins for brain and neurological traits.

  View details for DOI 10.1038/s41588-024-01972-8

  View details for PubMedID 39528825

  View details for PubMedCentralID 9605867

• APOE3 Christchurch Heterozygosity and Autosomal Dominant Alzheimer's Disease. The New England journal of medicine Cochran, J. N., Greicius, M. D., Goate, A. M. 2024; 391 (17): 1660-1661

  View details for DOI 10.1056/NEJMc2409320

  View details for PubMedID 39476352

• Role of the X Chromosome in Alzheimer Disease Genetics. JAMA neurology Belloy, M. E., Le Guen, Y., Stewart, I., Williams, K., Herz, J., Sherva, R., Zhang, R., Merritt, V., Panizzon, M. S., Hauger, R. L., Gaziano, J. M., Logue, M., Napolioni, V., Greicius, M. D. 2024

  Abstract

  The X chromosome has remained enigmatic in Alzheimer disease (AD), yet it makes up 5% of the genome and carries a high proportion of genes expressed in the brain, making it particularly appealing as a potential source of unexplored genetic variation in AD.To perform the first large-scale X chromosome-wide association study (XWAS) of AD.This was a meta-analysis of genetic association studies in case-control, family-based, population-based, and longitudinal AD-related cohorts from the US Alzheimer's Disease Genetics Consortium, the Alzheimer's Disease Sequencing Project, the UK Biobank, the Finnish health registry, and the US Million Veterans Program. Risk of AD was evaluated through case-control logistic regression analyses. Data were analyzed between January 2023 and March 2024. Genetic data available from high-density single-nucleotide variant microarrays and whole-genome sequencing and summary statistics for multitissue expression and protein quantitative trait loci available from published studies were included, enabling follow-up genetic colocalization analyses. A total of 1 629 863 eligible participants were selected from referred and volunteer samples, 477 596 of whom were excluded for analysis exclusion criteria. The number of participants who declined to participate in original studies was not available.Risk of AD, reported as odds ratios (ORs) with 95% CIs. Associations were considered at X chromosome-wide (P < 1 × 10-5) and genome-wide (P < 5 × 10-8) significance. Primary analyses are nonstratified, while secondary analyses evaluate sex-stratified effects.Analyses included 1 152 284 participants of non-Hispanic White, European ancestry (664 403 [57.7%] female and 487 881 [42.3%] male), including 138 558 individuals with AD. Six independent genetic loci passed X chromosome-wide significance, with 4 showing support for links between the genetic signal for AD and expression of nearby genes in brain and nonbrain tissues. One of these 4 loci passed conservative genome-wide significance, with its lead variant centered on an intron of SLC9A7 (OR, 1.03; 95% CI, 1.02-1.04) and colocalization analyses prioritizing both the SLC9A7 and nearby CHST7 genes. Of these 6 loci, 4 displayed evidence for escape from X chromosome inactivation with regard to AD risk.This large-scale XWAS of AD identified the novel SLC9A7 locus. SLC9A7 regulates pH homeostasis in Golgi secretory compartments and is anticipated to have downstream effects on amyloid β accumulation. Overall, this study advances our knowledge of AD genetics and may provide novel biological drug targets. The results further provide initial insights into elucidating the role of the X chromosome in sex-based differences in AD.

  View details for DOI 10.1001/jamaneurol.2024.2843

  View details for PubMedID 39250132

• Deciphering glial contributions to CSF1R-related disorder via single-nuclear transcriptomic profiling: a case study. Acta neuropathologica communications Pan, J., Fores-Martos, J., Delpirou Nouh, C., Jensen, T. D., Vallejo, K., Cayrol, R., Ahmadian, S., Ashley, E. A., Greicius, M. D., Cobos, I. 2024; 12 (1): 139

  Abstract

  CSF1R-related disorder (CSF1R-RD) is a neurodegenerative condition that predominantly affects white matter due to genetic alterations in the CSF1R gene, which is expressed by microglia. We studied an elderly man with a hereditary, progressive dementing disorder of unclear etiology. Standard genetic testing for leukodystrophy and other neurodegenerative conditions was negative. Brain autopsy revealed classic features of adult-onset leukoencephalopathy with axonal spheroids and pigmented glia (ALSP), including confluent white matter degeneration with axonal spheroids and pigmented glial cells in the affected white matter, consistent with CSF1R-RD. Subsequent long-read sequencing identified a novel deletion in CSF1R that was not detectable with short-read exome sequencing. To gain insight into potential mechanisms underlying white matter degeneration in CSF1R-RD, we studied multiple brain regions exhibiting varying degrees of white matter pathology. We found decreased CSF1R transcript and protein across brain regions, including intact white matter. Single nuclear RNA sequencing (snRNAseq) identified two disease-associated microglial cell states: lipid-laden microglia (expressing GPNMB, ATG7, LGALS1, LGALS3) and inflammatory microglia (expressing IL2RA, ATP2C1, FCGBP, VSIR, SESN3), along with a small population of CD44+ peripheral monocyte-derived macrophages exhibiting migratory and phagocytic signatures. GPNMB+ lipid-laden microglia with ameboid morphology represented the end-stage disease microglia state. Disease-associated oligodendrocytes exhibited cell stress signatures and dysregulated apoptosis-related genes. Disease-associated oligodendrocyte precursor cells (OPCs) displayed a failure in their differentiation into mature myelin-forming oligodendrocytes, as evidenced by upregulated LRP1, PDGFRA, SOX5, NFIA, and downregulated NKX2-2, NKX6.2, SOX4, SOX8, TCF7L2, YY1, ZNF488. Overall, our findings highlight microglia-oligodendroglia crosstalk in demyelination, with CSF1R dysfunction promoting phagocytic and inflammatory microglia states, an arrest in OPC differentiation, and oligodendrocyte depletion.

  View details for DOI 10.1186/s40478-024-01853-5

  View details for PubMedID 39217398

  View details for PubMedCentralID 9288387

• Temporal tau asymmetry spectrum influences divergent behavior and language patterns in Alzheimer's disease. Brain, behavior, and immunity Younes, K., Smith, V., Johns, E., Carlson, M. L., Winer, J., He, Z., Henderson, V. W., Greicius, M. D., Young, C. B., Mormino, E. C. 2024

  Abstract

  Understanding the psychiatric symptoms of Alzheimer s disease (AD) is crucial for advancing precision medicine and therapeutic strategies. The relationship between AD behavioral symptoms and asymmetry in spatial tau PET patterns is not well-known. Braak tau progression implicates the temporal lobes early. However, the clinical and pathological implications of temporal tau laterality remain unexplored. This cross-sectional study investigated the correlation between temporal tau PET asymmetry and behavior assessed using the neuropsychiatric inventory and composite scores for memory, executive function, and language, using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. In the entire cohort, continuous right and left temporal tau contributions to behavior and cognition were evaluated, controlling for age, sex, education, and tau burden on the contralateral side. Additionally, a temporal tau laterality index was calculated to define "asymmetry-extreme" groups (individuals with laterality indices greater than two standard deviations from the mean). 695 individuals (age = 73.9 ± 7.6 years, 372(53.5 %) females) were included, comprising 281(40 %) cognitively unimpaired (CU) amyloid negative, 185(27 %) CU amyloid positive, and 229(33 %) impaired (CI) amyloid positive participants. In the full cohort analysis, right temporal tau was associated with worse behavior (B = 8.14, p-value = 0.007), and left temporal tau was associated with worse language (B = 1.4, p-value < 0.001). Categorization into asymmetry-extreme groups revealed 20 right- and 27 left-asymmetric participants. Within these extreme groups, there was additional heterogeneity along the anterior-posterior dimension. Asymmetrical tau burden is associated with distinct behavioral and cognitive profiles. Wide multi-cultural implementation of social cognition measures is needed to understand right-sided asymmetry in AD.

  View details for DOI 10.1016/j.bbi.2024.05.002

  View details for PubMedID 38710339

• Rare genetic variation in fibronectin 1 (FN1) protects against APOEepsilon4 in Alzheimer's disease. Acta neuropathologica Bhattarai, P., Gunasekaran, T. I., Belloy, M. E., Reyes-Dumeyer, D., Julich, D., Tayran, H., Yilmaz, E., Flaherty, D., Turgutalp, B., Sukumar, G., Alba, C., McGrath, E. M., Hupalo, D. N., Bacikova, D., Le Guen, Y., Lantigua, R., Medrano, M., Rivera, D., Recio, P., Nuriel, T., Ertekin-Taner, N., Teich, A. F., Dickson, D. W., Holley, S., Greicius, M., Dalgard, C. L., Zody, M., Mayeux, R., Kizil, C., Vardarajan, B. N. 2024; 147 (1): 70

  Abstract

  The risk of developing Alzheimer's disease (AD) significantly increases in individuals carrying the APOEepsilon4 allele. Elderly cognitively healthy individuals with APOEepsilon4 also exist, suggesting the presence of cellular mechanisms that counteract the pathological effects of APOEepsilon4; however, these mechanisms are unknown. We hypothesized that APOEepsilon4 carriers without dementia might carry genetic variations that could protect them from developing APOEepsilon4-mediated AD pathology. To test this, we leveraged whole-genome sequencing (WGS) data in the NationalInstitute on Aging Alzheimer's Disease Family Based Study (NIA-ADFBS), Washington Heights/Inwood Columbia Aging Project (WHICAP), and Estudio Familiar de Influencia Genetica en Alzheimer (EFIGA) cohorts and identified potentially protective variants segregating exclusively among unaffected APOEepsilon4 carriers. In homozygous unaffected carriers above 70 years old, we identified 510 rare coding variants. Pathway analysis of the genes harboring these variants showed significant enrichment in extracellular matrix (ECM)-related processes, suggesting protective effects of functional modifications in ECM proteins. We prioritized two genes that were highly represented in the ECM-related gene ontology terms, (FN1) and collagen type VI alpha 2 chain (COL6A2) and are known to be expressed at the blood-brain barrier (BBB), for postmortem validation and in vivo functional studies. An independent analysis in a large cohort of 7185 APOEepsilon4 homozygous carriers found that rs140926439 variant in FN1 was protective of AD (OR=0.29; 95% CI [0.11, 0.78], P=0.014) and delayed age at onset of disease by 3.37 years (95% CI [0.42, 6.32], P=0.025). The FN1 and COL6A2 protein levels were increased at the BBB in APOEepsilon4 carriers with AD. Brain expression of cognitively unaffected homozygous APOEepsilon4 carriers had significantly lower FN1 deposition and less reactive gliosis compared to homozygous APOEepsilon4 carriers with AD, suggesting that FN1 might be a downstream driver of APOEepsilon4-mediated AD-related pathology and cognitive decline. To validate our findings, we used zebrafish models with loss-of-function (LOF) mutations in fn1b-the ortholog for human FN1. We found that fibronectin LOF reduced gliosis, enhanced gliovascular remodeling, and potentiated the microglial response, suggesting that pathological accumulation of FN1 could impair toxic protein clearance, which is ameliorated with FN1 LOF. Our study suggests that vascular deposition of FN1 is related to the pathogenicity of APOEepsilon4, and LOF variants in FN1 may reduce APOEepsilon4-related AD risk, providing novel clues to potential therapeutic interventions targeting the ECM to mitigate AD risk.

  View details for DOI 10.1007/s00401-024-02721-1

  View details for PubMedID 38598053

• TREM1 disrupts myeloid bioenergetics and cognitive function in aging and Alzheimer disease mouse models. Nature neuroscience Wilson, E. N., Wang, C., Swarovski, M. S., Zera, K. A., Ennerfelt, H. E., Wang, Q., Chaney, A., Gauba, E., Ramos Benitez, J. A., Le Guen, Y., Minhas, P. S., Panchal, M., Tan, Y. J., Blacher, E., A Iweka, C., Cropper, H., Jain, P., Liu, Q., Mehta, S. S., Zuckerman, A. J., Xin, M., Umans, J., Huang, J., Durairaj, A. S., Serrano, G. E., Beach, T. G., Greicius, M. D., James, M. L., Buckwalter, M. S., McReynolds, M. R., Rabinowitz, J. D., Andreasson, K. I. 2024

  Abstract

  Human genetics implicate defective myeloid responses in the development of late-onset Alzheimer disease. A decline in peripheral and brain myeloid metabolism, triggering maladaptive immune responses, is a feature of aging. The role of TREM1, a pro-inflammatory factor, in neurodegenerative diseases is unclear. Here we show that Trem1 deficiency prevents age-dependent changes in myeloid metabolism, inflammation and hippocampal memory function in mice. Trem1 deficiency rescues age-associated declines in ribose 5-phosphate. In vitro, Trem1-deficient microglia are resistant to amyloid-β42 oligomer-induced bioenergetic changes, suggesting that amyloid-β42 oligomer stimulation disrupts homeostatic microglial metabolism and immune function via TREM1. In the 5XFAD mouse model, Trem1 haploinsufficiency prevents spatial memory loss, preserves homeostatic microglial morphology, and reduces neuritic dystrophy and changes in the disease-associated microglial transcriptomic signature. In aging APPSwe mice, Trem1 deficiency prevents hippocampal memory decline while restoring synaptic mitochondrial function and cerebral glucose uptake. In postmortem Alzheimer disease brain, TREM1 colocalizes with Iba1+ cells around amyloid plaques and its expression is associated with Alzheimer disease clinical and neuropathological severity. Our results suggest that TREM1 promotes cognitive decline in aging and in the context of amyloid pathology.

  View details for DOI 10.1038/s41593-024-01610-w

  View details for PubMedID 38539014

  View details for PubMedCentralID 4369837

• Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease. medRxiv : the preprint server for health sciences Jensen, T. D., Ni, B., Reuter, C. M., Gorzynski, J. E., Fazal, S., Bonner, D., Ungar, R. A., Goddard, P. C., Raja, A., Ashley, E. A., Bernstein, J. A., Zuchner, S., Greicius, M. D., Montgomery, S. B., Schatz, M. C., Wheeler, M. T., Battle, A. 2024

  Abstract

  Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.

  View details for DOI 10.1101/2024.03.22.24304565

  View details for PubMedID 38585781

  View details for PubMedCentralID PMC10996727

• APOE loss-of-function variants: Compatible with longevity and associated with resistance to Alzheimer's disease pathology. Neuron Chemparathy, A., Le Guen, Y., Chen, S., Lee, E. G., Leong, L., Gorzynski, J. E., Jensen, T. D., Ferrasse, A., Xu, G., Xiang, H., Belloy, M. E., Kasireddy, N., Peña-Tauber, A., Williams, K., Stewart, I., Talozzi, L., Wingo, T. S., Lah, J. J., Jayadev, S., Hales, C. M., Peskind, E., Child, D. D., Roeber, S., Keene, C. D., Cong, L., Ashley, E. A., Yu, C. E., Greicius, M. D. 2024

  Abstract

  The ε4 allele of apolipoprotein E (APOE) is the strongest genetic risk factor for sporadic Alzheimer's disease (AD). Knockdown of ε4 may provide a therapeutic strategy for AD, but the effect of APOE loss of function (LoF) on AD pathogenesis is unknown. We searched for APOE LoF variants in a large cohort of controls and patients with AD and identified seven heterozygote carriers of APOE LoF variants. Five carriers were controls (aged 71-90 years), one carrier was affected by progressive supranuclear palsy, and one carrier was affected by AD with an unremarkable age at onset of 75 years. Two APOE ε3/ε4 controls carried a stop-gain affecting ε4: one was cognitively normal at 90 years and had no neuritic plaques at autopsy; the other was cognitively healthy at 79 years, and lumbar puncture at 76 years showed normal levels of amyloid. These results suggest that ε4 drives AD risk through the gain of abnormal function and support ε4 knockdown as a viable therapeutic option.

  View details for DOI 10.1016/j.neuron.2024.01.008

  View details for PubMedID 38301647

• Report of the APOE4 National Institute on Aging/Alzheimer Disease Sequencing Project Consortium Working Group: Reducing APOE4 in Carriers is a Therapeutic Goal for Alzheimer's Disease. Annals of neurology Vance, J. M., Farrer, L. A., Huang, Y., Cruchaga, C., Hyman, B. T., Pericak-Vance, M. A., Goate, A. M., Greicius, M. D., Griswold, A. J., Haines, J. L., Tcw, J., Schellenberg, G. D., Tsai, L. H., Herz, J., Holtzman, D. M. 2024

  Abstract

  Alzheimer's disease (AD) is the most common neurodegenerative disorder and one of the leading causes of disability worldwide. The apolipoprotein E4 gene (APOE4) is the strongest genetic risk factor for AD. In 2023, the APOE4 National Institute on Aging/Alzheimer's Disease Sequencing Project working group came together to gather data and discuss the question of whether to reduce or increase APOE4 as a therapeutic intervention for AD. It was the unanimous consensus that cumulative data from multiple studies in humans and animal models support that lowering APOE4 should be a target for therapeutic approaches for APOE4 carriers. ANN NEUROL 2024.

  View details for DOI 10.1002/ana.26864

  View details for PubMedID 38180638

• Substantial Doubt Remains about the Efficacy of Anti-Amyloid Antibodies. Journal of Alzheimer's disease : JAD Digma, L. A., Winer, J. R., Greicius, M. D. 2024; 97 (2): 567-572

  Abstract

  With the FDA approval of aducanumab and lecanemab, and with the recent statistically significant phase 3 clinical trial for donanemab, there is growing enthusiasm for anti-amyloid antibodies in the treatment of Alzheimer's disease. Here, we discuss three substantial limitations regarding recent anti-amyloid clinical trials: 1) there is little evidence that amyloid reduction correlates with clinical outcome, 2) the reported efficacy of anti-amyloid therapies may be explained by functional unblinding, and 3) donanemab had no effect on tau burden in its phase 3 trial. Taken together, these observations call into question the efficacy of anti-amyloid therapies.

  View details for DOI 10.3233/JAD-231198

  View details for PubMedID 38250779

• A mitochondrial inside-out iron-calcium signal reveals drug targets for Parkinson's disease. Cell reports Bharat, V., Durairaj, A. S., Vanhauwaert, R., Li, L., Muir, C. M., Chandra, S., Kwak, C. S., Le Guen, Y., Nandakishore, P., Hsieh, C. H., Rensi, S. E., Altman, R. B., Greicius, M. D., Feng, L., Wang, X. 2023; 42 (12): 113544

  Abstract

  Dysregulated iron or Ca2+ homeostasis has been reported in Parkinson's disease (PD) models. Here, we discover a connection between these two metals at the mitochondria. Elevation of iron levels causes inward mitochondrial Ca2+ overflow, through an interaction of Fe2+ with mitochondrial calcium uniporter (MCU). In PD neurons, iron accumulation-triggered Ca2+ influx across the mitochondrial surface leads to spatially confined Ca2+ elevation at the outer mitochondrial membrane, which is subsequently sensed by Miro1, a Ca2+-binding protein. A Miro1 blood test distinguishes PD patients from controls and responds to drug treatment. Miro1-based drug screens in PD cells discover Food and Drug Administration-approved T-type Ca2+-channel blockers. Human genetic analysis reveals enrichment of rare variants in T-type Ca2+-channel subtypes associated with PD status. Our results identify a molecular mechanism in PD pathophysiology and drug targets and candidates coupled with a convenient stratification method.

  View details for DOI 10.1016/j.celrep.2023.113544

  View details for PubMedID 38060381

• Organ aging signatures in the plasma proteome track health and disease. Nature Oh, H. S., Rutledge, J., Nachun, D., Pálovics, R., Abiose, O., Moran-Losada, P., Channappa, D., Urey, D. Y., Kim, K., Sung, Y. J., Wang, L., Timsina, J., Western, D., Liu, M., Kohlfeld, P., Budde, J., Wilson, E. N., Guen, Y., Maurer, T. M., Haney, M., Yang, A. C., He, Z., Greicius, M. D., Andreasson, K. I., Sathyan, S., Weiss, E. F., Milman, S., Barzilai, N., Cruchaga, C., Wagner, A. D., Mormino, E., Lehallier, B., Henderson, V. W., Longo, F. M., Montgomery, S. B., Wyss-Coray, T. 2023; 624 (7990): 164-172

  Abstract

  Animal studies show aging varies between individuals as well as between organs within an individual1-4, but whether this is true in humans and its effect on age-related diseases is unknown. We utilized levels of human blood plasma proteins originating from specific organs to measure organ-specific aging differences in living individuals. Using machine learning models, we analysed aging in 11 major organs and estimated organ age reproducibly in five independent cohorts encompassing 5,676 adults across the human lifespan. We discovered nearly 20% of the population show strongly accelerated age in one organ and 1.7% are multi-organ agers. Accelerated organ aging confers 20-50% higher mortality risk, and organ-specific diseases relate to faster aging of those organs. We find individuals with accelerated heart aging have a 250% increased heart failure risk and accelerated brain and vascular aging predict Alzheimer's disease (AD) progression independently from and as strongly as plasma pTau-181 (ref. 5), the current best blood-based biomarker for AD. Our models link vascular calcification, extracellular matrix alterations and synaptic protein shedding to early cognitive decline. We introduce a simple and interpretable method to study organ aging using plasma proteomics data, predicting diseases and aging effects.

  View details for DOI 10.1038/s41586-023-06802-1

  View details for PubMedID 38057571

  View details for PubMedCentralID PMC10700136

• APOE Genotype and Alzheimer Disease Risk Across Age, Sex, and Population Ancestry. JAMA neurology Belloy, M. E., Andrews, S. J., Le Guen, Y., Cuccaro, M., Farrer, L. A., Napolioni, V., Greicius, M. D. 2023

  Abstract

  Apolipoprotein E (APOE)*2 and APOE*4 are, respectively, the strongest protective and risk-increasing, common genetic variants for late-onset Alzheimer disease (AD), making APOE status highly relevant toward clinical trial design and AD research broadly. The associations of APOE genotypes with AD are modulated by age, sex, race and ethnicity, and ancestry, but these associations remain unclear, particularly among racial and ethnic groups understudied in the AD and genetics research fields.To assess the stratified associations of APOE genotypes with AD risk across sex, age, race and ethnicity, and global population ancestry.This genetic association study included case-control, family-based, population-based, and longitudinal AD-related cohorts that recruited referred and volunteer participants. Data were analyzed between March 2022 and April 2023. Genetic data were available from high-density, single-nucleotide variant microarrays, exome microarrays, and whole-exome and whole-genome sequencing. Summary statistics were ascertained from published AD genetic studies.The main outcomes were risk for AD (odds ratios [ORs]) and risk of conversion to AD (hazard ratios [HRs]), with 95% CIs. Risk for AD was evaluated through case-control logistic regression analyses. Risk of conversion to AD was evaluated through Cox proportional hazards regression survival analyses.Among 68 756 unique individuals, analyses included 21 852 East Asian (demographic data not available), 5738 Hispanic (68.2% female; mean [SD] age, 75.4 [8.8] years), 7145 non-Hispanic Black (hereafter referred to as Black) (70.8% female; mean [SD] age, 78.4 [8.2] years), and 34 021 non-Hispanic White (hereafter referred to as White) (59.3% female; mean [SD] age, 77.0 [9.1] years) individuals. There was a general, stepwise pattern of ORs for APOE*4 genotypes and AD risk across race and ethnicity groups. Odds ratios for APOE*34 and AD risk attenuated following East Asian (OR, 4.54; 95% CI, 3.99-5.17),White (OR, 3.46; 95% CI, 3.27-3.65), Black (OR, 2.18; 95% CI, 1.90-2.49) and Hispanic (OR, 1.90; 95% CI, 1.65-2.18) individuals. Similarly, ORs for APOE*22+23 and AD risk attenuated following White (OR, 0.53, 95% CI, 0.48-0.58), Black (OR, 0.69, 95% CI, 0.57-0.84), and Hispanic (OR, 0.89; 95% CI, 0.72-1.10) individuals, with no association for Hispanic individuals. Deviating from the global pattern of ORs, APOE*22+23 was not associated with AD risk in East Asian individuals (OR, 0.97; 95% CI, 0.77-1.23). Global population ancestry could not explain why Hispanic individuals showed APOE associations with less pronounced AD risk compared with Black and White individuals. Within Black individuals, decreased global African ancestry or increased global European ancestry showed a pattern of APOE*4 dosage associated with increasing AD risk, but no such pattern was apparent for APOE*2 dosage with AD risk. The sex-by-age-specific interaction effect of APOE*34 among White individuals (higher risk in women) was reproduced but shifted to ages 60 to 70 years (OR, 1.48; 95% CI, 1.10-2.01) and was additionally replicated in a meta-analysis of Black individuals and Hispanic individuals (OR, 1.72; 95% CI, 1.01-2.94).Through recent advances in AD-related genetic cohorts, this study provided the largest-to-date overview of the association of APOE with AD risk across age, sex, race and ethnicity, and population ancestry. These novel insights are critical to guide AD clinical trial design and research.

  View details for DOI 10.1001/jamaneurol.2023.3599

  View details for PubMedID 37930705

  View details for PubMedCentralID PMC10628838

• Loop diuretics association with Alzheimer's disease risk. Frontiers in aging Graber-Naidich, A., Lee, J., Younes, K., Greicius, M. D., Le Guen, Y., He, Z. 2023; 4: 1211571

  Abstract

  Objectives: To investigate whether exposure history to two common loop diuretics, bumetanide and furosemide, affects the risk of developing Alzheimer's disease (AD) after accounting for socioeconomic status and congestive heart failure. Methods: Individuals exposed to bumetanide or furosemide were identified in the Stanford University electronic health record using the de-identified Observational Medical Outcomes Partnership platform. We matched the AD case cohort to a control cohort (1:20 case:control) on gender, race, ethnicity, and hypertension, and controlled for variables that could potentially be collinear with bumetanide exposure and/or AD diagnosis. Among individuals older than 65 years, 5,839 AD cases and 116,103 matched controls were included. A total of 1,759 patients (54 cases and 1,705 controls) were exposed to bumetanide. Results: After adjusting for socioeconomic status and other confounders, the exposure of bumetanide and furosemide was significantly associated with reduced AD risk (respectively, bumetanide odds ratio [OR] = 0.23; 95% confidence interval [CI], 0.15-0.36; p = 4.0 × 10-11; furosemide OR = 0.42; 95% CI, 0.38-0.47; p < 2.0 × 10-16). Discussion: Our study replicates in an independent sample that a history of bumetanide exposure is associated with reduced AD risk while also highlighting an association of the most common loop diuretic (furosemide) with reduced AD risk. These associations need to be additionally replicated, and the mechanism of action remains to be investigated.

  View details for DOI 10.3389/fragi.2023.1211571

  View details for PubMedID 37822457

  View details for PubMedCentralID PMC10563814

• APOE-ε4 and BIN1 increase risk of Alzheimer's disease pathology but not specifically of Lewy body pathology. Acta neuropathologica communications Talyansky, S., Le Guen, Y., Kasireddy, N., Belloy, M. E., Greicius, M. D. 2023; 11 (1): 149

  Abstract

  Lewy body (LB) pathology commonly occurs in individuals with Alzheimer's disease (AD) pathology. However, it remains unclear which genetic risk factors underlie AD pathology, LB pathology, or AD-LB co-pathology. Notably, whether APOE-ε4 affects risk of LB pathology independently from AD pathology is controversial. We adapted criteria from the literature to classify 4,985 subjects from the National Alzheimer's Coordinating Center (NACC) and the Rush University Medical Center as AD-LB co-pathology (AD+LB+), sole AD pathology (AD+LB-), sole LB pathology (AD-LB+), or no pathology (AD-LB-). We performed a meta-analysis of a genome-wide association study (GWAS) per subpopulation (NACC/Rush) for each disease phenotype compared to the control group (AD-LB-), and compared the AD+LB+ to AD+LB- groups. APOE-ε4 was significantly associated with risk of AD+LB- and AD+LB+ compared to AD-LB-. However, APOE-ε4 was not associated with risk of AD-LB+ compared to AD-LB- or risk of AD+LB+ compared to AD+LB-. Associations at the BIN1 locus exhibited qualitatively similar results. These results suggest that APOE-ε4 is a risk factor for AD pathology, but not for LB pathology when decoupled from AD pathology. The same holds for BIN1 risk variants. These findings, in the largest AD-LB neuropathology GWAS to date, distinguish the genetic risk factors for sole and dual AD-LB pathology phenotypes. Our GWAS meta-analysis summary statistics, derived from phenotypes based on postmortem pathologic evaluation, may provide more accurate disease-specific polygenic risk scores compared to GWAS based on clinical diagnoses, which are likely confounded by undetected dual pathology and clinical misdiagnoses of dementia type.

  View details for DOI 10.1186/s40478-023-01626-6

  View details for PubMedID 37700353

  View details for PubMedCentralID PMC10496176

• Multiancestry analysis of the HLA locus in Alzheimer's and Parkinson's diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes. Proceedings of the National Academy of Sciences of the United States of America Le Guen, Y., Luo, G., Ambati, A., Damotte, V., Jansen, I., Yu, E., Nicolas, A., de Rojas, I., Peixoto Leal, T., Miyashita, A., Bellenguez, C., Lian, M. M., Parveen, K., Morizono, T., Park, H., Grenier-Boley, B., Naito, T., Küçükali, F., Talyansky, S. D., Yogeshwar, S. M., Sempere, V., Satake, W., Alvarez, V., Arosio, B., Belloy, M. E., Benussi, L., Boland, A., Borroni, B., Bullido, M. J., Caffarra, P., Clarimon, J., Daniele, A., Darling, D., Debette, S., Deleuze, J. F., Dichgans, M., Dufouil, C., During, E., Düzel, E., Galimberti, D., Garcia-Ribas, G., García-Alberca, J. M., García-González, P., Giedraitis, V., Goldhardt, O., Graff, C., Grünblatt, E., Hanon, O., Hausner, L., Heilmann-Heimbach, S., Holstege, H., Hort, J., Jung, Y. J., Jürgen, D., Kern, S., Kuulasmaa, T., Lee, K. H., Lin, L., Masullo, C., Mecocci, P., Mehrabian, S., de Mendonça, A., Boada, M., Mir, P., Moebus, S., Moreno, F., Nacmias, B., Nicolas, G., Niida, S., Nordestgaard, B. G., Papenberg, G., Papma, J., Parnetti, L., Pasquier, F., Pastor, P., Peters, O., Pijnenburg, Y. A., Piñol-Ripoll, G., Popp, J., Porcel, L. M., Puerta, R., Pérez-Tur, J., Rainero, I., Ramakers, I., Real, L. M., Riedel-Heller, S., Rodriguez-Rodriguez, E., Ross, O. A., Luís Royo, J., Rujescu, D., Scarmeas, N., Scheltens, P., Scherbaum, N., Schneider, A., Seripa, D., Skoog, I., Solfrizzi, V., Spalletta, G., Squassina, A., van Swieten, J., Sánchez-Valle, R., Tan, E. K., Tegos, T., Teunissen, C., Thomassen, J. Q., Tremolizzo, L., Vyhnalek, M., Verhey, F., Waern, M., Wiltfang, J., Zhang, J., Zetterberg, H., Blennow, K., He, Z., Williams, J., Amouyel, P., Jessen, F., Kehoe, P. G., Andreassen, O. A., Van Duin, C., Tsolaki, M., Sánchez-Juan, P., Frikke-Schmidt, R., Sleegers, K., Toda, T., Zettergren, A., Ingelsson, M., Okada, Y., Rossi, G., Hiltunen, M., Gim, J., Ozaki, K., Sims, R., Foo, J. N., van der Flier, W., Ikeuchi, T., Ramirez, A., Mata, I., Ruiz, A., Gan-Or, Z., Lambert, J. C., Greicius, M. D., Mignot, E. 2023; 120 (36): e2302720120

  Abstract

  Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson's disease (PD) and Alzheimer's disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues.

  View details for DOI 10.1073/pnas.2302720120

  View details for PubMedID 37643212

• Sex- and APOE-specific genetic risk factors for late-onset Alzheimer's disease: Evidence from gene-gene interaction of longevity-related loci. Aging cell Dato, S., De Rango, F., Crocco, P., Pallotti, S., Belloy, M. E., Le Guen, Y., Greicius, M. D., Passarino, G., Rose, G., Napolioni, V. 2023: e13938

  Abstract

  Advanced age is the largest risk factor for late-onset Alzheimer's disease (LOAD), a disease in which susceptibility correlates to almost all hallmarks of aging. Shared genetic signatures between LOAD and longevity were frequently hypothesized, likely characterized by distinctive epistatic and pleiotropic interactions. Here, we applied a multidimensional reduction approach to detect gene-gene interactions affecting LOAD in a large dataset of genomic variants harbored by genes in the insulin/IGF1 signaling, DNA repair, and oxidative stress pathways, previously investigated in human longevity. The dataset was generated from a collection of publicly available Genome Wide Association Studies, comprising a total of 2,469 gene variants genotyped in 20,766 subjects of Northwestern European ancestry (11,038 LOAD cases and 9,728 controls). The stratified analysis according to APOE*4 status and sex corroborated evidence that pathways leading to longevity also contribute to LOAD. Among the significantly interacting genes, PTPN1, TXNRD1, and IGF1R were already found enriched in gene-gene interactions affecting survival to old age. Furthermore, interacting variants associated with LOAD in a sex- and APOE-specific way. Indeed, while in APOE*4 female carriers we found several inter-pathway interactions, no significant epistasis was found in APOE*4 negative females; conversely, in males, significant intra- and inter-pathways epistasis emerged according to APOE*4 status. These findings suggest that interactions of risk factors may drive different trajectories of cognitive aging. Beyond helping to disentangle the genetic architecture of LOAD, such knowledge may improve precision in predicting the risk of dementia and enable effective sex- and APOE-stratified preventive and therapeutic interventions for LOAD.

  View details for DOI 10.1111/acel.13938

  View details for PubMedID 37621137

• APOE - ε 4 and BIN1 increase risk of Alzheimer's disease pathology but not specifically of Lewy body pathology. medRxiv : the preprint server for health sciences Talyansky, S., Guen, Y. L., Kasireddy, N., Belloy, M. E., Greicius, M. D. 2023

  Abstract

  Lewy body (LB) pathology commonly occurs in individuals with Alzheimer's disease (AD) pathology. However, it remains unclear which genetic risk factors underlie AD pathology, LB pathology, or AD-LB co-pathology. Notably, whether APOE - ε 4 affects risk of LB pathology independently from AD pathology is controversial. We adapted criteria from the literature to classify 4,985 subjects from the National Alzheimer's Coordinating Center (NACC) and the Rush University Medical Center as AD-LB co-pathology (AD + LB + ), sole AD pathology (AD + LB - ), sole LB pathology (AD - LB + ), or no pathology (AD - LB - ). We performed a meta-analysis of a genome-wide association study (GWAS) per subpopulation (NACC/Rush) for each disease phenotype compared to the control group (AD - LB - ), and compared the AD + LB + to AD + LB - groups. APOE - ε 4 was significantly associated with risk of AD + LB - and AD + LB + compared to AD - LB - . However, APOE - ε 4 was not associated with risk of AD - LB + compared to AD - LB - or risk of AD + LB + compared to AD + LB - . Associations at the BIN1 locus exhibited qualitatively similar results. These results suggest that APOE - ε 4 is a risk factor for AD pathology, but not for LB pathology when decoupled from AD pathology. The same holds for BIN1 risk variants. These findings, in the largest AD-LB neuropathology GWAS to date, distinguish the genetic risk factors for sole and dual AD-LB pathology phenotypes. Our GWAS meta-analysis summary statistics, derived from phenotypes based on postmortem pathologic evaluation, may provide more accurate disease-specific polygenic risk scores compared to GWAS based on clinical diagnoses, which are likely confounded by undetected dual pathology and clinical misdiagnoses of dementia type.

  View details for DOI 10.1101/2023.04.21.23288938

  View details for PubMedID 37503074

  View details for PubMedCentralID PMC10371184

• Bumetanide Exposure Association with Alzheimer's Disease Risk. Research square Graber-Naidich, A., Lee, J., Younes, K., Greicius, M. D., Le Guen, Y., He, Z. 2023

  Abstract

  To investigate whether exposure history to two common loop diuretics affects the risk of developing Alzheimer's disease (AD) after accounting for socioeconomic status and congestive heart failure.Individuals exposed to bumetanide or furosemide were identified in the Stanford University electronic health record using the deidentified Observational Medical Outcomes Partnership platform. We matched the AD case cohort to a control cohort (1:20 case:control) on gender, race, ethnicity, hypertension and controlled for variables that could potentially be collinear with bumetanide exposure and/or AD diagnosis. Among individuals older than 65 years, 5,839 AD cases and 116,103 matched controls were included. A total of 1,759 patients (54 cases, 1,705 controls) were exposed to bumetanide.After adjusting for socioeconomic status and other confounders, bumetanide exposure was significantly associated with reduced AD risk (odds ratio = 0.50; 95% confidence interval, 0.37-0.68; p = 9.9×10-6), while the most common loop diuretics, furosemide, was not associated with AD risk.Our study replicates in an independent sample that history of bumetanide exposure is associated with reduced risk of AD and emphasizes that this association is not confounded by difference in socioeconomic status, which was an important caveat given the cost difference between bumetanide and furosemide.

  View details for DOI 10.21203/rs.3.rs-2574215/v1

  View details for PubMedID 36909637

  View details for PubMedCentralID PMC10002844

• Association of African Ancestry-Specific APOE Missense Variant R145C With Risk of Alzheimer Disease. JAMA Le Guen, Y., Raulin, A., Logue, M. W., Sherva, R., Belloy, M. E., Eger, S. J., Chen, A., Kennedy, G., Kuchenbecker, L., O'Leary, J. P., Zhang, R., Merritt, V. C., Panizzon, M. S., Hauger, R. L., Gaziano, J. M., Bu, G., Thornton, T. A., Farrer, L. A., Napolioni, V., He, Z., Greicius, M. D. 2023; 329 (7): 551-560

  Abstract

  Importance: Numerous studies have established the association of the common APOE epsilon2 and APOE epsilon4 alleles with Alzheimer disease (AD) risk across ancestries. Studies of the interaction of these alleles with other amino acid changes on APOE in non-European ancestries are lacking and may improve ancestry-specific risk prediction.Objective: To determine whether APOE amino acid changes specific to individuals of African ancestry modulate AD risk.Design, Setting, and Participants: Case-control study including 31 929 participants and using a sequenced discovery sample (Alzheimer Disease Sequencing Project; stage 1) followed by 2 microarray imputed data sets derived from the Alzheimer Disease Genetic Consortium (stage 2, internal replication) and the Million Veteran Program (stage 3, external validation). This study combined case-control, family-based, population-based, and longitudinal AD cohorts, which recruited participants (1991-2022) in primarily US-based studies with 1 US/Nigerian study. Across all stages, individuals included in this study were of African ancestry.Exposures: Two APOE missense variants (R145C and R150H) were assessed, stratified by APOE genotype.Main Outcomes and Measures: The primary outcome was AD case-control status, and secondary outcomes included age at AD onset.Results: Stage 1 included 2888 cases (median age, 77 [IQR, 71-83] years; 31.3% male) and 4957 controls (median age, 77 [IQR, 71-83] years; 28.0% male). In stage 2, across multiple cohorts, 1201 cases (median age, 75 [IQR, 69-81] years; 30.8% male) and 2744 controls (median age, 80 [IQR, 75-84] years; 31.4% male) were included. In stage 3, 733 cases (median age, 79.4 [IQR, 73.8-86.5] years; 97.0% male) and 19 406 controls (median age, 71.9 [IQR, 68.4-75.8] years; 94.5% male) were included. In epsilon3/epsilon4-stratified analyses of stage 1, R145C was present in 52 individuals with AD (4.8%) and 19 controls (1.5%); R145C was associated with an increased risk of AD (odds ratio [OR], 3.01; 95% CI, 1.87-4.85; P=6.0*10-6) and was associated with a reported younger age at AD onset (beta, -5.87 years; 95% CI, -8.35 to -3.4 years; P=3.4*10-6). Association with increased AD risk was replicated in stage 2 (R145C was present in 23 individuals with AD [4.7%] and 21 controls [2.7%]; OR, 2.20; 95% CI, 1.04-4.65; P=.04) and was concordant in stage 3 (R145C was present in 11 individuals with AD [3.8%] and 149 controls [2.7%]; OR, 1.90; 95% CI, 0.99-3.64; P=.051). Association with earlier AD onset was replicated in stage 2 (beta, -5.23 years; 95% CI, -9.58 to -0.87 years; P=.02) and stage 3 (beta, -10.15 years; 95% CI, -15.66 to -4.64 years; P=4.0*10-4). No significant associations were observed in other APOE strata for R145C or in any APOE strata for R150H.Conclusions and Relevance: In this exploratory analysis, the APOE epsilon3[R145C] missense variant was associated with an increased risk of AD among individuals of African ancestry with the epsilon3/epsilon4 genotype. With additional external validation, these findings may inform AD genetic risk assessment in individuals of African ancestry.

  View details for DOI 10.1001/jama.2023.0268

  View details for PubMedID 36809323

• APOE effects on regional tau in preclinical Alzheimer's disease. Molecular neurodegeneration Young, C. B., Johns, E., Kennedy, G., Belloy, M. E., Insel, P. S., Greicius, M. D., Sperling, R. A., Johnson, K. A., Poston, K. L., Mormino, E. C., Alzheimers Disease Neuroimaging Initiative, A4 Study Team 2023; 18 (1): 1

  Abstract

  BACKGROUND: APOE variants are strongly associated with abnormal amyloid aggregation and additional direct effects of APOE on tau aggregation are reported in animal and human cell models. The degree to which these effects are present in humans when individuals are clinically unimpaired (CU) but have abnormal amyloid (Abeta+) remains unclear.METHODS: We analyzed data from CU individuals in the Anti-Amyloid Treatment in Asymptomatic AD (A4) and Longitudinal Evaluation of Amyloid Risk and Neurodegeneration (LEARN) studies. Amyloid PET data were available for 4486 participants (3163 Abeta-, 1323 Abeta+) and tau PET data were available for a subset of 447 participants (55 Abeta-, 392 Abeta+). Linear models examined APOE (number of e2 and e4 alleles) associations with global amyloid and regional tau burden in medial temporal lobe (entorhinal, amygdala) and early neocortical regions (inferior temporal, inferior parietal, precuneus). Consistency of APOE4 effects on regional tau were examined in 220 Abeta+CU and mild cognitive impairment (MCI) participants from the Alzheimer's Disease Neuroimaging Initiative (ADNI).RESULTS: APOE2 and APOE4 were associated with lower and higher amyloid positivity rates, respectively. Among Abeta+CU, e2 and e4 were associated with reduced (-12 centiloidsper allele) and greater (+15 centiloidsper allele) continuous amyloid burden, respectively. APOE2 was associated with reduced regional tau in all regions (-0.05 to -0.09 SUVR per allele), whereas APOE4 was associated with greater regional tau (+0.02 to +0.07 SUVR per allele). APOE differences were confirmed by contrasting e3/e3 with e2/e3 and e3/e4. Mediation analyses among Abeta+s showed that direct effects of e2 on regional tau were present in medial temporal lobe and early neocortical regions, beyond an indirect pathway mediated by continuous amyloid burden. For e4, direct effects on regional tau were only significant in medial temporal lobe. The magnitude of protective e2 effects on regional tau was consistent across brain regions, whereas detrimental e4 effects were greatest in medial temporal lobe. APOE4 patterns were confirmed in Abeta+ADNI participants.CONCLUSIONS: APOE influences early regional tau PET burden, above and beyond effects related to cross-sectional amyloid PET burden. Therapeutic strategies targeting underlying mechanisms related to APOE may modify tau accumulation among Abeta+individuals.

  View details for DOI 10.1186/s13024-022-00590-4

  View details for PubMedID 36597122

• GhostKnockoff inference empowers identification of putative causal variants in genome-wide association studies. Nature communications He, Z., Liu, L., Belloy, M. E., Le Guen, Y., Sossin, A., Liu, X., Qi, X., Ma, S., Gyawali, P. K., Wyss-Coray, T., Tang, H., Sabatti, C., Candes, E., Greicius, M. D., Ionita-Laza, I. 2022; 13 (1): 7209

  Abstract

  Recent advances in genome sequencing and imputation technologies provide an exciting opportunity to comprehensively study the contribution of genetic variants to complex phenotypes. However, our ability to translate genetic discoveries into mechanistic insights remains limited at this point. In this paper, we propose an efficient knockoff-based method, GhostKnockoff, for genome-wide association studies (GWAS) that leads to improved power and ability to prioritize putative causal variants relative to conventional GWAS approaches. The method requires only Z-scores from conventional GWAS and hence can be easily applied to enhance existing and future studies. The method can also be applied to meta-analysis of multiple GWAS allowing for arbitrary sample overlap. We demonstrate its performance using empirical simulations and two applications: (1) a meta-analysis for Alzheimer's disease comprising nine overlapping large-scale GWAS, whole-exome and whole-genome sequencing studies and (2) analysis of 1403 binary phenotypes from the UK Biobank data in 408,961 samples of European ancestry. Our results demonstrate that GhostKnockoff can identify putatively functional variants with weaker statistical effects that are missed by conventional association tests.

  View details for DOI 10.1038/s41467-022-34932-z

  View details for PubMedID 36418338

• Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer's disease. Nature genetics Holstege, H., Hulsman, M., Charbonnier, C., Grenier-Boley, B., Quenez, O., Grozeva, D., van Rooij, J. G., Sims, R., Ahmad, S., Amin, N., Norsworthy, P. J., Dols-Icardo, O., Hummerich, H., Kawalia, A., Amouyel, P., Beecham, G. W., Berr, C., Bis, J. C., Boland, A., Bosso, P., Bouwman, F., Bras, J., Campion, D., Cochran, J. N., Daniele, A., Dartigues, J., Debette, S., Deleuze, J., Denning, N., DeStefano, A. L., Farrer, L. A., Fernandez, M. V., Fox, N. C., Galimberti, D., Genin, E., Gille, J. J., Le Guen, Y., Guerreiro, R., Haines, J. L., Holmes, C., Ikram, M. A., Ikram, M. K., Jansen, I. E., Kraaij, R., Lathrop, M., Lemstra, A. W., Lleo, A., Luckcuck, L., Mannens, M. M., Marshall, R., Martin, E. R., Masullo, C., Mayeux, R., Mecocci, P., Meggy, A., Mol, M. O., Morgan, K., Myers, R. M., Nacmias, B., Naj, A. C., Napolioni, V., Pasquier, F., Pastor, P., Pericak-Vance, M. A., Raybould, R., Redon, R., Reinders, M. J., Richard, A., Riedel-Heller, S. G., Rivadeneira, F., Rousseau, S., Ryan, N. S., Saad, S., Sanchez-Juan, P., Schellenberg, G. D., Scheltens, P., Schott, J. M., Seripa, D., Seshadri, S., Sie, D., Sistermans, E. A., Sorbi, S., van Spaendonk, R., Spalletta, G., Tesi, N., Tijms, B., Uitterlinden, A. G., van der Lee, S. J., Visser, P. J., Wagner, M., Wallon, D., Wang, L., Zarea, A., Clarimon, J., van Swieten, J. C., Greicius, M. D., Yokoyama, J. S., Cruchaga, C., Hardy, J., Ramirez, A., Mead, S., van der Flier, W. M., van Duijn, C. M., Williams, J., Nicolas, G., Bellenguez, C., Lambert, J. 2022

  Abstract

  Alzheimer's disease (AD), the leading cause of dementia, has an estimated heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome sequencing data from 32,558 individuals-16,036 AD cases and 16,522 controls. Next to variants in TREM2, SORL1 and ABCA7, we observed a significant association of rare, predicted damaging variants in ATP8B4 and ABCA1 with AD risk, and a suggestive signal in ADAM10. Additionally, the rare-variant burden in RIN3, CLU, ZCWPW1 and ACE highlighted these genes as potential drivers of respective AD-genome-wide association study loci. Variants associated with the strongest effect on AD risk, in particular loss-of-function variants, are enriched in early-onset AD cases. Our results provide additional evidence for a major role for amyloid-beta precursor protein processing, amyloid-beta aggregation, lipid metabolism and microglial function in AD.

  View details for DOI 10.1038/s41588-022-01208-7

  View details for PubMedID 36411364

• Performance of a fully-automated Lumipulse plasma phospho-tau181 assay for Alzheimer's disease. Alzheimer's research & therapy Wilson, E. N., Young, C. B., Ramos Benitez, J., Swarovski, M. S., Feinstein, I., Vandijck, M., Le Guen, Y., Kasireddy, N. M., Shahid, M., Corso, N. K., Wang, Q., Kennedy, G., Trelle, A. N., Lind, B., Channappa, D., Belnap, M., Ramirez, V., Skylar-Scott, I., Younes, K., Yutsis, M. V., Le Bastard, N., Quinn, J. F., van Dyck, C. H., Nairn, A., Fredericks, C. A., Tian, L., Kerchner, G. A., Montine, T. J., Sha, S. J., Davidzon, G., Henderson, V. W., Longo, F. M., Greicius, M. D., Wagner, A. D., Wyss-Coray, T., Poston, K. L., Mormino, E. C., Andreasson, K. I. 2022; 14 (1): 172

  Abstract

  BACKGROUND: The recent promise of disease-modifying therapies for Alzheimer's disease (AD) has reinforced the need for accurate biomarkers for early disease detection, diagnosis and treatment monitoring. Advances in the development of novel blood-based biomarkers for AD have revealed that plasma levels of tau phosphorylated at various residues are specific and sensitive to AD dementia. However, the currently available tests have shortcomings in access, throughput, and scalability that limit widespread implementation.METHODS: We evaluated the diagnostic and prognostic performance of a high-throughput and fully-automated Lumipulse plasma p-tau181 assay for the detection of AD. Plasma from older clinically unimpaired individuals (CU, n = 463) and patients with mild cognitive impairment (MCI, n = 107) or AD dementia (n = 78) were obtained from the longitudinal Stanford University Alzheimer's Disease Research Center (ADRC) and the Stanford Aging and Memory Study (SAMS) cohorts. We evaluated the discriminative accuracy of plasma p-tau181 for clinical AD diagnosis, association with amyloid beta peptides and p-tau181 concentrations in CSF, association with amyloid positron emission tomography (PET), and ability to predict longitudinal cognitive and functional change.RESULTS: The assay showed robust performance in differentiating AD from control participants (AUC 0.959, CI: 0.912 to 0.990), and was strongly associated with CSF p-tau181, CSF Abeta42/Abeta40 ratio, and amyloid-PET global SUVRs. Associations between plasma p-tau181 with CSF biomarkers were significant when examined separately in Abeta+ and Abeta- groups. Plasma p-tau181 significantly increased over time in CU and AD diagnostic groups. After controlling for clinical diagnosis, age, sex, and education, baseline plasma p-tau181 predicted change in MoCA overall and change in CDR Sum of Boxes in the AD group over follow-up of up to 5 years.CONCLUSIONS: This fully-automated and available blood-based biomarker assay therefore may be useful for early detection, diagnosis, prognosis, and treatment monitoring of AD.

  View details for DOI 10.1186/s13195-022-01116-2

  View details for PubMedID 36371232

• A Fast and Robust Strategy to Remove Variant-Level Artifacts in Alzheimer Disease Sequencing Project Data. Neurology. Genetics Belloy, M. E., Le Guen, Y., Eger, S. J., Napolioni, V., Greicius, M. D., He, Z. 2022; 8 (5): e200012

  Abstract

  Background and Objectives: Exome sequencing (ES) and genome sequencing (GS) are expected to be critical to further elucidate the missing genetic heritability of Alzheimer disease (AD) risk by identifying rare coding and/or noncoding variants that contribute to AD pathogenesis. In the United States, the Alzheimer Disease Sequencing Project (ADSP) has taken a leading role in sequencing AD-related samples at scale, with the resultant data being made publicly available to researchers to generate new insights into the genetic etiology of AD. To achieve sufficient power, the ADSP has adapted a study design where subsets of larger AD cohorts are collected and sequenced across multiple centers, using a variety of sequencing platforms. This approach may lead to variable variant quality across sequencing centers and/or platforms. In this study, we sought to implement and evaluate filters that can be applied fast to robustly remove variant-level artifacts in the ADSP data.Methods: We implemented a robust quality control procedure to handle ADSP data. We evaluated this procedure while performing exome-wide and genome-wide association analyses on AD risk using the latest ADSP whole ES (WES) and whole GS (WGS) data releases (NG00067.v5).Results: We observed that many variants displayed large variation in allele frequencies across sequencing centers/platforms and contributed to spurious association signals with AD risk. We also observed that sequencing platform/center adjustment in association models could not fully account for these spurious signals. To address this issue, we designed and implemented variant filters that could capture and remove these center-specific/platform-specific artifactual variants.Discussion: We derived a fast and robust approach to filter variants that represent sequencing center-related or platform-related artifacts underlying spurious associations with AD risk in ADSP WES and WGS data. This approach will be important to support future robust genetic association studies on ADSP data, as well as other studies with similar designs.

  View details for DOI 10.1212/NXG.0000000000200012

  View details for PubMedID 35966919

• Association of Rare APOE Missense Variants V236E and R251G With Risk of Alzheimer Disease. JAMA neurology Le Guen, Y., Belloy, M. E., Grenier-Boley, B., de Rojas, I., Castillo-Morales, A., Jansen, I., Nicolas, A., Bellenguez, C., Dalmasso, C., Küçükali, F., Eger, S. J., Rasmussen, K. L., Thomassen, J. Q., Deleuze, J. F., He, Z., Napolioni, V., Amouyel, P., Jessen, F., Kehoe, P. G., van Duijn, C., Tsolaki, M., Sánchez-Juan, P., Sleegers, K., Ingelsson, M., Rossi, G., Hiltunen, M., Sims, R., van der Flier, W. M., Ramirez, A., Andreassen, O. A., Frikke-Schmidt, R., Williams, J., Ruiz, A., Lambert, J. C., Greicius, M. D., Arosio, B., Benussi, L., Boland, A., Borroni, B., Caffarra, P., Daian, D., Daniele, A., Debette, S., Dufouil, C., Düzel, E., Galimberti, D., Giedraitis, V., Grimmer, T., Graff, C., Grünblatt, E., Hanon, O., Hausner, L., Heilmann-Heimbach, S., Holstege, H., Hort, J., Jürgen, D., Kuulasmaa, T., van der Lugt, A., Masullo, C., Mecocci, P., Mehrabian, S., de Mendonça, A., Moebus, S., Nacmias, B., Nicolas, G., Olaso, R., Papenberg, G., Parnetti, L., Pasquier, F., Peters, O., Pijnenburg, Y. A., Popp, J., Rainero, I., Ramakers, I., Riedel-Heller, S., Scarmeas, N., Scheltens, P., Scherbaum, N., Schneider, A., Seripa, D., Soininen, H., Solfrizzi, V., Spalletta, G., Squassina, A., van Swieten, J., Tegos, T. J., Tremolizzo, L., Verhey, F., Vyhnalek, M., Wiltfang, J., Boada, M., García-González, P., Puerta, R., Real, L. M., Álvarez, V., Bullido, M. J., Clarimon, J., García-Alberca, J. M., Mir, P., Moreno, F., Pastor, P., Piñol-Ripoll, G., Molina-Porcel, L., Pérez-Tur, J., Rodríguez-Rodríguez, E., Royo, J. L., Sánchez-Valle, R., Dichgans, M., Rujescu, D. 2022

  Abstract

  The APOE ε2 and APOE ε4 alleles are the strongest protective and risk-increasing, respectively, genetic variants for late-onset Alzheimer disease (AD). However, the mechanisms linking APOE to AD-particularly the apoE protein's role in AD pathogenesis and how this is affected by APOE variants-remain poorly understood. Identifying missense variants in addition to APOE ε2 and APOE ε4 could provide critical new insights, but given the low frequency of additional missense variants, AD genetic cohorts have previously been too small to interrogate this question robustly.To determine whether rare missense variants on APOE are associated with AD risk.Association with case-control status was tested in a sequenced discovery sample (stage 1) and followed up in several microarray imputed cohorts as well as the UK Biobank whole-exome sequencing resource using a proxy-AD phenotype (stages 2 and 3). This study combined case-control, family-based, population-based, and longitudinal AD-related cohorts that recruited referred and volunteer participants. Stage 1 included 37 409 nonunique participants of European or admixed European ancestry, with 11 868 individuals with AD and 11 934 controls passing analysis inclusion criteria. In stages 2 and 3, 475 473 participants were considered across 8 cohorts, of which 84 513 individuals with AD and proxy-AD and 328 372 controls passed inclusion criteria. Selection criteria were cohort specific, and this study was performed a posteriori on individuals who were genotyped. Among the available genotypes, 76 195 were excluded. All data were retrieved between September 2015 and November 2021 and analyzed between April and November 2021.In primary analyses, the AD risk associated with each missense variant was estimated, as appropriate, with either linear mixed-model regression or logistic regression. In secondary analyses, associations were estimated with age at onset using linear mixed-model regression and risk of conversion to AD using competing-risk regression.A total of 544 384 participants were analyzed in the primary case-control analysis; 312 476 (57.4%) were female, and the mean (SD; range) age was 64.9 (15.2; 40-110) years. Two missense variants were associated with a 2-fold to 3-fold decreased AD risk: APOE ε4 (R251G) (odds ratio, 0.44; 95% CI, 0.33-0.59; P = 4.7 × 10-8) and APOE ε3 (V236E) (odds ratio, 0.37; 95% CI, 0.25-0.56; P = 1.9 × 10-6). Additionally, the cumulative incidence of AD in carriers of these variants was found to grow more slowly with age compared with noncarriers.In this genetic association study, a novel variant associated with AD was identified: R251G always coinherited with ε4 on the APOE gene, which mitigates the ε4-associated AD risk. The protective effect of the V236E variant, which is always coinherited with ε3 on the APOE gene, was also confirmed. The location of these variants confirms that the carboxyl-terminal portion of apoE plays an important role in AD pathogenesis. The large risk reductions reported here suggest that protein chemistry and functional assays of these variants should be pursued, as they have the potential to guide drug development targeting APOE.

  View details for DOI 10.1001/jamaneurol.2022.1166

  View details for PubMedID 35639372

• Divergent Cortical Tau Positron Emission Tomography Patterns Among Patients With Preclinical Alzheimer Disease. JAMA neurology Young, C. B., Winer, J. R., Younes, K., Cody, K. A., Betthauser, T. J., Johnson, S. C., Schultz, A., Sperling, R. A., Greicius, M. D., Cobos, I., Poston, K. L., Mormino, E. C., Alzheimers Disease Neuroimaging Initiative and the Harvard Aging Brain Study, Weiner, M. W., Aisen, P., Petersen, R., Jack, C. R., Jagust, W., Trojanowki, J. Q., Toga, A. W., Beckett, L., Green, R. C., Saykin, A. J., Morris, J. C., Perrin, R. J., Shaw, L. M., Khachaturian, Z., Carrillo, M., Potter, W., Barnes, L., Bernard, M., Gonzalez, H., Ho, C., Hsiao, J. K., Jackson, J., Masliah, E., Masterman, D., Okonkwo, O., Ryan, L., Silverberg, N., Fleisher, A., Sacrey, D. T., Fockler, J., Conti, C., Veitch, D., Neuhaus, J., Jin, C., Nosheny, R., Ashford, M., Flenniken, D., Kormos, A., Montine, T., Rafii, M., Raman, R., Jimenez, G., Donohue, M., Gessert, D., Salazar, J., Zimmerman, C., Cabrera, Y., Walter, S., Miller, G., Coker, G., Clanton, T., Hergesheimer, L., Smith, S., Adegoke, O., Mahboubi, P., Moore, S., Pizzola, J., Shaffer, E., Harvey, D., Forghanian-Arani, A., Borowski, B., Ward, C., Schwarz, C., Jones, D., Gunter, J., Kantarci, K., Senjem, M., Vemuri, P., Reid, R., Fox, N. C., Malone, I., Thompson, P., Thomopoulos, S. I., Nir, T. M., Jahanshad, N., DeCarli, C., Knaack, A., Fletcher, E., Tosun-Turgut, D., Chen, S. R., Choe, M., Crawford, K., Yuschkevich, P. A., Das, S., Koeppe, R. A., Reiman, E. M., Chen, K., Mathis, C., Landau, S., Cairns, N. J., Householder, E., Franklin, E., Bernhardt, H., Taylor-Reinwald, L., Korecka, M., Figurski, M., Neu, S., Nho, K., Risacher, S. L., Apostolova, L. G., Shen, L., Foroud, T. M., Nudelman, K., Faber, K., Wilmes, K., Thal, L., Johnson, K. A., Sperling, R. A. 2022

  Abstract

  Importance: Characterization of early tau deposition in individuals with preclinical Alzheimer disease (AD) is critical for prevention trials that aim to select individuals at risk for AD and halt the progression of disease.Objective: To evaluate the prevalence of cortical tau positron emission tomography (PET) heterogeneity in a large cohort of clinically unimpaired older adults with elevated beta-amyloid (A+).Design, Setting, and Participants: This cross-sectional study examined prerandomized tau PET, amyloid PET, structural magnetic resonance imaging, demographic, and cognitive data from the Anti-Amyloid Treatment in Asymptomatic AD (A4) Study from April 2014 to December 2017. Follow-up analyses used observational tau PET data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), the Harvard Aging Brain Study (HABS), and the Wisconsin Registry for Alzheimer's Prevention and the Wisconsin Alzheimer's Disease Research Center (together hereinafter referred to as Wisconsin) to evaluate consistency. Participants were clinically unimpaired at the study visit closest to the tau PET scan and had available amyloid and tau PET data (A4 Study, n=447; ADNI, n=433; HABS, n=190; and Wisconsin, n=328). No participants who met eligibility criteria were excluded. Data were analyzed from May 11, 2021, to January 25, 2022.Main Outcomes and Measures: Individuals with preclinical AD with heterogeneous cortical tau PET patterns (A+T cortical+) were identified by examining asymmetrical cortical tau signal and disproportionate cortical tau signal relative to medial temporal lobe (MTL) tau. Voxelwise tau patterns, amyloid, neurodegeneration, cognition, and demographic characteristics were examined.Results: The 447 A4 participants (A+ group, 392; and normal beta-amyloid group, 55), with a mean (SD) age of 71.8 (4.8) years, included 239 women (54%). A total of 36 individuals in the A+ group (9% of the A+ group) exhibited heterogeneous cortical tau patterns and were further categorized into 3 subtypes: asymmetrical left, precuneus dominant, and asymmetrical right. A total of 116 individuals in the A+ group (30% of the A+ group) showed elevated MTL tau (A+T MTL+). Individuals in the A+T cortical+ group were younger than those in the A+T MTL+ group (t61.867=-2.597; P=.03). Across the A+T cortical+ and A+T MTL+ groups, increased regional tau was associated with reduced hippocampal volume and MTL thickness but not with cortical thickness. Memory scores were comparable between the A+T cortical+ and A+T MTL+ groups, whereas executive functioning scores were lower for the A+T cortical+ group than for the A+T MTL+ group. The prevalence of the A+T cortical+ group and tau patterns within the A+T cortical+ group were consistent in ADNI, HABS, and Wisconsin.Conclusions and Relevance: This study suggests that early tau deposition may follow multiple trajectories during preclinical AD and may involve several cortical regions. Staging procedures, especially those based on neuropathology, that assume a uniform trajectory across individuals are insufficient for disease monitoring with tau imaging.

  View details for DOI 10.1001/jamaneurol.2022.0676

  View details for PubMedID 35435938

• Confirming Pathogenicity of the F386L PSEN1 Variant in a South Asian Family With Early-Onset Alzheimer Disease. Neurology. Genetics Eger, S. J., Le Guen, Y., Khan, R. R., Hall, J. N., Kennedy, G., Zaharchuk, G., Couthouis, J., Brooks, W. S., Velakoulis, D., Napolioni, V., Belloy, M. E., Dalgard, C. L., Mormino, E. C., Gitler, A. D., Greicius, M. D. 1800; 8 (1): e647

  Abstract

  Objectives: The F386L PSEN1 variant has been reported in 1 Japanese family with limited clinical information. We aimed to prove that F386L is pathogenic by demonstrating that it segregates with early-onset Alzheimer disease (AD).Methods: Eight individuals in a South Asian family provided DNA for genetic testing and underwent a neurologic examination.Results: The female proband was diagnosed with AD at age 45 years and died at age 49 years. She had a CSF biomarker profile consistent with AD, and her florbetaben PET scan was amyloid positive with high uptake in the striatum. Her MRI showed no prominent white matter disease. Her affected relatives had an age at onset range of 38-57 years and had imaging and biomarker profiles similar to hers.Discussion: The results presented here, in conjunction with the prior report, confirm the pathogenicity of F386L. Furthermore, our study highlights the importance of studying families from underrepresented populations to identify or confirm the pathogenicity of rare variants that may be specific to certain genetic ancestries.

  View details for DOI 10.1212/NXG.0000000000000647

  View details for PubMedID 34901437

• Phenotypic Heterogeneity among GBA p.R202X Carriers in Lewy Body Spectrum Disorders. Biomedicines Napolioni, V., Fredericks, C. A., Kim, Y., Channappa, D., Khan, R. R., Kim, L. H., Zafar, F., Couthouis, J., Davidzon, G. A., Mormino, E. C., Gitler, A. D., Montine, T. J., Schule, B., Greicius, M. D. 1800; 10 (1)

  Abstract

  We describe the clinical and neuropathologic features of patients with Lewy body spectrum disorder (LBSD) carrying a nonsense variant, c.604C>T; p.R202X, in the glucocerebrosidase 1 (GBA) gene. While this GBA variant is causative for Gaucher's disease, the pathogenic role of this mutation in LBSD is unclear. Detailed neuropathologic evaluation was performed for one index case and a structured literature review of other GBA p.R202X carriers was conducted. Through the systematic literature search, we identified three additional reported subjects carrying the same GBA mutation, including one Parkinson's disease (PD) patient with early disease onset, one case with neuropathologically-verified LBSD, and one unaffected relative of a Gaucher's disease patient. Among the affected subjects carrying the GBA p.R202X, all males were diagnosed with Lewy body dementia, while the two females presented as PD. The clinical penetrance of GBA p.R202X in LBSD patients and families argues strongly for a pathogenic role for this variant, although presenting with a striking phenotypic heterogeneity of clinical and pathological features.

  View details for DOI 10.3390/biomedicines10010160

  View details for PubMedID 35052839

• Challenges at the APOE locus: a robust quality control approach for accurate APOE genotyping. Alzheimer's research & therapy Belloy, M. E., Eger, S. J., Le Guen, Y., Damotte, V., Ahmad, S., Ikram, M. A., Ramirez, A., Tsolaki, A. C., Rossi, G., Jansen, I. E., de Rojas, I., Parveen, K., Sleegers, K., Ingelsson, M., Hiltunen, M., Amin, N., Andreassen, O., Sánchez-Juan, P., Kehoe, P., Amouyel, P., Sims, R., Frikke-Schmidt, R., van der Flier, W. M., Lambert, J. C., He, Z., Han, S. S., Napolioni, V., Greicius, M. D. 2022; 14 (1): 22

  Abstract

  Genetic variants within the APOE locus may modulate Alzheimer's disease (AD) risk independently or in conjunction with APOE*2/3/4 genotypes. Identifying such variants and mechanisms would importantly advance our understanding of APOE pathophysiology and provide critical guidance for AD therapies aimed at APOE. The APOE locus however remains relatively poorly understood in AD, owing to multiple challenges that include its complex linkage structure and uncertainty in APOE*2/3/4 genotype quality. Here, we present a novel APOE*2/3/4 filtering approach and showcase its relevance on AD risk association analyses for the rs439401 variant, which is located 1801 base pairs downstream of APOE and has been associated with a potential regulatory effect on APOE.We used thirty-two AD-related cohorts, with genetic data from various high-density single-nucleotide polymorphism microarrays, whole-genome sequencing, and whole-exome sequencing. Study participants were filtered to be ages 60 and older, non-Hispanic, of European ancestry, and diagnosed as cognitively normal or AD (n = 65,701). Primary analyses investigated AD risk in APOE*4/4 carriers. Additional supporting analyses were performed in APOE*3/4 and 3/3 strata. Outcomes were compared under two different APOE*2/3/4 filtering approaches.Using more conventional APOE*2/3/4 filtering criteria (approach 1), we showed that, when in-phase with APOE*4, rs439401 was variably associated with protective effects on AD case-control status. However, when applying a novel filter that increases the certainty of the APOE*2/3/4 genotypes by applying more stringent criteria for concordance between the provided APOE genotype and imputed APOE genotype (approach 2), we observed that all significant effects were lost.We showed that careful consideration of APOE genotype and appropriate sample filtering were crucial to robustly interrogate the role of the APOE locus on AD risk. Our study presents a novel APOE filtering approach and provides important guidelines for research into the APOE locus, as well as for elucidating genetic interaction effects with APOE*2/3/4.

  View details for DOI 10.1186/s13195-022-00962-4

  View details for PubMedID 35120553

• Plasma Biomarkers of Tau and Neurodegeneration During Major Cardiac and Noncardiac Surgery. JAMA neurology Feinstein, I., Wilson, E. N., Swarovski, M. S., Andreasson, K. I., Angst, M. S., Greicius, M. D. 2021

  View details for DOI 10.1001/jamaneurol.2021.2823

  View details for PubMedID 34542578

• Rare genetic coding variants associated with human longevity and protection against age-related diseases NATURE AGING Lin, J., Sin-Chan, P., Napolioni, V., Torres, G. G., Mitra, J., Zhang, Q., Jabalameli, M., Wang, Z., Nha Nguyen, Gao, T., Laudes, M., Goerg, S., Franke, A., Nebel, A., Greicius, M. D., Atzmon, G., Ye, K., Gorbunova, V., Ladiges, W. C., Shuldiner, A. R., Niedernhofer, L. J., Robbins, P. D., Milman, S., Suh, Y., Vijg, J., Barzilai, N., Zhang, Z. D., Regeneron Genetics Ctr 2021; 1 (9): 783-+

  View details for DOI 10.1038/s43587-021-00108-5

  View details for Web of Science ID 000916569100008

• Will CMS Find Aducanumab Reasonable and Necessary for Alzheimer Disease After FDA Approval? JAMA Schulman, K. A., Greicius, M. D., Richman, B. 2021

  View details for DOI 10.1001/jama.2021.11768

  View details for PubMedID 34279572

• Medicare should not cover aducanumab as a treatment for Alzheimer's disease. Annals of neurology Moghavem, N., Henderson, V. W., Greicius, M. D. 2021

  View details for DOI 10.1002/ana.26167

  View details for PubMedID 34278596

• Identification of putative causal loci in whole-genome sequencing data via knockoff statistics. Nature communications He, Z., Liu, L., Wang, C., Le Guen, Y., Lee, J., Gogarten, S., Lu, F., Montgomery, S., Tang, H., Silverman, E. K., Cho, M. H., Greicius, M., Ionita-Laza, I. 2021; 12 (1): 3152

  Abstract

  The analysis of whole-genome sequencing studies is challenging due to the large number of rare variants in noncoding regions and the lack of natural units for testing. We propose a statistical method to detect and localize rare and common risk variants in whole-genome sequencing studies based on a recently developed knockoff framework. It can (1) prioritize causal variants over associations due to linkage disequilibrium thereby improving interpretability; (2) help distinguish the signal due to rare variants from shadow effects of significant common variants nearby; (3) integrate multiple knockoffs for improved power, stability, and reproducibility; and (4) flexibly incorporate state-of-the-art and future association tests to achieve the benefits proposed here. In applications to whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (ADSP) and COPDGene samples from NHLBI Trans-Omics for Precision Medicine (TOPMed) Program we show that our method compared with conventional association tests can lead to substantially more discoveries.

  View details for DOI 10.1038/s41467-021-22889-4

  View details for PubMedID 34035245

• A Robust Test for Additive Gene-Environment Interaction Under the Trend Effect of Genotype Using an Empirical Bayes-Type Shrinkage Estimator. American journal of epidemiology Sanyal, N., Napolioni, V., de Rochemonteix, M., Belloy, M. E., Caporaso, N. E., Landi, M. T., Greicius, M. D., Chatterjee, N., Han, S. S. 2021

  Abstract

  Evaluating gene by environment (G$\times$E) interaction under an additive risk model (i.e. additive interaction) has gained wider attention. Recently, statistical tests have been proposed for detecting additive interaction that utilize an assumption on G-E independence to boost power, which do not rely on restrictive genetic models such as dominant or recessive models. However, a major limitation of these methods is a sharp increase in type I error when this assumption is violated. Our goal is to develop a robust test for additive G$\times$E interaction under the trend effect of genotype, applying an empirical Bayes-type shrinkage estimator of the relative excess risk due to interaction. The proposed method uses a set of constraints to impose the trend effect of genotype and builds an estimator that data-adaptively shrinks a RERI estimator obtained under a general model for G-E dependence using a retrospective likelihood framework. Numerical study under varying levels of departures from G-E independence shows that the proposed method is robust against the violation of the independence assumption while providing an adequate balance between bias and efficiency compared to existing methods. We applied the proposed method to the genetic data of Alzheimer's disease and lung cancer.

  View details for DOI 10.1093/aje/kwab124

  View details for PubMedID 33942053

• A novel age-informed approach for genetic association analysis in Alzheimer's disease. Alzheimer's research & therapy Le Guen, Y., Belloy, M. E., Napolioni, V., Eger, S. J., Kennedy, G., Tao, R., He, Z., Greicius, M. D., Alzheimers Disease Neuroimaging Initiative 2021; 13 (1): 72

  Abstract

  BACKGROUND: Many Alzheimer's disease (AD) genetic association studies disregard age or incorrectly account for it, hampering variant discovery.METHODS: Using simulated data, we compared the statistical power of several models: logistic regression on AD diagnosis adjusted and not adjusted for age; linear regression on a score integrating case-control status and age; and multivariate Cox regression on age-at-onset. We applied these models to real exome-wide data of 11,127 sequenced individuals (54% cases) and replicated suggestive associations in 21,631 genotype-imputed individuals (51% cases).RESULTS: Modeling variable AD risk across age results in 5-10% statistical power gain compared to logistic regression without age adjustment, while incorrect age adjustment leads to critical power loss. Applying our novel AD-age score and/or Cox regression, we discovered and replicated novel variants associated with AD on KIF21B, USH2A, RAB10, RIN3, and TAOK2 genes.CONCLUSION: Our AD-age score provides a simple means for statistical power gain and is recommended for future AD studies.

  View details for DOI 10.1186/s13195-021-00808-5

  View details for PubMedID 33794991

• Common X-chromosome variants are associated with Parkinson's disease risk. Annals of neurology Le Guen, Y., Napolioni, V., Belloy, M. E., Yu, E., Krohn, L., Ruskey, J. A., Gan-Or, Z., Kennedy, G., Eger, S. J., Greicius, M. D. 2021

  Abstract

  OBJECTIVE: Identify genetic variants on the X-chromosome associated with Parkinson's disease (PD) risk.METHODS: We performed an X-chromosome-wide association study (XWAS) of PD risk by meta-analyzing results from sex-stratified analyses. To avoid spurious associations, we designed a specific harmonization pipeline for the X-chromosome and focused on a European ancestry sample. We included 11,142 cases, 280,164 controls, and 5,379 proxy cases, based on parental history of PD. Additionally, we tested the association of significant variants with: (i) PD risk in an independent replication with 1,561 cases and 2,465 controls, and (ii) putamen volume in 33,360 individuals from the UK Biobank.RESULTS: In the discovery meta-analysis, we identified: rs7066890 (OR=1.10 [1.06-1.14]; P=2.2x10-9 ) intron of GPM6B, and rs28602900 (OR=1.10 [1.07-1.14]; P=1.6x10-8 ) in a high gene density region including RPL10, ATP6A1, FAM50A, PLXNA3. The rs28602900 association with PD was replicated (OR=1.16 [1.03-1.30]; P=0.016) and shown to colocalize with a significant expression quantitative locus (eQTL) regulating RPL10 expression in the putamen and other brain tissues in GTEx. Additionally, the rs28602900 locus was found to be associated with reduced brain putamen volume. No results reached genome-wide significance in the sex-stratified analyses.INTERPRETATION: We report the first XWAS of PD and identify two genome-wide significant loci. The rs28602900 association replicated in an independent PD dataset and showed concordant effects in its association with putamen volume. Critically, rs26802900 is a significant eQTL of RPL10.These results support a role for ribosomal proteins in PD pathogenesis and show that the X-chromosome contributes to PD genetic risk. This article is protected by copyright. All rights reserved.

  View details for DOI 10.1002/ana.26051

  View details for PubMedID 33583074

• Amyloid PET imaging in self-identified non-Hispanic Blacks from the Anti-Amyloid in Asymptomatic Alzheimer's Disease (A4) Study. Neurology Deters, K., Napolioni, V., Sperling, R. A., Greicius, M. D., Mayeux, R., Hohman, T., Mormino, E. C. 2021

  Abstract

  OBJECTIVE: To examine whether amyloid PET in CN individuals that were screened for the Anti-Amyloid in Asymptomatic AD (A4) study differed across self-identified, non-Hispanic White and Black (NHW and NHB) groups.METHODS: We examined 3689 NHW and 144 NHB that passed initial screening for the A4 study and underwent amyloid PET. The effect of race on amyloid PET was examined using logistic (dichotomous groups) and linear (continuous values) regression controlling for age, sex, and number of APOE epsilon4 and APOE epsilon2 alleles. Associations between amyloid and genetically determined ancestry (reflecting African, South Asian, East Asian, American, European populations) were tested within the NHB group. Potential interactions with APOE were assessed.RESULTS: NHB had lower rates of amyloid-positivity and lower continuous amyloid levels compared to NHW. This race effect on amyloid was strongest in the APOE epsilon4 group. Within NHB, those with a lower percentage of African ancestry had higher amyloid. A greater proportion of NHB did not pass initial screening compared to NHW, suggesting potential sources of bias related to race in the A4 PET data.CONCLUSION: Reduced amyloid was observed in self-identified non-Hispanic Blacks that passed initial eligibility criteria for the A4 Study. This work stresses the importance of investigating AD biomarkers in ancestrally diverse samples as well as the need for careful consideration regarding study eligibility criteria in AD prevention trials.

  View details for DOI 10.1212/WNL.0000000000011599

  View details for PubMedID 33568538

• KLVS heterozygosity reduces brain amyloid in asymptomatic at-risk APOE4 carriers. Neurobiology of aging Belloy, M. E., Eger, S. J., Le Guen, Y., Napolioni, V., Deters, K. D., Yang, H., Scelsi, M. A., Porter, T., James, S., Wong, A., Schott, J. M., Sperling, R. A., Laws, S. M., Mormino, E. C., He, Z., Han, S. S., Altmann, A., Greicius, M. D., A4 Study Team, Insight 46 Study Team, Australian Imaging Biomarkers and Lifestyle (AIBL) Study, Alzheimer's Disease Neuroimaging Initiative 2021; 101: 123–29

  Abstract

  KLOTHOVS heterozygosity (KLVSHET+) was recently shown to be associated with reduced risk of Alzheimer's disease (AD) in APOE4 carriers. Additional studies suggest that KLVSHET+ protects against amyloid burden in cognitively normal older subjects, but sample sizes were too small to draw definitive conclusions. We performed a well-powered meta-analysis across 5 independent studies, comprising 3581 pre-clinical participants ages 60-80, to investigate whether KLVSHET+ reduces the risk of having an amyloid-positive positron emission tomography scan. Analyses were stratified by APOE4 status. KLVSHET+ reduced the risk of amyloid positivity in APOE4 carriers (odds ratio= 0.67 [0.52-0.88]; p= 3.5*10-3), but not in APOE4 non-carriers (odds ratio= 0.94 [0.73-1.21]; p= 0.63). The combination of APOE4 and KLVS genotypes should help enrich AD clinical trials for pre-symptomatic subjects at increased risk of developing amyloid aggregation and AD. KL-related pathways may help elucidate protective mechanisms against amyloid accumulation and merit exploration for novel AD drug targets. Future investigation of the biological mechanisms by which KL interacts with APOE4 and AD are warranted.

  View details for DOI 10.1016/j.neurobiolaging.2021.01.008

  View details for PubMedID 33610961

• Network propagation of rare variants in Alzheimer's disease reveals tissue-specific hub genes and communities. PLoS computational biology Scelsi, M. A., Napolioni, V. n., Greicius, M. D., Altmann, A. n. 2021; 17 (1): e1008517

  Abstract

  State-of-the-art rare variant association testing methods aggregate the contribution of rare variants in biologically relevant genomic regions to boost statistical power. However, testing single genes separately does not consider the complex interaction landscape of genes, nor the downstream effects of non-synonymous variants on protein structure and function. Here we present the NETwork Propagation-based Assessment of Genetic Events (NETPAGE), an integrative approach aimed at investigating the biological pathways through which rare variation results in complex disease phenotypes. We applied NETPAGE to sporadic, late-onset Alzheimer's disease (AD), using whole-genome sequencing from the AD Neuroimaging Initiative (ADNI) cohort, as well as whole-exome sequencing from the AD Sequencing Project (ADSP). NETPAGE is based on network propagation, a framework that models information flow on a graph and simulates the percolation of genetic variation through tissue-specific gene interaction networks. The result of network propagation is a set of smoothed gene scores that can be tested for association with disease status through sparse regression. The application of NETPAGE to AD enabled the identification of a set of connected genes whose smoothed variation profile was robustly associated to case-control status, based on gene interactions in the hippocampus. Additionally, smoothed scores significantly correlated with risk of conversion to AD in Mild Cognitive Impairment (MCI) subjects. Lastly, we investigated tissue-specific transcriptional dysregulation of the core genes in two independent RNA-seq datasets, as well as significant enrichments in terms of gene sets with known connections to AD. We present a framework that enables enhanced genetic association testing for a wide range of traits, diseases, and sample sizes.

  View details for DOI 10.1371/journal.pcbi.1008517

  View details for PubMedID 33411734

• Genome-wide analysis of common and rare variants via multiple knockoffs at biobank scale, with an application to Alzheimer disease genetics. American journal of human genetics He, Z., Le Guen, Y., Liu, L., Lee, J., Ma, S., Yang, A. C., Liu, X., Rutledge, J., Losada, P. M., Song, B., Belloy, M. E., Butler, R. R., Longo, F. M., Tang, H., Mormino, E. C., Wyss-Coray, T., Greicius, M. D., Ionita-Laza, I. 2021

  Abstract

  Knockoff-based methods have become increasingly popular due to their enhanced power for locus discovery and their ability to prioritize putative causal variants in a genome-wide analysis. However, because of the substantial computational cost for generating knockoffs, existing knockoff approaches cannot analyze millions of rare genetic variants in biobank-scale whole-genome sequencing and whole-genome imputed datasets. We propose a scalable knockoff-based method for the analysis of common and rare variants across the genome, KnockoffScreen-AL, that is applicable to biobank-scale studies with hundreds of thousands of samples and millions of genetic variants. The application of KnockoffScreen-AL to the analysis of Alzheimer disease (AD) in 388,051 WG-imputed samples from the UK Biobank resulted in 31 significant loci, including 14 loci that are missed by conventional association tests on these data. We perform replication studies in an independent meta-analysis of clinically diagnosed AD with 94,437 samples, and additionally leverage single-cell RNA-sequencing data with 143,793 single-nucleus transcriptomes from 17 control subjects and AD-affected individuals, and proteomics data from 735 control subjects and affected indviduals with AD and related disorders to validate the genes at these significant loci. These multi-omics analyses show that 79.1% of the proximal genes at these loci and 76.2% of the genes at loci identified only by KnockoffScreen-AL exhibit at least suggestive signal (p < 0.05) in the scRNA-seq or proteomics analyses. We highlight a potentially causal gene in AD progression, EGFR, that shows significant differences in expression and protein levels between AD-affected individuals and healthy control subjects.

  View details for DOI 10.1016/j.ajhg.2021.10.009

  View details for PubMedID 34767756

• Failure to demonstrate efficacy of aducanumab: An analysis of the EMERGE and ENGAGE trials as reported by Biogen, December 2019. Alzheimer's & dementia : the journal of the Alzheimer's Association Knopman, D. S., Jones, D. T., Greicius, M. D. 2020

  Abstract

  Aducanumab recently underwent two large phase III clinical trials that were stopped prematurely by the sponsor Biogen. One trial was trending positive while the other showed no benefits from aducanumab. Post hoc analyses led the sponsor to assert that there was a sufficient efficacy signal to justify a new drug application as a treatment for Alzheimer's disease. The sponsor claimed that subsets of participants receiving sufficiently high doses of aducanumab demonstrated benefits in both trials. In contrast, we identified alternative accounts for the apparent drug benefits in post hoc subgroups that are unrelated to dose effects. Biomarker data were consistent with target engagement, but no evidence was presented to correlate biomarker changes to cognitive benefits. Our analysis supports the conduct of a third, phase III trial with high-dose aducanumab. Aducanumab's efficacy as a treatment for the cognitive dysfunction in Alzheimer's disease cannot be proven by clinical trials with divergent outcomes.

  View details for DOI 10.1002/alz.12213

  View details for PubMedID 33135381

• A Likelihood Ratio Test for Gene-Environment Interaction Based on the Trend Effect of Genotype Under an Additive Risk Model Using the Gene-Environment Independence Assumption. American journal of epidemiology de Rochemonteix, M., Napolioni, V., Sanyal, N., Belloy, M. E., Caporaso, N. E., Landi, M. T., Greicius, M. D., Chatterjee, N., Han, S. S. 2020

  Abstract

  Several statistical methods have been proposed for testing gene(G)-environment(E) interactions under additive risk models using genome-wide association study data. However, these approaches have strong assumptions on underlying genetic models such as dominant or recessive effects that are known to be less robust when the true genetic model is unknown. We aim to develop a robust trend test employing a likelihood ratio test for detecting G-E interaction under an additive risk model, while incorporating the G-E independence assumption to increase power. We used a constrained likelihood to impose two sets of constraints for (i) the linear trend effect of genotype and (ii) the additive joint effects of G and E. To incorporate the G-E independence assumption, a retrospective likelihood was used versus a standard prospective likelihood. Numerical investigation suggests that the proposed tests are more powerful than tests assuming dominant, recessive, or general models under various parameter settings and under both likelihoods. Incorporation of the independence assumption enhances efficiency by 2.5- fold. We applied the proposed methods to examine gene-smoking interaction for lung cancer and gene-APOE*4 interaction for Alzheimer's disease, which identified two interactions between APOE*4 and loci MS4A and BIN1 at genome-wide significance that were replicated using independent data.

  View details for DOI 10.1093/aje/kwaa132

  View details for PubMedID 32870973

• Clonally expanded CD8 T cells patrol the cerebrospinal fluid in Alzheimer's disease. Nature Gate, D., Saligrama, N., Leventhal, O., Yang, A. C., Unger, M. S., Middeldorp, J., Chen, K., Lehallier, B., Channappa, D., De Los Santos, M. B., McBride, A., Pluvinage, J., Elahi, F., Tam, G. K., Kim, Y., Greicius, M., Wagner, A. D., Aigner, L., Galasko, D. R., Davis, M. M., Wyss-Coray, T. 2020

  Abstract

  Alzheimer's disease is an incurable neurodegenerative disorder in which neuroinflammation has a critical function1. However, little is known about the contribution of the adaptive immune response in Alzheimer's disease2. Here, using integrated analyses of multiple cohorts, we identify peripheral and central adaptive immune changes in Alzheimer's disease. First, we performed mass cytometry of peripheral blood mononuclear cells and discovered an immune signature of Alzheimer's disease that consists of increased numbers of CD8+ T effector memory CD45RA+ (TEMRA) cells. In a second cohort, we found that CD8+ TEMRA cells were negatively associated with cognition. Furthermore, single-cell RNA sequencing revealed that T cell receptor (TCR) signalling was enhanced in these cells. Notably, by using several strategies of single-cell TCR sequencing in a third cohort, we discovered clonally expanded CD8+ TEMRA cells in the cerebrospinal fluid of patients with Alzheimer's disease. Finally, we used machine learning, cloning and peptide screens to demonstrate the specificity of clonally expanded TCRs in the cerebrospinal fluid of patients with Alzheimer's disease to two separate Epstein-Barr virus antigens. These results reveal an adaptive immune response in the blood and cerebrospinal fluid in Alzheimer's disease and provide evidence of clonal, antigen-experienced T cells patrolling the intrathecal space of brains affected by age-related neurodegeneration.

  View details for DOI 10.1038/s41586-019-1895-7

  View details for PubMedID 31915375

• Tau PET imaging with 18F-PI-2620 in aging and neurodegenerative diseases. European journal of nuclear medicine and molecular imaging Mormino, E. C., Toueg, T. N., Azevedo, C. n., Castillo, J. B., Guo, W. n., Nadiadwala, A. n., Corso, N. K., Hall, J. N., Fan, A. n., Trelle, A. N., Harrison, M. B., Hunt, M. P., Sha, S. J., Deutsch, G. n., James, M. n., Fredericks, C. A., Koran, M. E., Zeineh, M. n., Poston, K. n., Greicius, M. D., Khalighi, M. n., Davidzon, G. A., Shen, B. n., Zaharchuk, G. n., Wagner, A. D., Chin, F. T. 2020

  Abstract

  In vivo measurement of the spatial distribution of neurofibrillary tangle pathology is critical for early diagnosis and disease monitoring of Alzheimer's disease (AD).Forty-nine participants were scanned with 18F-PI-2620 PET to examine the distribution of this novel PET ligand throughout the course of AD: 36 older healthy controls (HC) (age range 61 to 86), 11 beta-amyloid+ (Aβ+) participants with cognitive impairment (CI; clinical diagnosis of either mild cognitive impairment or AD dementia, age range 57 to 86), and 2 participants with semantic variant primary progressive aphasia (svPPA, age 66 and 78). Group differences in brain regions relevant in AD (medial temporal lobe, posterior cingulate cortex, and lateral parietal cortex) were examined using standardized uptake value ratios (SUVRs) normalized to the inferior gray matter of the cerebellum.SUVRs in target regions were relatively stable 60 to 90 min post-injection, with the exception of very high binders who continued to show increases over time. Robust elevations in 18F-PI-2620 were observed between HC and Aβ+ CI across all AD regions. Within the HC group, older age was associated with subtle elevations in target regions. Mildly elevated focal uptake was observed in the anterior temporal pole in one svPPA patient.Preliminary results suggest strong differences in the medial temporal lobe and cortical regions known to be impacted in AD using 18F-PI-2620 in patients along the AD trajectory. This work confirms that 18F-PI-2620 holds promise as a tool to visualize tau aggregations in AD.

  View details for DOI 10.1007/s00259-020-04923-7

  View details for PubMedID 32572562

• Recent Consanguinity and Outbred Autozygosity Are Associated With Increased Risk of Late-Onset Alzheimer's Disease. Frontiers in genetics Napolioni, V., Scelsi, M. A., Khan, R. R., Altmann, A., Greicius, M. D. 2020; 11: 629373

  Abstract

  Prior work in late-onset Alzheimer's disease (LOAD) has resulted in discrepant findings as to whether recent consanguinity and outbred autozygosity are associated with LOAD risk. In the current study, we tested the association between consanguinity and outbred autozygosity with LOAD in the largest such analysis to date, in which 20 LOAD GWAS datasets were retrieved through public databases. Our analyses were restricted to eight distinct ethnic groups: African-Caribbean, Ashkenazi-Jewish European, European-Caribbean, French-Canadian, Finnish European, North-Western European, South-Eastern European, and Yoruba African for a total of 21,492 unrelated subjects (11,196 LOAD and 10,296 controls). Recent consanguinity determination was performed using FSuite v1.0.3, according to subjects' ancestral background. The level of autozygosity in the outbred population was assessed by calculating inbreeding estimates based on the proportion (FROH) and the number (NROH) of runs of homozygosity (ROHs). We analyzed all eight ethnic groups using a fixed-effect meta-analysis, which showed a significant association of recent consanguinity with LOAD (N = 21,481; OR = 1.262, P = 3.6 * 10-4), independently of APOE 4 (N = 21,468, OR = 1.237, P = 0.002), and years of education (N = 9,257; OR = 1.274, P = 0.020). Autozygosity in the outbred population was also associated with an increased risk of LOAD, both for F ROH (N = 20,237; OR = 1.204, P = 0.030) and N ROH metrics (N = 20,237; OR = 1.019, P = 0.006), independently of APOE 4 [(F ROH, N = 20,225; OR = 1.222, P = 0.029) (N ROH, N = 20,225; OR = 1.019, P = 0.007)]. By leveraging the Alzheimer's Disease Sequencing Project (ADSP) whole-exome sequencing (WES) data, we determined that LOAD subjects do not show an enrichment of rare, risk-enhancing minor homozygote variants compared to the control population. A two-stage recessive GWAS using ADSP data from 201 consanguineous subjects in the discovery phase followed by validation in 10,469 subjects led to the identification of RPH3AL p.A303V (rs117190076) as a rare minor homozygote variant increasing the risk of LOAD [discovery: Genotype Relative Risk (GRR) = 46, P = 2.16 * 10-6; validation: GRR = 1.9, P = 8.0 * 10-4]. These results confirm that recent consanguinity and autozygosity in the outbred population increase risk for LOAD. Subsequent work, with increased samples sizes of consanguineous subjects, should accelerate the discovery of non-additive genetic effects in LOAD.

  View details for DOI 10.3389/fgene.2020.629373

  View details for PubMedID 33584820

• Association of Klotho-VS Heterozygosity With Risk of Alzheimer Disease in Individuals Who Carry APOE4. JAMA neurology Belloy, M. E., Napolioni, V. n., Han, S. S., Le Guen, Y. n., Greicius, M. D. 2020

  Abstract

  Identification of genetic factors that interact with the apolipoprotein e4 (APOE4) allele to reduce risk for Alzheimer disease (AD) would accelerate the search for new AD drug targets. Klotho-VS heterozygosity (KL-VSHET+ status) protects against aging-associated phenotypes and cognitive decline, but whether it protects individuals who carry APOE4 from AD remains unclear.To determine if KL-VSHET+ status is associated with reduced AD risk and β-amyloid (Aβ) pathology in individuals who carry APOE4.This study combined 25 independent case-control, family-based, and longitudinal AD cohorts that recruited referred and volunteer participants and made data available through public repositories. Analyses were stratified by APOE4 status. Three cohorts were used to evaluate conversion risk, 1 provided longitudinal measures of Aβ CSF and PET, and 3 provided cross-sectional measures of Aβ CSF. Genetic data were available from high-density single-nucleotide variant microarrays. All data were collected between September 2015 and September 2019 and analyzed between April 2019 and December 2019.The risk of AD was evaluated through logistic regression analyses under a case-control design. The risk of conversion to mild cognitive impairment (MCI) or AD was evaluated through competing risks regression. Associations with Aβ, measured from cerebrospinal fluid (CSF) or brain positron emission tomography (PET), were evaluated using linear regression and mixed-effects modeling.Of 36 530 eligible participants, 13 782 were excluded for analysis exclusion criteria or refusal to participate. Participants were men and women aged 60 years and older who were non-Hispanic and of Northwestern European ancestry and had been diagnosed as being cognitively normal or having MCI or AD. The sample included 20 928 participants in case-control studies, 3008 in conversion studies, 556 in Aβ CSF regression analyses, and 251 in PET regression analyses. The genotype KL-VSHET+ was associated with reduced risk for AD in individuals carrying APOE4 who were 60 years or older (odds ratio, 0.75 [95% CI, 0.67-0.84]; P = 7.4 × 10-7), and this was more prominent at ages 60 to 80 years (odds ratio, 0.69 [95% CI, 0.61-0.79]; P = 3.6 × 10-8). Additionally, control participants carrying APOE4 with KL-VS heterozygosity were at reduced risk of converting to MCI or AD (hazard ratio, 0.64 [95% CI, 0.44-0.94]; P = .02). Finally, in control participants who carried APOE4 and were aged 60 to 80 years, KL-VS heterozygosity was associated with higher Aβ in CSF (β, 0.06 [95% CI, 0.01-0.10]; P = .03) and lower Aβ on PET scans (β, -0.04 [95% CI, -0.07 to -0.00]; P = .04).The genotype KL-VSHET+ is associated with reduced AD risk and Aβ burden in individuals who are aged 60 to 80 years, cognitively normal, and carrying APOE4. Molecular pathways associated with KL merit exploration for novel AD drug targets. The KL-VS genotype should be considered in conjunction with the APOE genotype to refine AD prediction models used in clinical trial enrichment and personalized genetic counseling.

  View details for DOI 10.1001/jamaneurol.2020.0414

  View details for PubMedID 32282020

• Rooting out racial stereotypes in Neurology (R) A commentary on "Lucky and the root doctor" NEUROLOGY Hamilton, R. H., McClean, J. C., Greicius, M. D., Gamaldo, C. E., Burrus, T. M., Charleston, L., Correa, D. J., Ebong, I. M., Hamilton, R., Lewis, S., Thomas, R. P., Vargas, A., Flippen, C. C. 2019; 92 (22): 1029–32

  View details for DOI 10.1212/WNL.0000000000007578

  View details for Web of Science ID 000480769900016

• A Quarter Century of APOE and Alzheimer's Disease: Progress to Date and the Path Forward NEURON Belloy, M. E., Napolioni, V., Greicius, M. D. 2019; 101 (5): 820–38

  View details for DOI 10.1016/j.neuron.2019.01.056

  View details for Web of Science ID 000460398100010

• Ultra-Low-Dose F-18-Florbetaben Amyloid PET Imaging Using Deep Learning with Multi-Contrast MRI Inputs RADIOLOGY Chen, K. T., Gong, E., Macruz, F., Xu, J., Boumis, A., Khalighi, M., Poston, K. L., Sha, S. J., Greicius, M. D., Mormino, E., Pauly, J. M., Srinivas, S., Zaharchuk, G. 2019; 290 (3): 649–56

  View details for DOI 10.1148/radiol.2018180940

  View details for Web of Science ID 000459261900009

• A Quarter Century of APOE and Alzheimer's Disease: Progress to Date and the Path Forward. Neuron Belloy, M. E., Napolioni, V. n., Greicius, M. D. 2019; 101 (5): 820–38

  Abstract

  Alzheimer's disease (AD) is considered a polygenic disorder. This view is clouded, however, by lingering uncertainty over how to treat the quasi "monogenic" role of apolipoprotein E (APOE). The APOE4 allele is not only the strongest genetic risk factor for AD, it also affects risk for cardiovascular disease, stroke, and other neurodegenerative disorders. This review, based mostly on data from human studies, ranges across a variety of APOE-related pathologies, touching on evolutionary genetics and risk mitigation by ethnicity and sex. The authors also address one of the most fundamental question pertaining to APOE4 and AD: does APOE4 increase AD risk via a loss or gain of function? The answer will be of the utmost importance in guiding future research in AD.

  View details for PubMedID 30844401

  View details for PubMedCentralID PMC6407643

• Ultra-Low-Dose 18F-Florbetaben Amyloid PET Imaging Using Deep Learning with Multi-Contrast MRI Inputs. Radiology Chen, K. T., Gong, E., de Carvalho Macruz, F. B., Xu, J., Boumis, A., Khalighi, M., Poston, K. L., Sha, S. J., Greicius, M. D., Mormino, E., Pauly, J. M., Srinivas, S., Zaharchuk, G. 2018: 180940

  Abstract

  Purpose To reduce radiotracer requirements for amyloid PET/MRI without sacrificing diagnostic quality by using deep learning methods. Materials and Methods Forty data sets from 39 patients (mean age ± standard deviation [SD], 67 years ± 8), including 16 male patients and 23 female patients (mean age, 66 years ± 6 and 68 years ± 9, respectively), who underwent simultaneous amyloid (fluorine 18 [18F]-florbetaben) PET/MRI examinations were acquired from March 2016 through October 2017 and retrospectively analyzed. One hundredth of the raw list-mode PET data were randomly chosen to simulate a low-dose (1%) acquisition. Convolutional neural networks were implemented with low-dose PET and multiple MR images (PET-plus-MR model) or with low-dose PET alone (PET-only) as inputs to predict full-dose PET images. Quality of the synthesized images was evaluated while Bland-Altman plots assessed the agreement of regional standard uptake value ratios (SUVRs) between image types. Two readers scored image quality on a five-point scale (5 = excellent) and determined amyloid status (positive or negative). Statistical analyses were carried out to assess the difference of image quality metrics and reader agreement and to determine confidence intervals (CIs) for reading results. Results The synthesized images (especially from the PET-plus-MR model) showed marked improvement on all quality metrics compared with the low-dose image. All PET-plus-MR images scored 3 or higher, with proportions of images rated greater than 3 similar to those for the full-dose images (-10% difference [eight of 80 readings], 95% CI: -15%, -5%). Accuracy for amyloid status was high (71 of 80 readings [89%]) and similar to intrareader reproducibility of full-dose images (73 of 80 [91%]). The PET-plus-MR model also had the smallest mean and variance for SUVR difference to full-dose images. Conclusion Simultaneously acquired MRI and ultra-low-dose PET data can be used to synthesize full-dose-like amyloid PET images. © RSNA, 2018 Online supplemental material is available for this article.

  View details for PubMedID 30526350

• Effect of Alzheimer's disease risk and protective factors on cognitive trajectories in subjective memory complainers: An INSIGHT-preAD study ALZHEIMERS & DEMENTIA Teipel, S. J., Cavedo, E., Lista, S., Habert, M., Potier, M., Grothe, M. J., Epelbaum, S., Sambati, L., Gagliardi, G., Toschi, N., Greicius, M. D., Dubois, B., Hampel, H., INSIGHT-preAD Study Grp, Alzheimer Precision Med Initiative 2018; 14 (9): 1126–36

  Abstract

  Cognitive change in people at risk of Alzheimer's disease (AD) such as subjective memory complainers is highly variable across individuals.We used latent class growth modeling to identify distinct classes of nonlinear trajectories of cognitive change over 2 years follow-up from 265 subjective memory complainers individuals (age 70 years and older) of the INSIGHT-preAD cohort. We determined the effect of cortical amyloid load, hippocampus and basal forebrain volumes, and education on the cognitive trajectory classes.Latent class growth modeling identified distinct nonlinear cognitive trajectories. Education was associated with higher performing trajectories, whereas global amyloid load and basal forebrain atrophy were associated with lower performing trajectories.Distinct classes of cognitive trajectories were associated with risk and protective factors of AD. These associations support the notion that the identified cognitive trajectories reflect different risk for AD that may be useful for selecting high-risk individuals for intervention trials.

  View details for PubMedID 29792873

• Genetic study of multimodal imaging Alzheimer's disease progression score implicates novel loci BRAIN Scelsi, M. A., Khan, R. R., Lorenzi, M., Christopher, L., Greicius, M. D., Schott, J. M., Ourselin, S., Altmann, A., Alzheimer's Dis Neuroimaging, Natl Alzheimer's Coordinating Ctr 2018; 141: 2167–80

  Abstract

  Identifying genetic risk factors underpinning different aspects of Alzheimer's disease has the potential to provide important insights into pathogenesis. Moving away from simple case-control definitions, there is considerable interest in using quantitative endophenotypes, such as those derived from imaging as outcome measures. Previous genome-wide association studies of imaging-derived biomarkers in sporadic late-onset Alzheimer's disease focused only on phenotypes derived from single imaging modalities. In contrast, we computed a novel multi-modal neuroimaging phenotype comprising cortical amyloid burden and bilateral hippocampal volume. Both imaging biomarkers were used as input to a disease progression modelling algorithm, which estimates the biomarkers' long-term evolution curves from population-based longitudinal data. Among other parameters, the algorithm computes the shift in time required to optimally align a subjects' biomarker trajectories with these population curves. This time shift serves as a disease progression score and it was used as a quantitative trait in a discovery genome-wide association study with n = 944 subjects from the Alzheimer's Disease Neuroimaging Initiative database diagnosed as Alzheimer's disease, mild cognitive impairment or healthy at the time of imaging. We identified a genome-wide significant locus implicating LCORL (rs6850306, chromosome 4; P = 1.03 × 10-8). The top variant rs6850306 was found to act as an expression quantitative trait locus for LCORL in brain tissue. The clinical role of rs6850306 in conversion from healthy ageing to mild cognitive impairment or Alzheimer's disease was further validated in an independent cohort comprising healthy, older subjects from the National Alzheimer's Coordinating Center database. Specifically, possession of a minor allele at rs6850306 was protective against conversion from mild cognitive impairment to Alzheimer's disease in the National Alzheimer's Coordinating Center cohort (hazard ratio = 0.593, 95% confidence interval = 0.387-0.907, n = 911, PBonf = 0.032), in keeping with the negative direction of effect reported in the genome-wide association study (βdisease progression score = -0.07 ± 0.01). The implicated locus is linked to genes with known connections to Alzheimer's disease pathophysiology and other neurodegenerative diseases. Using multimodal imaging phenotypes in association studies may assist in unveiling the genetic drivers of the onset and progression of complex diseases.

  View details for PubMedID 29860282

  View details for PubMedCentralID PMC6022660

• PINK1 Phosphorylates MIC60/Mitofilin to Control Structural Plasticity of Mitochondrial Crista Junctions. Molecular cell Tsai, P. I., Lin, C. H., Hsieh, C. H., Papakyrikos, A. M., Kim, M. J., Napolioni, V. n., Schoor, C. n., Couthouis, J. n., Wu, R. M., Wszolek, Z. K., Winter, D. n., Greicius, M. D., Ross, O. A., Wang, X. n. 2018

  Abstract

  Mitochondrial crista structure partitions vital cellular reactions and is precisely regulated by diverse cellular signals. Here, we show that, in Drosophila, mitochondrial cristae undergo dynamic remodeling among distinct subcellular regions and the Parkinson's disease (PD)-linked Ser/Thr kinase PINK1 participates in their regulation. Mitochondria increase crista junctions and numbers in selective subcellular areas, and this remodeling requires PINK1 to phosphorylate the inner mitochondrial membrane protein MIC60/mitofilin, which stabilizes MIC60 oligomerization. Expression of MIC60 restores crista structure and ATP levels of PINK1-null flies and remarkably rescues their behavioral defects and dopaminergic neurodegeneration. In an extension to human relevance, we discover that the PINK1-MIC60 pathway is conserved in human neurons, and expression of several MIC60 coding variants in the mitochondrial targeting sequence found in PD patients in Drosophila impairs crista junction formation and causes locomotion deficits. These findings highlight the importance of maintenance and plasticity of crista junctions to cellular homeostasis in vivo.

  View details for PubMedID 29456190

• Mnemonic Training Reshapes Brain Networks to Support Superior Memory NEURON Dresler, M., Shirer, W. R., Konrad, B. N., Mueller, N. C., Wagner, I. C., Fernandez, G., Czisch, M., Greicius, M. D. 2017; 93 (5): 1227-?

  Abstract

  Memory skills strongly differ across the general population; however, little is known about the brain characteristics supporting superior memory performance. Here we assess functional brain network organization of 23 of the world's most successful memory athletes and matched controls with fMRI during both task-free resting state baseline and active memory encoding. We demonstrate that, in a group of naive controls, functional connectivity changes induced by 6 weeks of mnemonic training were correlated with the network organization that distinguishes athletes from controls. During rest, this effect was mainly driven by connections between rather than within the visual, medial temporal lobe and default mode networks, whereas during task it was driven by connectivity within these networks. Similarity with memory athlete connectivity patterns predicted memory improvements up to 4 months after training. In conclusion, mnemonic training drives distributed rather than regional changes, reorganizing the brain's functional network organization to enable superior memory performance.

  View details for DOI 10.1016/j.neuron.2017.02.003

  View details for Web of Science ID 000396429800022

  View details for PubMedID 28279356

• Dissociated patterns of anti-correlations with dorsal and ventral default-mode networks at rest. Human brain mapping Chen, J. E., Glover, G. H., Greicius, M. D., Chang, C. 2017

  Abstract

  Previous studies of resting state functional connectivity have demonstrated that the default-mode network (DMN) is negatively correlated with a set of brain regions commonly activated during goal-directed tasks. However, the location and extent of anti-correlations are inconsistent across different studies, which has been posited to result largely from differences in whether or not global signal regression (GSR) was applied as a pre-processing step. Notably, coordinates of seed regions-of-interest defined within the posterior cingulate cortex (PCC)/precuneus, an area often employed to study functional connectivity of the DMN, have been inconsistent across studies. Taken together with recent observations that the DMN contains functionally heterogeneous subdivisions, it is presently unclear whether these seeds map to different DMN subnetworks, whose patterns of anti-correlation may differ. If so, then seed location may be a non-negligible factor that, in addition to differences in preprocessing steps, contributes to the inconsistencies reported among published studies regarding DMN correlations/anti-correlations. In this study, they examined anti-correlations of different subnetworks within the DMN during rest using both seed-based and point process analyses, and discovered that: (1) the ventral branch of the DMN (vDMN) yielded significantly weaker anti-correlations than that associated with the dorsal branch of the DMN (dDMN); (2) vDMN anti-correlations introduced by GSR were distinct from dDMN anti-correlations; (3) PCC/precuneus seeds employed by earlier studies mapped to different DMN subnetworks, which may explain some of the inconsistency (in addition to preprocessing steps) in the reported DMN anti-correlations. Hum Brain Mapp, 2017. © 2017 Wiley Periodicals, Inc.

  View details for DOI 10.1002/hbm.23532

  View details for PubMedID 28150892

• Ruminative brooding is associated with salience network coherence in early pubertal youth SOCIAL COGNITIVE AND AFFECTIVE NEUROSCIENCE Ordaz, S. J., LeMoult, J., Colich, N. L., Prasad, G., Pollak, M., Popolizio, M., Price, A., Greicius, M., Gotlib, I. H. 2017; 12 (2): 298-310

  Abstract

  Rumination, and particularly ruminative brooding, perpetuates dysphoric mood states and contributes to the emergence of depression. Studies of adults and older adolescents have characterized the association between rumination and intrinsic functional connectivity within default mode (DMN), salience (SN) and executive control (ECN) networks; we know little, however, about the brain network basis of rumination during early puberty, a sensitive period for network reorganization. 112 early puberty boys and girls completed resting-state scans, the Ruminative Response Scale, and the Youth Self-Report questionnaire. Using independent components analysis and dual regression, we quantified coherence for each individual in networks of interest (SN, ECN, DMN) and in non-relevant networks (motor, visual) in which we predicted no correlations with behavioral measures. Boys and girls did not differ in levels of rumination or internalizing symptoms, or in coherence for any network. The relation between SN network coherence and rumination; however, and specifically ruminative brooding, was moderated by sex: greater SN coherence was associated with higher levels of brooding in girls but not in boys. Further, in girls, brooding mediated the relation between SN coherence and internalizing symptoms. These results point to coherence within the SN as a potential neurodevelopmental marker of risk for depression in early pubertal girls.

  View details for DOI 10.1093/scan/nsw133

  View details for Web of Science ID 000397312200011

  View details for PubMedCentralID PMC5390708

• A variant in PPP4R3A protects against Alzheimer-related metabolic decline. Annals of neurology Christopher, L. n., Napolioni, V. n., Khan, R. R., Han, S. S., Greicius, M. D. 2017

  Abstract

  A reduction in glucose metabolism in the posterior cingulate cortex (PCC) predicts conversion to Alzheimer's disease (AD) and tracks disease progression, signifying its importance in AD. We aimed to use decline in PCC glucose metabolism as a proxy for the development and progression of AD to discover common genetic variants associated with disease vulnerability.We performed a genome-wide association study (GWAS) of decline in PCC [18 F] FDG PET measured in Alzheimer's Disease Neuroimaging Initiative (ADNI) participants (n=606). We then performed follow-up analyses to assess the impact of significant single nucleotide polymorphisms (SNPs) on disease risk and longitudinal cognitive performance in a large independent dataset (n=870). Lastly, we assessed whether significant SNPs influence gene expression using two RNA sequencing (RNA-Seq) datasets (n=210 & n=159).We demonstrate a novel genome-wide significant association between rs2273647-T in the gene PPP4R3A and reduced [18 F] FDG decline (p= 4.44 x 10-8 ). In a follow-up analysis using an independent dataset, we demonstrate a protective effect of this variant against risk of conversion to MCI or AD (p=0.038) and against cognitive decline in individuals who develop dementia (p = 3.41 x 10-15 ). Furthermore, this variant is associated with altered gene expression in peripheral blood and altered PPPP4R3A transcript expression in temporal cortex, suggesting a role at the molecular level.PPP4R3A is a gene involved in AD risk and progression. Given the protective effect of this variant PPP4R3A should be further investigated as a gene of interest in neurodegenerative diseases and as a potential target for AD therapies. This article is protected by copyright. All rights reserved.

  View details for PubMedID 29130521

• Overdominant effect of a CHRNA4 polymorphism on cingulo-opercular network activity and cognitive control. The Journal of neuroscience : the official journal of the Society for Neuroscience Sadaghiani, S. n., Ng, B. n., Altmann, A. n., Poline, J. B., Banaschewski, T. n., Bokde, A. L., Bromberg, U. n., Büchel, C. n., Burke Quinlan, E. n., Conrod, P. n., Desrivières, S. n., Flor, H. n., Frouin, V. n., Garavan, H. n., Gowland, P. n., Gallinat, J. n., Heinz, A. n., Ittermann, B. n., Martinot, J. L., Paillère Martinot, M. L., Lemaitre, H. n., Nees, F. n., Papadopoulos Orfanos, D. n., Paus, T. n., Poustka, L. n., Millenet, S. n., Fröhner, J. H., Smolka, M. N., Walter, H. n., Whelan, R. n., Schumann, G. n., Napolioni, V. n., Greicius, M. n. 2017

  Abstract

  The nicotinic system plays an important role in cognitive control, and is implicated in several neuropsychiatric conditions. Yet, the contributions of genetic variability in this system to individuals' cognitive control abilities are poorly understood, and the brain processes that mediate such genetic contributions remain largely unidentified. In this first large-scale neuroimaging genetics study of the human nicotinic receptor system (two cohorts, males and females, fMRI total N=1586, behavioral total N=3650), we investigated a common polymorphism of the high-affinity nicotinic receptor α4β2 (rs1044396 on the CHRNA4 gene) previously implicated in behavioral and nicotine-related studies (albeit with inconsistent major/minor allele impacts). Based on our prior neuroimaging findings, we expected this polymorphism to impact neural activity in the cingulo-opercular network involved in core cognitive control processes including maintenance of alertness. Consistent across the cohorts, all cortical areas of the cingulo-opercular network showed higher activity in heterozygotes compared to both types of homozygotes during cognitive engagement. This inverted U-shaped relation reflects an overdominant effect, i.e. allelic interaction (cumulative evidence p=1.33*10(-5)). Furthermore, heterozygotes performed more accurately in behavioral tasks that primarily depend on sustained alertness. No effects were observed for haplotypes of the surrounding CHRNA4 region, supporting a true overdominant effect at rs1044396. As a possible mechanism, we observed that this polymorphism is an expression quantitative trait locus (eQTL) modulating CHRNA4 expression levels. This is the first report of overdominance in the nicotinic system. These findings connect CHRNA4 genotype, cingulo-opercular network activation and sustained alertness, providing insights into how genetics shapes individuals' cognitive control abilities.Significance Statement:The nicotinic acetylcholine system plays a central role in neuromodulatory regulation of cognitive control processes, and is dysregulated in several neuropsychiatric disorders. In spite of this functional importance, no large-scale neuroimaging genetics studies have targeted the contributions of genetic variability in this system to human brain activity. Here, we show impact of a common polymorphism of the high-affinity nicotinic receptor α4β2, consistent across brain activity and behavior in two large human cohorts. We report a hitherto unknown overdominant effect (allelic interaction) at this locus, where the heterozygotes show higher activity in the cingulo-opercular network underlying alertness maintenance, and higher behavioral alertness performance than both homozygous groups. This gene-brain-behavior relationship informs about the biological basis of inter-individual differences in cognitive control.

  View details for PubMedID 28877969

• Distinct alterations in Parkinson's medication-state and disease-state connectivity NEUROIMAGE-CLINICAL Ng, B., Varoquaux, G., Poline, J., Thirion, B., Greicius, M. D., Poston, K. L. 2017; 16: 575–85

  Abstract

  Altered brain connectivity has been described in people with Parkinson's disease and in response to dopaminergic medications. However, it is unclear whether dopaminergic medications primarily 'normalize' disease related connectivity changes or if they induce unique alterations in brain connectivity. Further, it is unclear how these disease- and medication-associated changes in brain connectivity relate differently to specific motor manifestations of disease, such as bradykinesia/rigidity and tremor. In this study, we applied a novel covariance projection approach in combination with a bootstrapped permutation test to resting state functional MRI data from 57 Parkinson's disease and 20 healthy control participants to determine the Parkinson's medication-state and disease-state connectivity changes associated with different motor manifestations of disease. First, we identified brain connections that best classified Parkinson's disease ON versus OFF dopamine and Parkinson's disease versus healthy controls, achieving 96.9 ± 5.9% and 72.7 ± 12.4% classification accuracy, respectively. Second, we investigated the connections that significantly contribute to the classifications. We found that the connections greater in Parkinson's disease OFF compared to ON dopamine are primarily between motor (cerebellum and putamen) and posterior cortical regions, such as the posterior cingulate cortex. By contrast, connections that are greater in ON compared to OFF dopamine are between the right and left medial prefrontal cortex. We also identified the connections that are greater in healthy control compared to Parkinson's disease and found the most significant connections are associated with primary motor regions, such as the striatum and the supplementary motor area. Notably, these are different connections than those identified in Parkinson's disease OFF compared to ON. Third, we determined which of the Parkinson's medication-state and disease-state connections are associated with the severity of different motor symptoms. We found two connections correlate with both bradykinesia/rigidity severity and tremor severity, whereas four connections correlate with only bradykinesia/rigidity severity, and five connections correlate with only tremor severity. Connections that correlate with only tremor severity are anchored by the cerebellum and the supplemental motor area, but only those connections that include the supplemental motor area predict dopaminergic improvement in tremor. Our results suggest that dopaminergic medications do not simply 'normalize' abnormal brain connectivity associated with Parkinson's disease, but rather dopamine drives distinct connectivity changes, only some of which are associated with improved motor symptoms. In addition, the dissociation between of connections related to severity of bradykinesia/rigidity versus tremor highlights the distinct abnormalities in brain circuitry underlying these specific motor symptoms.

  View details for PubMedID 28971008

• Identification of Mood-Relevant Brain Connections Using a Continuous, Subject-Driven Rumination Paradigm. Cerebral cortex Milazzo, A., Ng, B., Jiang, H., Shirer, W., Varoquaux, G., Poline, J. B., Thirion, B., Greicius, M. D. 2016; 26 (3): 933-942

  Abstract

  Rumination, an internal cognitive state characterized by recursive thinking of current self-distress and past negative events, has been found to correlate with the development of depressive disorders. Here, we investigated the feasibility of using connectivity for distinguishing different emotional states induced by a novel free-streaming, subject-driven experimental paradigm. Connectivity between 78 functional regions of interest (ROIs) within 14 large-scale networks and 6 structural ROIs particularly relevant to emotional processing were used for classifying 4 mental states in 19 healthy controls. The 4 mental states comprised: An unconstrained period of mind wandering; a ruminative mental state self-induced by recalling a time of personal disappointment; a euphoric mental state self-induced by recalling what brings the subject joy; and a sequential episodic recollection of the events of the day. A support vector machine achieved accuracies ranging from 89% to 94% in classifying pairs of different mental states. We reported the most significant brain connections that best discriminated these mental states. In particular, connectivity changes involving the amygdala were found to be important for distinguishing the rumination condition from the other mental states. Our results demonstrated that connectivity-based classification of subject-driven emotional states constitutes a novel and effective approach for studying ruminative behavior.

  View details for DOI 10.1093/cercor/bhu255

  View details for PubMedID 25331601

  View details for PubMedCentralID PMC4737600

• Validation of non-REM sleep stage decoding from resting state fMRI using linear support vector machines NEUROIMAGE Altmann, A., Schroeter, M. S., Spoormaker, V. I., Kiem, S. A., Jordan, D., Ilg, R., Bullmore, E. T., Greicius, M. D., Czisch, M., Saemann, P. G. 2016; 125: 544-555

  View details for DOI 10.1016/j.neuroimage.2015.09.072

  View details for PubMedID 26596551

• Transport on Riemannian Manifold for Connectivity-Based Brain Decoding IEEE TRANSACTIONS ON MEDICAL IMAGING Ng, B., Varoquaux, G., Poline, J. B., Greicius, M., Thirion, B. 2016; 35 (1): 208-216

  Abstract

  There is a recent interest in using functional magnetic resonance imaging (fMRI) for decoding more naturalistic, cognitive states, in which subjects perform various tasks in a continuous, self-directed manner. In this setting, the set of brain volumes over the entire task duration is usually taken as a single sample with connectivity estimates, such as Pearson's correlation, employed as features. Since covariance matrices live on the positive semidefinite cone, their elements are inherently inter-related. The assumption of uncorrelated features implicit in most classifier learning algorithms is thus violated. Coupled with the usual small sample sizes, the generalizability of the learned classifiers is limited, and the identification of significant brain connections from the classifier weights is nontrivial. In this paper, we present a Riemannian approach for connectivity-based brain decoding. The core idea is to project the covariance estimates onto a common tangent space to reduce the statistical dependencies between their elements. For this, we propose a matrix whitening transport, and compare it against parallel transport implemented via the Schild's ladder algorithm. To validate our classification approach, we apply it to fMRI data acquired from twenty four subjects during four continuous, self-driven tasks. We show that our approach provides significantly higher classification accuracy than directly using Pearson's correlation and its regularized variants as features. To facilitate result interpretation, we further propose a non-parametric scheme that combines bootstrapping and permutation testing for identifying significantly discriminative brain connections from the classifier weights. Using this scheme, a number of neuro-anatomically meaningful connections are detected, whereas no significant connections are found with pure permutation testing.

  View details for DOI 10.1109/TMI.2015.2463723

  View details for Web of Science ID 000367624800018

• Resting-State Functional MRI: A Novel Tool for Understanding Brain Networks in Neuropsychiatric Disorders GENOMICS, CIRCUITS, AND PATHWAYS IN CLINICAL NEUROPSYCHIATRY Greicius, M., Lehner, T., Miller, B. L., State, M. W. 2016: 247–62

  View details for DOI 10.1016/B978-0-12-800105-9.00016-0

  View details for Web of Science ID 000416943300017

• Regional brain hypometabolism is unrelated to regional amyloid plaque burden BRAIN Altmann, A., Ng, B., Landau, S. M., Jagust, W. J., Greicius, M. D. 2015; 138: 3734-3746

  Abstract

  In its original form, the amyloid cascade hypothesis of Alzheimer's disease holds that fibrillar deposits of amyloid are an early, driving force in pathological events leading ultimately to neuronal death. Early clinicopathological investigations highlighted a number of inconsistencies leading to an updated hypothesis in which amyloid plaques give way to amyloid oligomers as the driving force in pathogenesis. Rather than focusing on the inconsistencies, amyloid imaging studies have tended to highlight the overlap between regions that show early amyloid plaque signal on positron emission tomography and that also happen to be affected early in Alzheimer's disease. Recent imaging studies investigating the regional dependency between metabolism and amyloid plaque deposition have arrived at conflicting results, with some showing regional associations and other not. We extracted multimodal neuroimaging data from the Alzheimer's disease neuroimaging database for 227 healthy controls and 434 subjects with mild cognitive impairment. We analysed regional patterns of amyloid deposition, regional glucose metabolism and regional atrophy using florbetapir ((18)F) positron emission tomography, (18)F-fluordeoxyglucose positron emission tomography and T1-weighted magnetic resonance imaging, respectively. Specifically, we derived grey matter density and standardized uptake value ratios for both positron emission tomography tracers in 404 functionally defined regions of interest. We examined the relation between regional glucose metabolism and amyloid plaques using linear models. For each region of interest, correcting for regional grey matter density, age, education and disease status, we tested the association of regional glucose metabolism with (i) cortex-wide florbetapir uptake; (ii) regional (i.e. in the same region of interest) florbetapir uptake; and (iii) regional florbetapir uptake while correcting in addition for cortex-wide florbetapir uptake. P-values for each setting were Bonferroni corrected for 404 tests. Regions showing significant hypometabolism with increasing cortex-wide amyloid burden were classic Alzheimer's disease-related regions: the medial and lateral parietal cortices. The associations between regional amyloid burden and regional metabolism were more heterogeneous: there were significant hypometabolic effects in posterior cingulate, precuneus, and parietal regions but also significant positive associations in bilateral hippocampus and entorhinal cortex. However, after correcting for global amyloid burden, few of the negative associations remained and the number of positive associations increased. Given the wide-spread distribution of amyloid plaques, if the canonical cascade hypothesis were true, we would expect wide-spread, cortical hypometabolism. Instead, cortical hypometabolism appears to be linked to global amyloid burden. Thus we conclude that regional fibrillar amyloid deposition has little to no association with regional hypometabolism.

  View details for DOI 10.1093/brain/awv278

  View details for Web of Science ID 000366384600030

  View details for PubMedID 26419799

  View details for PubMedCentralID PMC4806718

• Loss of functional connectivity is greater outside the default mode network in nonfamilial early-onset Alzheimer's disease variants. Neurobiology of aging Lehmann, M., Madison, C., Ghosh, P. M., Miller, Z. A., Greicius, M. D., Kramer, J. H., Coppola, G., Miller, B. L., Jagust, W. J., Gorno-Tempini, M. L., Seeley, W. W., Rabinovici, G. D. 2015; 36 (10): 2678-2686

  Abstract

  The common and specific involvement of brain networks in clinical variants of Alzheimer's disease (AD) is not well understood. We performed task-free ("resting-state") functional imaging in 60 nonfamilial AD patients, including 20 early-onset AD (age at onset <65 years, amnestic/dysexecutive deficits), 24 logopenic aphasia (language deficits), and 16 posterior cortical atrophy patients (visual deficits), as well as 60 healthy controls. Seed-based connectivity analyses were conducted to assess differences between groups in 3 default mode network (DMN) components (anterior, posterior, and ventral) and 4 additional non-DMN networks: left and right executive-control, language, and higher visual networks. Significant decreases in connectivity were found across AD variants compared with controls in the non-DMN networks. Within the DMN components, patients showed higher connectivity in the anterior DMN, in particular in logopenic aphasia. No significant differences were found for the posterior and ventral DMN. Our findings suggest that loss of functional connectivity is greatest in networks outside the DMN in early-onset and nonamnestic AD variants and may thus be a better biomarker in these patients.

  View details for DOI 10.1016/j.neurobiolaging.2015.06.029

  View details for PubMedID 26242705

• Modulation of Creutzfeldt-Jakob disease prion propagation by the A224V mutation. Annals of neurology Watts, J. C., Giles, K., Serban, A., Patel, S., Oehler, A., Bhardwaj, S., Guan, S., Greicius, M. D., Miller, B. L., DeArmond, S. J., Geschwind, M. D., Prusiner, S. B. 2015; 78 (4): 540-553

  Abstract

  Mutations in the gene encoding the prion protein (PrP) are responsible for approximately 10 to 15% of cases of prion disease in humans, including Creutzfeldt-Jakob disease (CJD). Here, we report on the discovery of a previously unreported C-terminal PrP mutation (A224V) in a CJD patient exhibiting a disease similar to the rare VV1 subtype of sporadic (s) CJD and investigate the role of this mutation in prion replication and transmission.We generated transgenic (Tg) mice expressing human PrP with the V129 polymorphism and A224V mutation, denoted Tg(HuPrP,V129,A224V) mice, and inoculated them with different subtypes of sCJD prions.Transmission of sCJD VV2 or MV2 prions was accelerated in Tg(HuPrP,V129,A224V) mice, compared to Tg(HuPrP,V129) mice, with incubation periods of ∼110 and ∼210 days, respectively. In contrast, sCJD MM1 prions resulted in longer incubation periods in Tg(HuPrP,V129,A224V) mice, compared to Tg(HuPrP,V129) mice (∼320 vs. ∼210 days). Prion strain fidelity was maintained in Tg(HuPrP,V129,A224V) mice inoculated with sCJD VV2 or MM1 prions, despite the altered replication kinetics.Our results suggest that A224V is a risk factor for prion disease and modulates the transmission behavior of CJD prions in a strain-specific manner, arguing that residues near the C-terminus of PrP are important for controlling the kinetics of prion replication.

  View details for DOI 10.1002/ana.24463

  View details for PubMedID 26094969

  View details for PubMedCentralID PMC4711268

• The posterior medial cortex in urologic chronic pelvic pain syndrome: detachment from default mode network-a resting-state study from the MAPP Research Network PAIN Martucci, K. T., Shirer, W. R., Bagarinao, E., Johnson, K. A., Farmer, M. A., Labus, J. S., Apkarian, A. V., Deutsch, G., Harris, R. E., Mayer, E. A., Clauw, D. J., Greicius, M. D., Mackey, S. C. 2015; 156 (9): 1755-1764

  Abstract

  Altered resting-state (RS) brain activity, as a measure of functional connectivity (FC), is commonly observed in chronic pain. Identifying a reliable signature pattern of altered RS activity for chronic pain could provide strong mechanistic insights and serve as a highly beneficial neuroimaging-based diagnostic tool. We collected and analyzed RS functional magnetic resonance imaging data from female patients with urologic chronic pelvic pain syndrome (N = 45) and matched healthy participants (N = 45) as part of an NIDDK-funded multicenter project (www.mappnetwork.org). Using dual regression and seed-based analyses, we observed significantly decreased FC of the default mode network to 2 regions in the posterior medial cortex (PMC): the posterior cingulate cortex (PCC) and the left precuneus (threshold-free cluster enhancement, family-wise error corrected P < 0.05). Further investigation revealed that patients demonstrated increased FC between the PCC and several brain regions implicated in pain, sensory, motor, and emotion regulation processes (eg, insular cortex, dorsolateral prefrontal cortex, thalamus, globus pallidus, putamen, amygdala, hippocampus). The left precuneus demonstrated decreased FC to several regions of pain processing, reward, and higher executive functioning within the prefrontal (orbitofrontal, anterior cingulate, ventromedial prefrontal) and parietal cortices (angular gyrus, superior and inferior parietal lobules). The altered PMC connectivity was associated with several phenotype measures, including pain and urologic symptom intensity, depression, anxiety, quality of relationships, and self-esteem levels in patients. Collectively, these findings indicate that in patients with urologic chronic pelvic pain syndrome, regions of the PMC are detached from the default mode network, whereas neurological processes of self-referential thought and introspection may be joined to pain and emotion regulatory processes.

  View details for DOI 10.1097/j.pain.0000000000000238

  View details for Web of Science ID 000360579400021

  View details for PubMedCentralID PMC4545714

• The posterior medial cortex in urologic chronic pelvic pain syndrome: detachment from default mode network-a resting-state study from the MAPP Research Network. Pain Martucci, K. T., Shirer, W. R., Bagarinao, E., Johnson, K. A., Farmer, M. A., Labus, J. S., Apkarian, A. V., Deutsch, G., Harris, R. E., Mayer, E. A., Clauw, D. J., Greicius, M. D., Mackey, S. C. 2015; 156 (9): 1755-1764

  Abstract

  Altered resting-state (RS) brain activity, as a measure of functional connectivity (FC), is commonly observed in chronic pain. Identifying a reliable signature pattern of altered RS activity for chronic pain could provide strong mechanistic insights and serve as a highly beneficial neuroimaging-based diagnostic tool. We collected and analyzed RS functional magnetic resonance imaging data from female patients with urologic chronic pelvic pain syndrome (N = 45) and matched healthy participants (N = 45) as part of an NIDDK-funded multicenter project (www.mappnetwork.org). Using dual regression and seed-based analyses, we observed significantly decreased FC of the default mode network to 2 regions in the posterior medial cortex (PMC): the posterior cingulate cortex (PCC) and the left precuneus (threshold-free cluster enhancement, family-wise error corrected P < 0.05). Further investigation revealed that patients demonstrated increased FC between the PCC and several brain regions implicated in pain, sensory, motor, and emotion regulation processes (eg, insular cortex, dorsolateral prefrontal cortex, thalamus, globus pallidus, putamen, amygdala, hippocampus). The left precuneus demonstrated decreased FC to several regions of pain processing, reward, and higher executive functioning within the prefrontal (orbitofrontal, anterior cingulate, ventromedial prefrontal) and parietal cortices (angular gyrus, superior and inferior parietal lobules). The altered PMC connectivity was associated with several phenotype measures, including pain and urologic symptom intensity, depression, anxiety, quality of relationships, and self-esteem levels in patients. Collectively, these findings indicate that in patients with urologic chronic pelvic pain syndrome, regions of the PMC are detached from the default mode network, whereas neurological processes of self-referential thought and introspection may be joined to pain and emotion regulatory processes.

  View details for DOI 10.1097/j.pain.0000000000000238

  View details for PubMedID 26010458

  View details for PubMedCentralID PMC4545714

• Optimization of rs-fMRI Pre-processing for Enhanced Signal-Noise Separation, Test-Retest Reliability, and Group Discrimination NEUROIMAGE Shirer, W. R., Jiang, H., Price, C. M., Ng, B., Greicius, M. D. 2015; 117: 67-79

  Abstract

  Resting-state functional magnetic resonance imaging (rs-fMRI) has become an increasingly important tool in mapping the functional networks of the brain. This tool has been used to examine network changes induced by cognitive and emotional states, neurological traits, and neuropsychiatric disorders. However, noise that remains in the rs-fMRI data after preprocessing has limited the reliability of individual-subject results, wherein scanner artifacts, subject movements, and other noise sources induce non-neural temporal correlations in the blood oxygen level-dependent (BOLD) timeseries. Numerous preprocessing methods have been proposed to isolate and remove these confounds; however, the field has not coalesced around a standard preprocessing pipeline. In comparisons, these preprocessing methods are often assessed with only a single metric of rs-fMRI data quality, such as reliability, without considering other aspects in tandem, such as signal-to-noise ratio and group discriminability. The present study seeks to identify the data preprocessing pipeline that optimizes rs-fMRI data across multiple outcome measures. Specifically, we aim to minimize the noise in the data and maximize result reliability, while retaining the unique features that characterize distinct groups. We examine how these metrics are influenced by bandpass filter selection and noise regression in four datasets, totaling 181 rs-fMRI scans and 38 subject-driven memory scans. Additionally, we perform two different rs-fMRI analysis methods - dual regression and region-of-interest based functional connectivity - and highlight the preprocessing parameters that optimize both approaches. Our results expand upon previous reports of individual-scan reliability, and demonstrate that preprocessing parameter selection can significantly change the noisiness, reliability, and heterogeneity of rs-fMRI data. The application of our findings to rs-fMRI data analysis should improve the validity and reliability of rs-fMRI results, both at the individual-subject level and the group level.

  View details for DOI 10.1016/j.neuroimage.2015.05.015

  View details for Web of Science ID 000358045100007

  View details for PubMedID 25987368

• Correlated gene expression supports synchronous activity in brain networks SCIENCE Richiardi, J., Altmann, A., Milazzo, A., Chang, C., Chakravarty, M. M., Banaschewski, T., Barker, G. J., Bokde, A. L., Bromberg, U., Buechel, C., Conrod, P., Fauth-Buehler, M., Flor, H., Frouin, V., Gallinat, J., Garavan, H., Gowland, P., Heinz, A., Lemaitre, H., Mann, K. F., Martinot, J., Nees, F., Paus, T., Pausova, Z., Rietschel, M., Robbins, T. W., Smolka, M. N., Spanagel, R., Stroehle, A., Schumann, G., Hawrylycz, M., Poline, J., Greicius, M. D. 2015; 348 (6240): 1241-1244

  Abstract

  During rest, brain activity is synchronized between different regions widely distributed throughout the brain, forming functional networks. However, the molecular mechanisms supporting functional connectivity remain undefined. We show that functional brain networks defined with resting-state functional magnetic resonance imaging can be recapitulated by using measures of correlated gene expression in a post mortem brain tissue data set. The set of 136 genes we identify is significantly enriched for ion channels. Polymorphisms in this set of genes significantly affect resting-state functional connectivity in a large sample of healthy adolescents. Expression levels of these genes are also significantly associated with axonal connectivity in the mouse. The results provide convergent, multimodal evidence that resting-state functional networks correlate with the orchestrated activity of dozens of genes linked to ion channel activity and synaptic function.

  View details for DOI 10.1126/science.1255905

  View details for Web of Science ID 000356011500051

• Introducing co-activation pattern metrics to quantify spontaneous brain network dynamics NEUROIMAGE Chen, J. E., Chang, C., Greicius, M. D., Glover, G. H. 2015; 111: 476-488

  Abstract

  Recently, fMRI researchers have begun to realize that the brain's intrinsic network patterns may undergo substantial changes during a single resting state (RS) scan. However, despite the growing interest in brain dynamics, metrics that can quantify the variability of network patterns are still quite limited. Here, we first introduce various quantification metrics based on the extension of co-activation pattern (CAP) analysis, a recently proposed point-process analysis that tracks state alternations at each individual time frame and relies on very few assumptions; then apply these proposed metrics to quantify changes of brain dynamics during a sustained 2-back working memory (WM) task compared to rest. We focus on the functional connectivity of two prominent RS networks, the default-mode network (DMN) and executive control network (ECN). We first demonstrate less variability of global Pearson correlations with respect to the two chosen networks using a sliding-window approach during WM task compared to rest; then we show that the macroscopic decrease in variations in correlations during a WM task is also well characterized by the combined effect of a reduced number of dominant CAPs, increased spatial consistency across CAPs, and increased fractional contributions of a few dominant CAPs. These CAP metrics may provide alternative and more straightforward quantitative means of characterizing brain network dynamics than time-windowed correlation analyses.

  View details for DOI 10.1016/j.neuroimage.2015.01.057

  View details for PubMedID 25662866

• Expert consensus document: Mind the gaps-advancing research into short-term and long-term neuropsychological outcomes of youth sports-related concussions. Nature reviews. Neurology Carman, A. J., Ferguson, R., Cantu, R., Comstock, R. D., Dacks, P. A., DeKosky, S. T., Gandy, S., Gilbert, J., Gilliland, C., Gioia, G., Giza, C., Greicius, M., Hainline, B., Hayes, R. L., Hendrix, J., Jordan, B., Kovach, J., Lane, R. F., Mannix, R., Murray, T., Seifert, T., Shineman, D. W., Warren, E., Wilde, E., Willard, H., Fillit, H. M. 2015; 11 (4): 230-244

  Abstract

  Sports-related concussions and repetitive subconcussive exposure are increasingly recognized as potential dangers to paediatric populations, but much remains unknown about the short-term and long-term consequences of these events, including potential cognitive impairment and risk of later-life dementia. This Expert Consensus Document is the result of a 1-day meeting convened by Safe Kids Worldwide, the Alzheimer's Drug Discovery Foundation, and the Andrews Institute for Orthopaedics and Sports Medicine. The goal is to highlight knowledge gaps and areas of critically needed research in the areas of concussion science, dementia, genetics, diagnostic and prognostic biomarkers, neuroimaging, sports injury surveillance, and information sharing. For each of these areas, we propose clear and achievable paths to improve the understanding, treatment and prevention of youth sports-related concussions.

  View details for DOI 10.1038/nrneurol.2015.30

  View details for PubMedID 25776822

• Bootstrapped Permutation Test for Multiresponse Inference on Brain Behavior Associations. Information processing in medical imaging : proceedings of the ... conference Ng, B., Poline, J. B., Thirion, B., Greicius, M. 2015; 24: 113-124

  Abstract

  Despite that diagnosis of neurological disorders commonly involves a collection of behavioral assessments, most neuroimaging studies investigating the associations between brain and behavior largely analyze each behavioral measure in isolation. To jointly model multiple behavioral scores, sparse multiresponse regression (SMR) is often used. However, directly applying SMR without statistically controlling for false positives could result in many spurious findings. For models, such as SMR, where the distribution of the model parameters is unknown, permutation test and stability selection are typically used to control for false positives. In this paper, we present another technique for inferring statistically significant features from models with unknown parameter distribution. We refer to this technique as bootstrapped permutation test (BPT), which uses Studentized statistics to exploit the intuition that the variability in parameter estimates associated with relevant features would likely be higher with responses permuted. On synthetic data, we show that BPT provides higher sensitivity in identifying relevant features from the SMR model than permutation test and stability selection, while retaining strong control on the false positive rate. We further apply BPT to study the associations between brain connectivity estimated from pseudo-rest fMRI data of 1139 fourteen year olds and behavioral measures related to ADHD. Significant connections are found between brain networks known to be implicated in the behavioral tasks involved. Moreover, we validate the identified connections by fitting a regression model on pseudo-rest data with only those connections and applying this model on resting state fMRI data of 337 left out subjects to predict their behavioral scores. The predicted scores significantly correlate with the actual scores, hence verifying the behavioral relevance of the found connections.

  View details for PubMedID 26221670

• Neuropathologic analysis of Tyr69His TTR variant meningovascular amyloidosis with dementia. Acta neuropathologica communications Ziskin, J. L., Greicius, M. D., Zhu, W., Okumu, A. N., Adams, C. M., Plowey, E. D. 2015; 3 (1): 43-?

  Abstract

  Transthyretin/TTR gene mutations usually cause systemic amyloidotic diseases. Few TTR variants preferentially affect the central nervous system, manifesting as oculoleptomeningeal amyloidosis. Patients with TTR meningovascular amyloidosis often show dementia, however the neuropathologic features of dementia in these cases have not been elucidated. We report the neuropathologic findings from a brain autopsy of a 72-year-old man with the rare Tyr69His (Y69H) TTR gene variant, dementia and ataxia. Severe amyloid deposits were observed in the leptomeninges and in a subpial and subependymal distribution. Mass spectrometry analysis demonstrated that the amyloid deposits were comprised of over 80 % of the variant TTR. TTR was undetectable by mass spectrometry in the neocortex subjacent to the subpial amyloid deposits. Subpial TTR amyloid deposits were associated with brisk superficial reactive gliosis and siderosis in the neocortex and cerebellar cortex. Subependymal TTR amyloid deposits were associated with subjacent myelin pallor in the hippocampal outflow tract structures including the alveus, fimbria and fornix. Phospho-tau immunostains demonstrated transentorhinal-stage neurofibrillary degeneration (Braak stage II) which, in the absence of neocortical amyloid-beta and neuritic plaques, was indicative of primary age-related tauopathy (PART). However, distinctive phospho-tau aggregates were observed subjacent to the subpial TTR amyloid deposits in all regions of the neocortex, including the primary motor and striate cortices, suggesting a potential link between TTR amyloid and neocortical tauopathy. Our report reveals novel insights into the potential neuropathologic substrates of dementia in variant TTR amyloidosis that need to be investigated in larger autopsy series.

  View details for DOI 10.1186/s40478-015-0216-0

  View details for PubMedID 26156087

  View details for PubMedCentralID PMC4496870

• Disentangling Dynamic Networks: Separated and Joint Expressions of Functional Connectivity Patterns in Time HUMAN BRAIN MAPPING Leonardi, N., Shirer, W. R., Greicius, M. D., Van De Ville, D. 2014; 35 (12): 5984-5995

  Abstract

  Resting-state functional connectivity (FC) is highly variable across the duration of a scan. Groups of coevolving connections, or reproducible patterns of dynamic FC (dFC), have been revealed in fluctuating FC by applying unsupervised learning techniques. Based on results from k-means clustering and sliding-window correlations, it has recently been hypothesized that dFC may cycle through several discrete FC states. Alternatively, it has been proposed to represent dFC as a linear combination of multiple FC patterns using principal component analysis. As it is unclear whether sparse or nonsparse combinations of FC patterns are most appropriate, and as this affects their interpretation and use as markers of cognitive processing, the goal of our study was to evaluate the impact of sparsity by performing an empirical evaluation of simulated, task-based, and resting-state dFC. To this aim, we applied matrix factorizations subject to variable constraints in the temporal domain and studied both the reproducibility of ensuing representations of dFC and the expression of FC patterns over time. During subject-driven tasks, dFC was well described by alternating FC states in accordance with the nature of the data. The estimated FC patterns showed a rich structure with combinations of known functional networks enabling accurate identification of three different tasks. During rest, dFC was better described by multiple FC patterns that overlap. The executive control networks, which are critical for working memory, appeared grouped alternately with externally or internally oriented networks. These results suggest that combinations of FC patterns can provide a meaningful way to disentangle resting-state dFC.

  View details for DOI 10.1002/hbm.22599

  View details for Web of Science ID 000344398900019

  View details for PubMedID 25081921

• Apolipoprotein E, gender, and Alzheimer's disease: an overlooked, but potent and promising interaction. Brain imaging and behavior Ungar, L., Altmann, A., Greicius, M. D. 2014; 8 (2): 262-273

  Abstract

  Alzheimer's disease (AD) is an increasingly prevalent, fatal neurodegenerative disease that has proven resistant, thus far, to all attempts to prevent it, forestall it, or slow its progression. The ε4 allele of the Apolipoprotein E gene (APOE4) is a potent genetic risk factor for sporadic and late-onset familial AD. While the link between APOE4 and AD is strong, many expected effects, like increasing the risk of conversion from MCI to AD, have not been widely replicable. One critical, and commonly overlooked, feature of the APOE4 link to AD is that several lines of evidence suggest it is far more pronounced in women than in men. Here we review previous literature on the APOE4 by gender interaction with a particular focus on imaging-related studies.

  View details for DOI 10.1007/s11682-013-9272-x

  View details for PubMedID 24293121

• Sex modifies the APOE-related risk of developing Alzheimer disease. Annals of neurology Altmann, A., Tian, L., Henderson, V. W., Greicius, M. D. 2014; 75 (4): 563-573

  Abstract

  The APOE4 allele is the strongest genetic risk factor for sporadic Alzheimer disease (AD). Case-control studies suggest the APOE4 link to AD is stronger in women. We examined the APOE4-by-sex interaction in conversion risk (from healthy aging to mild cognitive impairment (MCI)/AD or from MCI to AD) and cerebrospinal fluid (CSF) biomarker levels.Cox proportional hazards analysis was used to compute hazard ratios (HRs) for an APOE-by-sex interaction on conversion in controls (n = 5,496) and MCI patients (n = 2,588). The interaction was also tested in CSF biomarker levels of 980 subjects from the Alzheimer's Disease Neuroimaging Initiative.Among controls, male and female carriers were more likely to convert to MCI/AD, but the effect was stronger in women (HR = 1.81 for women; HR = 1.27 for men; interaction: p = 0.011). The interaction remained significant in a predefined subanalysis restricted to APOE3/3 and APOE3/4 genotypes. Among MCI patients, both male and female APOE4 carriers were more likely to convert to AD (HR = 2.16 for women; HR = 1.64 for men); the interaction was not significant (p = 0.14). In the subanalysis restricted to APOE3/3 and APOE3/4 genotypes, the interaction was significant (p = 0.02; HR = 2.17 for women; HR = 1.51 for men). The APOE4-by-sex interaction on biomarker levels was significant for MCI patients for total tau and the tau-to-Aβ ratio (p = 0.009 and p = 0.02, respectively; more AD-like in women).APOE4 confers greater AD risk in women. Biomarker results suggest that increased APOE-related risk in women may be associated with tau pathology. These findings have important clinical implications and suggest novel research approaches into AD pathogenesis.

  View details for DOI 10.1002/ana.24135

  View details for PubMedID 24623176

• Transport on Riemannian manifold for functional connectivity-based classification. Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention Ng, B., Dressler, M., Varoquaux, G., Poline, J. B., Greicius, M., Thirion, B. 2014; 17: 405-412

  Abstract

  We present a Riemannian approach for classifying fMRI connectivity patterns before and after intervention in longitudinal studies. A fundamental difficulty with using connectivity as features is that covariance matrices live on the positive semi-definite cone, which renders their elements inter-related. The implicit independent feature assumption in most classifier learning algorithms is thus violated. In this paper, we propose a matrix whitening transport for projecting the covariance estimates onto a common tangent space to reduce the statistical dependencies between their elements. We show on real data that our approach provides significantly higher classification accuracy than directly using Pearson's correlation. We further propose a non-parametric scheme for identifying significantly discriminative connections from classifier weights. Using this scheme, a number of neuroanatomically meaningful connections are found, whereas no significant connections are detected with pure permutation testing.

  View details for PubMedID 25485405

• Transport on Riemannian Manifold for Functional Connectivity-Based Classification 17th International Conference on Medical Image Computing and Computer-Assisted Intervention (MICCAI) Ng, B., Dressler, M., Varoquaux, G., Poline, J. B., Greicius, M., Thirion, B. SPRINGER-VERLAG BERLIN. 2014: 405–12

  Abstract

  We present a Riemannian approach for classifying fMRI connectivity patterns before and after intervention in longitudinal studies. A fundamental difficulty with using connectivity as features is that covariance matrices live on the positive semi-definite cone, which renders their elements inter-related. The implicit independent feature assumption in most classifier learning algorithms is thus violated. In this paper, we propose a matrix whitening transport for projecting the covariance estimates onto a common tangent space to reduce the statistical dependencies between their elements. We show on real data that our approach provides significantly higher classification accuracy than directly using Pearson's correlation. We further propose a non-parametric scheme for identifying significantly discriminative connections from classifier weights. Using this scheme, a number of neuroanatomically meaningful connections are found, whereas no significant connections are detected with pure permutation testing.

  View details for Web of Science ID 000347686400051

• The will to persevere induced by electrical stimulation of the human cingulate gyrus. Neuron Parvizi, J., Rangarajan, V., Shirer, W. R., Desai, N., Greicius, M. D. 2013; 80 (6): 1359-1367

  Abstract

  Anterior cingulate cortex (ACC) is known to be involved in functions such as emotion, pain, and cognitive control. While studies in humans and nonhuman mammals have advanced our understanding of ACC function, the subjective correlates of ACC activity have remained largely unexplored. In the current study, we show that electrical charge delivery in the anterior midcingulate cortex (aMCC) elicits autonomic changes and the expectation of an imminent challenge coupled with a determined attitude to overcome it. Seed-based, resting-state connectivity analysis revealed that the site of stimulation in both patients was at the core of a large-scale distributed network linking aMCC to the frontoinsular and frontopolar as well as some subcortical regions. This report provides compelling, first-person accounts of electrical stimulation of this brain network and suggests its possible involvement in psychopathological conditions that are characterized by a reduced capacity to endure psychological or physical distress.

  View details for DOI 10.1016/j.neuron.2013.10.057

  View details for PubMedID 24316296

  View details for PubMedCentralID PMC3877748

• Identifying large-scale brain networks in fragile x syndrome. JAMA psychiatry Hall, S. S., Jiang, H., Reiss, A. L., Greicius, M. D. 2013; 70 (11): 1215-1223

  Abstract

  Fragile X syndrome (FXS) is an X-linked neurogenetic disorder characterized by a cognitive and behavioral phenotype resembling features of autism spectrum disorder. Until now, research has focused largely on identifying regional differences in brain structure and function between individuals with FXS and various control groups. Very little is known about the large-scale brain networks that may underlie the cognitive and behavioral symptoms of FXS.To identify large-scale, resting-state networks in FXS that differ from control individuals matched on age, IQ, and severity of behavioral and cognitive symptoms.Cross-sectional, in vivo neuroimaging study conducted in an academic medical center. Participants (aged 10-23 years) included 17 males and females with FXS and 16 males and females serving as controls.Univariate voxel-based morphometric analyses, fractional amplitude of low-frequency fluctuations (fALFF) analysis, and group-independent component analysis with dual regression.Patients with FXS showed decreased functional connectivity in the salience, precuneus, left executive control, language, and visuospatial networks compared with controls. Decreased fALFF in the bilateral insular, precuneus, and anterior cingulate cortices also was found in patients with FXS compared with control participants. Furthermore, fALFF in the left insular cortex was significantly positively correlated with IQ in patients with FXS. Decreased gray matter density, resting-state connectivity, and fALFF converged in the left insular cortex in patients with FXS.Fragile X syndrome results in widespread reductions in functional connectivity across multiple cognitive and affective brain networks. Converging structural and functional abnormalities in the left insular cortex, a region also implicated in individuals diagnosed with autism spectrum disorder, suggests that insula integrity and connectivity may be compromised in FXS. This method could prove useful in establishing an imaging biomarker for FXS.

  View details for DOI 10.1001/jamapsychiatry.2013.247

  View details for PubMedID 24068330

• Disordered reward processing and functional connectivity in trichotillomania: A pilot study JOURNAL OF PSYCHIATRIC RESEARCH White, M. P., Shirer, W. R., Molfino, M. J., Tenison, C., Damoiseaux, J. S., Greicius, M. D. 2013; 47 (9): 1264-1272

  Abstract

  The neurobiology of Trichotillomania is poorly understood, although there is increasing evidence to suggest that TTM may involve alterations of reward processing. The current study represents the first exploration of reward processing in TTM and the first resting state fMRI study in TTM. We incorporate both event-related fMRI using a monetary incentive delay (MID) task, and resting state fMRI, using two complementary resting state analysis methodologies (functional connectivity to the nucleus accumbens and dual regression within a reward network) in a pilot study to investigate differences in reward processing between TTM and healthy controls (HC).21 unmedicated subjects with TTM and 14 HC subjects underwent resting state fMRI scans. A subset (13 TTM and 12 HC) also performed the MID task.For the MID task, TTM subjects showed relatively decreased nucleus accumbens (NAcc) activation to reward anticipation, but relative over-activity of the NAcc to both gain and loss outcomes. Resting state functional connectivity analysis showed decreased connectivity of the dorsal anterior cingulate (dACC) to the NAcc in TTM. Dual regression analysis of a reward network identified through independent component analysis (ICA) also showed decreased dACC connectivity and more prominently decreased basolateral amygdala connectivity within the reward network in TTM.Disordered reward processing at the level of NAcc, also involving decreased modulatory input from the dACC and the basolateral amygdala may play a role in the pathophysiology of TTM.

  View details for DOI 10.1016/j.jpsychires.2013.05.014

  View details for Web of Science ID 000322413800021

  View details for PubMedID 23777938

• Intrinsic connectivity networks in healthy subjects explain clinical variability in Alzheimer's disease PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Lehmann, M., Madison, C. M., Ghosh, P. M., Seeley, W. W., Mormino, E., Greicius, M. D., Gorno-Tempini, M. L., Kramer, J. H., Miller, B. L., Jagust, W. J., Rabinovici, G. D. 2013; 110 (28): 11606-11611

  Abstract

  Although previous studies have emphasized the vulnerability of the default mode network (DMN) in Alzheimer's disease (AD), little is known about the involvement of other functional networks and their relationship to clinical phenotype. To test whether clinicoanatomic heterogeneity in AD is driven by the involvement of specific networks, network connectivity was assessed in healthy subjects by seeding regions commonly and specifically atrophied in three clinical AD variants: early-onset AD (age at onset, <65 y; memory and executive deficits), logopenic variant primary progressive aphasia (language deficits), and posterior cortical atrophy (visuospatial deficits). Four-millimeter seed regions of interest were used to obtain intrinsic connectivity maps in 131 healthy controls (age, 65.5 ± 3.5 y). Atrophy patterns in independent cohorts of AD variant patients and their correspondence to connectivity networks in controls were also assessed. The connectivity maps of commonly atrophied regions of interest support posterior DMN and precuneus network involvement across AD variants, whereas seeding regions specifically atrophied in each AD variant revealed distinct, syndrome-specific connectivity patterns. Goodness-of-fit analysis of each connectivity map with network templates showed the highest correspondence between the early-onset AD seed connectivity map and anterior salience and right executive-control networks, the logopenic aphasia seed connectivity map and the language network, and the posterior cortical atrophy seed connectivity map and the higher visual network. Connectivity maps derived from controls matched regions commonly and specifically atrophied in the patients. Our findings indicate that the posterior DMN and precuneus network are commonly affected in AD variants, whereas syndrome-specific neurodegenerative patterns are driven by the involvement of specific networks outside the DMN.

  View details for DOI 10.1073/pnas.1221536110

  View details for Web of Science ID 000321827000086

  View details for PubMedID 23798398

  View details for PubMedCentralID PMC3710820

• Altered resting state network activity in complex regional pain syndrome Martucci, K., BARAD, M., Shirer, W., Greicius, M., Mackey, S. CHURCHILL LIVINGSTONE. 2013: S48–S48

  View details for Web of Science ID 000317639400189

• Diverging patterns of amyloid deposition and hypometabolism in clinical variants of probable Alzheimer's disease BRAIN Lehmann, M., Ghosh, P. M., Madison, C., Laforce, R., Corbetta-Rastelli, C., Weiner, M. W., Greicius, M. D., Seeley, W. W., Gorno-Tempini, M. L., Rosen, H. J., Miller, B. L., Jagust, W. J., Rabinovici, G. D. 2013; 136: 844-858

  Abstract

  The factors driving clinical heterogeneity in Alzheimer's disease are not well understood. This study assessed the relationship between amyloid deposition, glucose metabolism and clinical phenotype in Alzheimer's disease, and investigated how these relate to the involvement of functional networks. The study included 17 patients with early-onset Alzheimer's disease (age at onset <65 years), 12 patients with logopenic variant primary progressive aphasia and 13 patients with posterior cortical atrophy [whole Alzheimer's disease group: age = 61.5 years (standard deviation 6.5 years), 55% male]. Thirty healthy control subjects [age = 70.8 (3.3) years, 47% male] were also included. Subjects underwent positron emission tomography with (11)C-labelled Pittsburgh compound B and (18)F-labelled fluorodeoxyglucose. All patients met National Institute on Ageing-Alzheimer's Association criteria for probable Alzheimer's disease and showed evidence of amyloid deposition on (11)C-labelled Pittsburgh compound B positron emission tomography. We hypothesized that hypometabolism patterns would differ across variants, reflecting involvement of specific functional networks, whereas amyloid patterns would be diffuse and similar across variants. We tested these hypotheses using three complimentary approaches: (i) mass-univariate voxel-wise group comparison of (18)F-labelled fluorodeoxyglucose and (11)C-labelled Pittsburgh compound B; (ii) generation of covariance maps across all subjects with Alzheimer's disease from seed regions of interest specifically atrophied in each variant, and comparison of these maps to functional network templates; and (iii) extraction of (11)C-labelled Pittsburgh compound B and (18)F-labelled fluorodeoxyglucose values from functional network templates. Alzheimer's disease clinical groups showed syndrome-specific (18)F-labelled fluorodeoxyglucose patterns, with greater parieto-occipital involvement in posterior cortical atrophy, and asymmetric involvement of left temporoparietal regions in logopenic variant primary progressive aphasia. In contrast, all Alzheimer's disease variants showed diffuse patterns of (11)C-labelled Pittsburgh compound B binding, with posterior cortical atrophy additionally showing elevated uptake in occipital cortex compared with early-onset Alzheimer's disease. The seed region of interest covariance analysis revealed distinct (18)F-labelled fluorodeoxyglucose correlation patterns that greatly overlapped with the right executive-control network for the early-onset Alzheimer's disease region of interest, the left language network for the logopenic variant primary progressive aphasia region of interest, and the higher visual network for the posterior cortical atrophy region of interest. In contrast, (11)C-labelled Pittsburgh compound B covariance maps for each region of interest were diffuse. Finally, (18)F-labelled fluorodeoxyglucose was similarly reduced in all Alzheimer's disease variants in the dorsal and left ventral default mode network, whereas significant differences were found in the right ventral default mode, right executive-control (both lower in early-onset Alzheimer's disease and posterior cortical atrophy than logopenic variant primary progressive aphasia) and higher-order visual network (lower in posterior cortical atrophy than in early-onset Alzheimer's disease and logopenic variant primary progressive aphasia), with a trend towards lower (18)F-labelled fluorodeoxyglucose also found in the left language network in logopenic variant primary progressive aphasia. There were no differences in (11)C-labelled Pittsburgh compound B binding between syndromes in any of the networks. Our data suggest that Alzheimer's disease syndromes are associated with degeneration of specific functional networks, and that fibrillar amyloid-β deposition explains at most a small amount of the clinico-anatomic heterogeneity in Alzheimer's disease.

  View details for DOI 10.1093/brain/aws327

  View details for Web of Science ID 000315624700016

  View details for PubMedID 23358601

  View details for PubMedCentralID PMC3580269

• Sporadic Jakob-Creutzfeldt Disease Presenting as Primary Progressive Aphasia JAMA NEUROLOGY Johnson, D. Y., Dunkelberger, D. L., Henry, M., Haman, A., Greicius, M. D., Wong, K., DeArmond, S. J., Miller, B. L., Gorno-Tempini, M. L., Geschwind, M. D. 2013; 70 (2): 254-257

  Abstract

  To report the clinical, neuropsychological, linguistic, imaging, and neuropathological features of a unique case of sporadic Jakob-Creutzfeldt disease in which the patient presented with a logopenic variant of primary progressive aphasia.Case report.Large referral center for atypical memory and aging disorders, particularly Jakob-Creutzfeldt disease.Patient presenting with logopenic variant primary progressive aphasia initially thought to be due to Alzheimer disease.Despite the long, slow 3.5-year course, the patient was shown to have pathology-proven sporadic Jakob-Creutzfeldt disease.These findings expand the differential of primary progressive aphasia to include prion disease.

  View details for DOI 10.1001/2013.jamaneurol.139

  View details for Web of Science ID 000316801300016

  View details for PubMedID 23400721

• Two test statistics for cross-modal graph community significance 3rd International Workshop on Pattern Recognition in NeuroImaging (PRNI) Richiardi, J., Altmann, A., Greicius, M. IEEE. 2013: 70–73

  View details for DOI 10.1109/PRNI.2013.27

  View details for Web of Science ID 000333958600018

• Neuroimaging insights into network-based neurodegeneration CURRENT OPINION IN NEUROLOGY Greicius, M. D., Kimmel, D. L. 2012; 25 (6): 727-734

  Abstract

  Convergent evidence from a number of neuroscience disciplines supports the hypothesis that Alzheimer's disease and other neurodegenerative disorders progress along brain networks. This review considers the role of neuroimaging in strengthening the case for network-based neurodegeneration and elucidating potential mechanisms.Advances in functional and structural MRI have recently enabled the delineation of multiple large-scale distributed brain networks. The application of these network-imaging modalities to neurodegenerative disease has shown that specific disorders appear to progress along specific networks. Recent work applying theoretical measures of network efficiency to in-vivo network imaging has allowed for the development and evaluation of models of disease spread along networks. Novel MRI acquisition and analysis methods are paving the way for in-vivo assessment of the layer-specific microcircuits first targeted by neurodegenerative diseases. These methodological advances coupled with large, longitudinal studies of subjects progressing from healthy aging into dementia will enable a detailed understanding of the seeding and spread of these disorders.Neuroimaging has provided ample evidence that neurodegenerative disorders progress along brain networks, and is now beginning to elucidate how they do so.

  View details for DOI 10.1097/WCO.0b013e32835a26b3

  View details for Web of Science ID 000311364500013

  View details for PubMedID 23108250

• Introduction to the Special Issue on Connectivity NEUROIMAGE Greicius, M. D., Seeley, W. W. 2012; 62 (4): 2181-2181

  View details for DOI 10.1016/j.neuroimage.2012.07.036

  View details for Web of Science ID 000308265200001

  View details for PubMedID 22902262

• Efficacy of Transcranial Magnetic Stimulation Targets for Depression Is Related to Intrinsic Functional Connectivity with the Subgenual Cingulate BIOLOGICAL PSYCHIATRY Fox, M. D., Buckner, R. L., White, M. P., Greicius, M. D., Pascual-Leone, A. 2012; 72 (7): 595-603

  Abstract

  Transcranial magnetic stimulation (TMS) to the left dorsolateral prefrontal cortex (DLPFC) is used clinically for the treatment of depression. However, the antidepressant mechanism remains unknown and its therapeutic efficacy remains limited. Recent data suggest that some left DLPFC targets are more effective than others; however, the reasons for this heterogeneity and how to capitalize on this information remain unclear.Intrinsic (resting state) functional magnetic resonance imaging data from 98 normal subjects were used to compute functional connectivity with various left DLPFC TMS targets employed in the literature. Differences in functional connectivity related to differences in previously reported clinical efficacy were identified. This information was translated into a connectivity-based targeting strategy to identify optimized left DLPFC TMS coordinates. Results in normal subjects were tested for reproducibility in an independent cohort of 13 patients with depression.Differences in functional connectivity were related to previously reported differences in clinical efficacy across a distributed set of cortical and limbic regions. Dorsolateral prefrontal cortex TMS sites with better clinical efficacy were more negatively correlated (anticorrelated) with the subgenual cingulate. Optimum connectivity-based stimulation coordinates were identified in Brodmann area 46. Results were reproducible in patients with depression.Reported antidepressant efficacy of different left DLPFC TMS sites is related to the anticorrelation of each site with the subgenual cingulate, potentially lending insight into the antidepressant mechanism of TMS and suggesting a role for intrinsically anticorrelated networks in depression. These results can be translated into a connectivity-based targeting strategy for focal brain stimulation that might be used to optimize clinical response.

  View details for DOI 10.1016/j.biopsych.2012.04.028

  View details for Web of Science ID 000308714000014

  View details for PubMedID 22658708

• Gender Modulates the APOE epsilon 4 Effect in Healthy Older Adults: Convergent Evidence from Functional Brain Connectivity and Spinal Fluid Tau Levels JOURNAL OF NEUROSCIENCE Damoiseaux, J. S., Seeley, W. W., Zhou, J., Shirer, W. R., Coppola, G., Karydas, A., Rosen, H. J., Miller, B. L., Kramer, J. H., Greicius, M. D. 2012; 32 (24): 8254-8262

  Abstract

  We examined whether the effect of the apolipoprotein E (APOE) genotype on functional brain connectivity is modulated by gender in healthy older human adults. Our results confirm significantly decreased connectivity in the default mode network in healthy older APOE ε4 carriers compared with ε3 homozygotes. More important, further testing revealed a significant interaction between APOE genotype and gender in the precuneus, a major default mode hub. Female ε4 carriers showed significantly reduced default mode connectivity compared with either female ε3 homozygotes or male ε4 carriers, whereas male ε4 carriers differed minimally from male ε3 homozygotes. An additional analysis in an independent sample of healthy elderly using an independent marker of Alzheimer's disease, i.e., spinal fluid levels of tau, provided corresponding evidence for this gender-by-APOE interaction. Together, these results converge with previous work showing a higher prevalence of the ε4 allele among women with Alzheimer's disease and, critically, demonstrate that this interaction between APOE genotype and gender is detectable in the preclinical period.

  View details for DOI 10.1523/JNEUROSCI.0305-12.2012

  View details for Web of Science ID 000305295600017

  View details for PubMedID 22699906

  View details for PubMedCentralID PMC3394933

• Functional connectivity tracks clinical deterioration in Alzheimer's disease NEUROBIOLOGY OF AGING Damoiseaux, J. S., Prater, K. E., Miller, B. L., Greicius, M. D. 2012; 33 (4)

  Abstract

  While resting state functional connectivity has been shown to decrease in patients with mild and/or moderate Alzheimer's disease, it is not yet known how functional connectivity changes in patients as the disease progresses. Furthermore, it has been noted that the default mode network is not as homogenous as previously assumed and several fractionations of the network have been proposed. Here, we separately investigated the modulation of 3 default mode subnetworks, as identified with group independent component analysis, by comparing Alzheimer's disease patients to healthy controls and by assessing connectivity changes over time. Our results showed decreased connectivity at baseline in patients versus controls in the posterior default mode network, and increased connectivity in the anterior and ventral default mode networks. At follow-up, functional connectivity decreased across all default mode systems in patients. Our results suggest that earlier in the disease, regions of the posterior default mode network start to disengage whereas regions within the anterior and ventral networks enhance their connectivity. However, as the disease progresses, connectivity within all systems eventually deteriorates.

  View details for DOI 10.1016/j.neurobiolaging.2011.06.024

  View details for Web of Science ID 000301506800029

  View details for PubMedID 21840627

  View details for PubMedCentralID PMC3218226

• Gender Modulates the APOE epsilon 4 Effect in Healthy Older Controls: Convergent Evidence from Functional Brain Connectivity and Spinal Fluid Tau Levels 64th Annual Meeting of the American-Academy-of-Neurology (AAN) Damoiseaux, J., Seeley, W., Shirer, W., Coppola, G., Karydas, A., Miller, B., Kramer, J., Greicius, M. LIPPINCOTT WILLIAMS & WILKINS. 2012

  View details for Web of Science ID 000303204801304

• Decoding Subject-Driven Cognitive States with Whole-Brain Connectivity Patterns CEREBRAL CORTEX SHIRER, W. R., RYALI, S., Rykhlevskaia, E., Menon, V., Greicius, M. D. 2012; 22 (1): 158-165

  Abstract

  Decoding specific cognitive states from brain activity constitutes a major goal of neuroscience. Previous studies of brain-state classification have focused largely on decoding brief, discrete events and have required the timing of these events to be known. To date, methods for decoding more continuous and purely subject-driven cognitive states have not been available. Here, we demonstrate that free-streaming subject-driven cognitive states can be decoded using a novel whole-brain functional connectivity analysis. Ninety functional regions of interest (ROIs) were defined across 14 large-scale resting-state brain networks to generate a 3960 cell matrix reflecting whole-brain connectivity. We trained a classifier to identify specific patterns of whole-brain connectivity as subjects rested quietly, remembered the events of their day, subtracted numbers, or (silently) sang lyrics. In a leave-one-out cross-validation, the classifier identified these 4 cognitive states with 84% accuracy. More critically, the classifier achieved 85% accuracy when identifying these states in a second, independent cohort of subjects. Classification accuracy remained high with imaging runs as short as 30-60 s. At all temporal intervals assessed, the 90 functionally defined ROIs outperformed a set of 112 commonly used structural ROIs in classifying cognitive states. This approach should enable decoding a myriad of subject-driven cognitive states from brief imaging data samples.

  View details for DOI 10.1093/cercor/bhr099

  View details for Web of Science ID 000298190500014

  View details for PubMedID 21616982

  View details for PubMedCentralID PMC3236795

• Relationships between Beta-Amyloid and Functional Connectivity in Different Components of the Default Mode Network in Aging CEREBRAL CORTEX Mormino, E. C., Smiljic, A., Hayenga, A. O., Onami, S. H., Greicius, M. D., Rabinovici, G. D., Janabi, M., Baker, S. L., Yen, I. V., Madison, C. M., Miller, B. L., Jagust, W. J. 2011; 21 (10): 2399-2407

  Abstract

  Although beta-amyloid (Aβ) deposition is a characteristic feature of Alzheimer's disease (AD), this pathology is commonly found in elderly normal controls (NC). The pattern of Aβ deposition as detected with Pittsburgh compound-B positron emission tomography (PIB-PET) imaging shows substantial spatial overlap with the default mode network (DMN), a group of brain regions that typically deactivates during externally driven cognitive tasks. In this study, we show that DMN functional connectivity (FC) during rest is altered with increasing levels of PIB uptake in NC. Specifically, FC decreases were identified in regions implicated in episodic memory (EM) processing (posteromedial cortex, ventral medial prefrontal cortex, and angular gyrus), whereas connectivity increases were detected in dorsal and anterior medial prefrontal and lateral temporal cortices. This pattern of decreases is consistent with previous studies that suggest heightened vulnerability of EM-related brain regions in AD, whereas the observed increases in FC may reflect a compensatory response.

  View details for DOI 10.1093/cercor/bhr025

  View details for Web of Science ID 000294808800020

  View details for PubMedID 21383234

  View details for PubMedCentralID PMC3169663

• Differential electrophysiological response during rest, self-referential, and non-self-referential tasks in human posteromedial cortex PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Dastjerdi, M., Foster, B. L., Nasrullah, S., Rauschecker, A. M., Dougherty, R. F., Townsend, J. D., Chang, C., Greicius, M. D., Menon, V., Kennedy, D. P., Parvizi, J. 2011; 108 (7): 3023-3028

  Abstract

  The electrophysiological basis for higher brain activity during rest and internally directed cognition within the human default mode network (DMN) remains largely unknown. Here we use intracranial recordings in the human posteromedial cortex (PMC), a core node within the DMN, during conditions of cued rest, autobiographical judgments, and arithmetic processing. We found a heterogeneous profile of PMC responses in functional, spatial, and temporal domains. Although the majority of PMC sites showed increased broad gamma band activity (30-180 Hz) during rest, some PMC sites, proximal to the retrosplenial cortex, responded selectively to autobiographical stimuli. However, no site responded to both conditions, even though they were located within the boundaries of the DMN identified with resting-state functional imaging and similarly deactivated during arithmetic processing. These findings, which provide electrophysiological evidence for heterogeneity within the core of the DMN, will have important implications for neuroimaging studies of the DMN.

  View details for DOI 10.1073/pnas.1017098108

  View details for Web of Science ID 000287377000073

  View details for PubMedID 21282630

  View details for PubMedCentralID PMC3041085

• Breakdown of within- and between-network Resting State Functional Magnetic Resonance Imaging Connectivity during Propofol-induced Loss of Consciousness ANESTHESIOLOGY Boveroux, P., Vanhaudenhuyse, A., Bruno, M., Noirhomme, Q., Lauwick, S., Luxen, A., Degueldre, C., Plenevaux, A., Schnakers, C., Phillips, C., Brichant, J., Bonhomme, V., Maquet, P., Greicius, M. D., Leureys, S., Boly, M. 2010; 113 (5): 1038-1053

  Abstract

  Mechanisms of anesthesia-induced loss of consciousness remain poorly understood. Resting-state functional magnetic resonance imaging allows investigating whole-brain connectivity changes during pharmacological modulation of the level of consciousness.Low-frequency spontaneous blood oxygen level-dependent fluctuations were measured in 19 healthy volunteers during wakefulness, mild sedation, deep sedation with clinical unconsciousness, and subsequent recovery of consciousness.Propofol-induced decrease in consciousness linearly correlates with decreased corticocortical and thalamocortical connectivity in frontoparietal networks (i.e., default- and executive-control networks). Furthermore, during propofol-induced unconsciousness, a negative correlation was identified between thalamic and cortical activity in these networks. Finally, negative correlations between default network and lateral frontoparietal cortices activity, present during wakefulness, decreased proportionally to propofol-induced loss of consciousness. In contrast, connectivity was globally preserved in low-level sensory cortices, (i.e., in auditory and visual networks across sedation stages). This was paired with preserved thalamocortical connectivity in these networks. Rather, waning of consciousness was associated with a loss of cross-modal interactions between visual and auditory networks.Our results shed light on the functional significance of spontaneous brain activity fluctuations observed in functional magnetic resonance imaging. They suggest that propofol-induced unconsciousness could be linked to a breakdown of cerebral temporal architecture that modifies both within- and between-network connectivity and thus prevents communication between low-level sensory and higher-order frontoparietal cortices, thought to be necessary for perception of external stimuli. They emphasize the importance of thalamocortical connectivity in higher-order cognitive brain networks in the genesis of conscious perception.

  View details for Web of Science ID 000283671300010

  View details for PubMedID 20885292

• Dissociable Connectivity within Human Angular Gyrus and Intraparietal Sulcus: Evidence from Functional and Structural Connectivity CEREBRAL CORTEX Uddin, L. Q., Supekar, K., Amin, H., Rykhlevskaia, E., Nguyen, D. A., Greicius, M. D., Menon, V. 2010; 20 (11): 2636-2646

  Abstract

  The inferior parietal lobule (IPL) of the human brain is a heterogeneous region involved in visuospatial attention, memory, and mathematical cognition. Detailed description of connectivity profiles of subdivisions within the IPL is critical for accurate interpretation of functional neuroimaging studies involving this region. We separately examined functional and structural connectivity of the angular gyrus (AG) and the intraparietal sulcus (IPS) using probabilistic cytoarchitectonic maps. Regions-of-interest (ROIs) included anterior and posterior AG subregions (PGa, PGp) and 3 IPS subregions (hIP2, hIP1, and hIP3). Resting-state functional connectivity analyses showed that PGa was more strongly linked to basal ganglia, ventral premotor areas, and ventrolateral prefrontal cortex, while PGp was more strongly connected with ventromedial prefrontal cortex, posterior cingulate, and hippocampus-regions comprising the default mode network. The anterior-most IPS ROIs, hIP2 and hIP1, were linked with ventral premotor and middle frontal gyrus, while the posterior-most IPS ROI, hIP3, showed connectivity with extrastriate visual areas. In addition, hIP1 was connected with the insula. Tractography using diffusion tensor imaging revealed structural connectivity between most of these functionally connected regions. Our findings provide evidence for functional heterogeneity of cytoarchitectonically defined subdivisions within IPL and offer a novel framework for synthesis and interpretation of the task-related activations and deactivations involving the IPL during cognition.

  View details for DOI 10.1093/cercor/bhq011

  View details for Web of Science ID 000282750600013

  View details for PubMedID 20154013

  View details for PubMedCentralID PMC2951845

• Development of functional and structural connectivity within the default mode network in young children NEUROIMAGE Supekar, K., Uddin, L. Q., Prater, K., Amin, H., Greicius, M. D., Menon, V. 2010; 52 (1): 290-301

  Abstract

  Functional and structural maturation of networks comprised of discrete regions is an important aspect of brain development. The default-mode network (DMN) is a prominent network which includes the posterior cingulate cortex (PCC), medial prefrontal cortex (mPFC), medial temporal lobes (MTL), and angular gyrus (AG). Despite increasing interest in DMN function, little is known about its maturation from childhood to adulthood. Here we examine developmental changes in DMN connectivity using a multimodal imaging approach by combining resting-state fMRI, voxel-based morphometry and diffusion tensor imaging-based tractography. We found that the DMN undergoes significant developmental changes in functional and structural connectivity, but these changes are not uniform across all DMN nodes. Convergent structural and functional connectivity analyses suggest that PCC-mPFC connectivity along the cingulum bundle is the most immature link in the DMN of children. Both PCC and mPFC also showed gray matter volume differences, as well as prominent macrostructural and microstructural differences in the dorsal cingulum bundle linking these regions. Notably, structural connectivity between PCC and left MTL was either weak or non-existent in children, even though functional connectivity did not differ from that of adults. These results imply that functional connectivity in children can reach adult-like levels despite weak structural connectivity. We propose that maturation of PCC-mPFC structural connectivity plays an important role in the development of self-related and social-cognitive functions that emerge during adolescence. More generally, our study demonstrates how quantitative multimodal analysis of anatomy and connectivity allows us to better characterize the heterogeneous development and maturation of brain networks.

  View details for DOI 10.1016/j.neuroimage.2010.04.009

  View details for Web of Science ID 000278637700029

  View details for PubMedID 20385244

  View details for PubMedCentralID PMC2976600

• Functional magnetic resonance imaging and estrogen effects on the brain: cautious interpretation of a BOLD finding MENOPAUSE-THE JOURNAL OF THE NORTH AMERICAN MENOPAUSE SOCIETY Henderson, V. W., Greicius, M. D. 2010; 17 (4): 669-671

  View details for DOI 10.1097/gme.0b013e3181e3a50e

  View details for Web of Science ID 000279799300002

  View details for PubMedID 20944455

• Divergent network connectivity changes in behavioural variant frontotemporal dementia and Alzheimer's disease BRAIN Zhou, J., Greicius, M. D., Gennatas, E. D., Growdon, M. E., Jang, J. Y., Rabinovici, G. D., Kramer, J. H., Weiner, M., Miller, B. L., Seeley, W. W. 2010; 133: 1352-1367

  Abstract

  Resting-state or intrinsic connectivity network functional magnetic resonance imaging provides a new tool for mapping large-scale neural network function and dysfunction. Recently, we showed that behavioural variant frontotemporal dementia and Alzheimer's disease cause atrophy within two major networks, an anterior 'Salience Network' (atrophied in behavioural variant frontotemporal dementia) and a posterior 'Default Mode Network' (atrophied in Alzheimer's disease). These networks exhibit an anti-correlated relationship with each other in the healthy brain. The two diseases also feature divergent symptom-deficit profiles, with behavioural variant frontotemporal dementia undermining social-emotional function and preserving or enhancing visuospatial skills, and Alzheimer's disease showing the inverse pattern. We hypothesized that these disorders would exert opposing connectivity effects within the Salience Network (disrupted in behavioural variant frontotemporal dementia but enhanced in Alzheimer's disease) and the Default Mode Network (disrupted in Alzheimer's disease but enhanced in behavioural variant frontotemporal dementia). With task-free functional magnetic resonance imaging, we tested these ideas in behavioural variant frontotemporal dementia, Alzheimer's disease and healthy age-matched controls (n = 12 per group), using independent component analyses to generate group-level network contrasts. As predicted, behavioural variant frontotemporal dementia attenuated Salience Network connectivity, most notably in frontoinsular, cingulate, striatal, thalamic and brainstem nodes, but enhanced connectivity within the Default Mode Network. Alzheimer's disease, in contrast, reduced Default Mode Network connectivity to posterior hippocampus, medial cingulo-parieto-occipital regions and the dorsal raphe nucleus, but intensified Salience Network connectivity. Specific regions of connectivity disruption within each targeted network predicted intrinsic connectivity enhancement within the reciprocal network. In behavioural variant frontotemporal dementia, clinical severity correlated with loss of right frontoinsular Salience Network connectivity and with biparietal Default Mode Network connectivity enhancement. Based on these results, we explored whether a combined index of Salience Network and Default Mode Network connectivity might discriminate between the three groups. Linear discriminant analysis achieved 92% clinical classification accuracy, including 100% separation of behavioural variant frontotemporal dementia and Alzheimer's disease. Patients whose clinical diagnoses were supported by molecular imaging, genetics, or pathology showed 100% separation using this method, including four diagnostically equivocal 'test' patients not used to train the algorithm. Overall, the findings suggest that behavioural variant frontotemporal dementia and Alzheimer's disease lead to divergent network connectivity patterns, consistent with known reciprocal network interactions and the strength and deficit profiles of the two disorders. Further developed, intrinsic connectivity network signatures may provide simple, inexpensive, and non-invasive biomarkers for dementia differential diagnosis and disease monitoring.

  View details for DOI 10.1093/brain/awq075

  View details for Web of Science ID 000277225700015

  View details for PubMedID 20410145

  View details for PubMedCentralID PMC2912696

• Default network connectivity reflects the level of consciousness in non-communicative brain-damaged patients BRAIN Vanhaudenhuyse, A., Noirhomme, Q., Tshibanda, L. J., Bruno, M., Boveroux, P., Schnakers, C., Soddu, A., Perlbarg, V., Ledoux, D., Brichant, J., Moonen, G., Maquet, P., Greicius, M. D., Laureys, S., Boly, M. 2010; 133: 161-171

  Abstract

  The 'default network' is defined as a set of areas, encompassing posterior-cingulate/precuneus, anterior cingulate/mesiofrontal cortex and temporo-parietal junctions, that show more activity at rest than during attention-demanding tasks. Recent studies have shown that it is possible to reliably identify this network in the absence of any task, by resting state functional magnetic resonance imaging connectivity analyses in healthy volunteers. However, the functional significance of these spontaneous brain activity fluctuations remains unclear. The aim of this study was to test if the integrity of this resting-state connectivity pattern in the default network would differ in different pathological alterations of consciousness. Fourteen non-communicative brain-damaged patients and 14 healthy controls participated in the study. Connectivity was investigated using probabilistic independent component analysis, and an automated template-matching component selection approach. Connectivity in all default network areas was found to be negatively correlated with the degree of clinical consciousness impairment, ranging from healthy controls and locked-in syndrome to minimally conscious, vegetative then coma patients. Furthermore, precuneus connectivity was found to be significantly stronger in minimally conscious patients as compared with unconscious patients. Locked-in syndrome patient's default network connectivity was not significantly different from controls. Our results show that default network connectivity is decreased in severely brain-damaged patients, in proportion to their degree of consciousness impairment. Future prospective studies in a larger patient population are needed in order to evaluate the prognostic value of the presented methodology.

  View details for DOI 10.1093/brain/awp313

  View details for Web of Science ID 000273492800014

  View details for PubMedID 20034928

  View details for PubMedCentralID PMC2801329

• Clinical applications of resting state functional connectivity. Frontiers in systems neuroscience Fox, M. D., Greicius, M. 2010; 4: 19-?

  Abstract

  During resting conditions the brain remains functionally and metabolically active. One manifestation of this activity that has become an important research tool is spontaneous fluctuations in the blood oxygen level-dependent (BOLD) signal of functional magnetic resonance imaging (fMRI). The identification of correlation patterns in these spontaneous fluctuations has been termed resting state functional connectivity (fcMRI) and has the potential to greatly increase the translation of fMRI into clinical care. In this article we review the advantages of the resting state signal for clinical applications including detailed discussion of signal to noise considerations. We include guidelines for performing resting state research on clinical populations, outline the different areas for clinical application, and identify important barriers to be addressed to facilitate the translation of resting state fcMRI into the clinical realm.

  View details for DOI 10.3389/fnsys.2010.00019

  View details for PubMedID 20592951

  View details for PubMedCentralID PMC2893721

• Episodic encephalopathy due to an occult spinal vascular malformation complicated by superficial siderosis CLINICAL NEUROLOGY AND NEUROSURGERY Gonella, M. C., Fischbein, N. J., Lane, B., Shuer, L. M., Greicius, M. D. 2010; 112 (1): 82-84

  Abstract

  Superficial siderosis (SS) of the central nervous system is a rare condition caused by chronic subarachnoid hemorrhage. Clinical manifestations typically include sensorineural hearing loss and cerebellar ataxia. Recurrent episodic encephalopathy in the setting of SS has not been reported. We describe a unique case of SS in a 67-year-old man with an 8-year history of episodic encephalopathy associated with headache and vomiting. The patient also had a history of progressive dementia, ataxia, and myelopathy. A diagnosis of superficial siderosis was made after magnetic resonance gradient-echo images showed diffuse hemosiderin staining over the cerebellum and cerebral convexities. No intracerebral source of hemorrhage was identified. The patient therefore underwent gadolinium-enhanced spinal MRI which suggested a possible vascular malformation. A therapeutic laminectomy subsequently confirmed an arteriovenous fistula which was resected. In SS, there are often long delays between symptom onset and definitive diagnosis. Early identification is facilitated by magnetic resonance imaging with gradient-echo sequences. When no source of hemorrhage is identified intracranially, then total spinal cord imaging is indicated to assess for an occult source of hemorrhage as occurred in our case.

  View details for DOI 10.1016/j.clineuro.2009.09.005

  View details for Web of Science ID 000273933700017

  View details for PubMedID 19857921

• Disrupted Amygdalar Subregion Functional Connectivity and Evidence of a Compensatory Network in Generalized Anxiety Disorder ARCHIVES OF GENERAL PSYCHIATRY Etkin, A., Prater, K. E., Schatzberg, A. F., Menon, V., Greicius, M. D. 2009; 66 (12): 1361-1372

  Abstract

  Little is known about the neural abnormalities underlying generalized anxiety disorder (GAD). Studies in other anxiety disorders have implicated the amygdala, but work in GAD has yielded conflicting results. The amygdala is composed of distinct subregions that interact with dissociable brain networks, which have been studied only in experimental animals. A functional connectivity approach at the subregional level may therefore yield novel insights into GAD.To determine whether distinct connectivity patterns can be reliably identified for the basolateral (BLA) and centromedial (CMA) subregions of the human amygdala, and to examine subregional connectivity patterns and potential compensatory amygdalar connectivity in GAD.Cross-sectional study.Academic medical center.Two cohorts of healthy control subjects (consisting of 17 and 31 subjects) and 16 patients with GAD.Functional connectivity with cytoarchitectonically determined BLA and CMA regions of interest, measured during functional magnetic resonance imaging performed while subjects were resting quietly in the scanner. Amygdalar gray matter volume was also investigated with voxel-based morphometry.Reproducible subregional differences in large-scale connectivity were identified in both cohorts of healthy controls. The BLA was differentially connected with primary and higher-order sensory and medial prefrontal cortices. The CMA was connected with the midbrain, thalamus, and cerebellum. In GAD patients, BLA and CMA connectivity patterns were significantly less distinct, and increased gray matter volume was noted primarily in the CMA. Across the subregions, GAD patients had increased connectivity with a previously characterized frontoparietal executive control network and decreased connectivity with an insula- and cingulate-based salience network.Our findings provide new insights into the functional neuroanatomy of the human amygdala and converge with connectivity studies in experimental animals. In GAD, we find evidence of an intra-amygdalar abnormality and engagement of a compensatory frontoparietal executive control network, consistent with cognitive theories of GAD.

  View details for Web of Science ID 000272494700011

  View details for PubMedID 19996041

• Greater than the sum of its parts: a review of studies combining structural connectivity and resting-state functional connectivity BRAIN STRUCTURE & FUNCTION Damoiseaux, J. S., Greicius, M. D. 2009; 213 (6): 525-533

  Abstract

  It is commonly assumed that functional brain connectivity reflects structural brain connectivity. The exact relationship between structure and function, however, might not be straightforward. In this review we aim to examine how our understanding of the relationship between structure and function in the 'resting' brain has advanced over the last several years. We discuss eight articles that directly compare resting-state functional connectivity with structural connectivity and three clinical case studies of patients with limited white matter connections between the cerebral hemispheres. All studies examined show largely convergent results: the strength of resting-state functional connectivity is positively correlated with structural connectivity strength. However, functional connectivity is also observed between regions where there is little or no structural connectivity, which most likely indicates functional correlations mediated by indirect structural connections (i.e. via a third region). As the methodologies for measuring structural and functional connectivity continue to improve and their complementary strengths are applied in parallel, we can expect important advances in our diagnostic and prognostic capacities in diseases like Alzheimer's, multiple sclerosis, and stroke.

  View details for DOI 10.1007/s00429-009-0208-6

  View details for Web of Science ID 000270437600004

  View details for PubMedID 19565262

• Distinct Cerebellar Contributions to Intrinsic Connectivity Networks JOURNAL OF NEUROSCIENCE Habas, C., Kamdar, N., Nguyen, D., Prater, K., Beckmann, C. F., Menon, V., Greicius, M. D. 2009; 29 (26): 8586-8594

  Abstract

  Convergent data from various scientific approaches strongly implicate cerebellar systems in nonmotor functions. The functional anatomy of these systems has been pieced together from disparate sources, such as animal studies, lesion studies in humans, and structural and functional imaging studies in humans. To better define this distinct functional anatomy, in the current study we delineate the role of the cerebellum in several nonmotor systems simultaneously and in the same subjects using resting state functional connectivity MRI. Independent component analysis was applied to resting state data from two independent datasets to identify common cerebellar contributions to several previously identified intrinsic connectivity networks (ICNs) involved in executive control, episodic memory/self-reflection, salience detection, and sensorimotor function. We found distinct cerebellar contributions to each of these ICNs. The neocerebellum participates in (1) the right and left executive control networks (especially crus I and II), (2) the salience network (lobule VI), and (3) the default-mode network (lobule IX). Little to no overlap was detected between these cerebellar regions and the sensorimotor cerebellum (lobules V-VI). Clusters were also located in pontine and dentate nuclei, prominent points of convergence for cerebellar input and output, respectively. The results suggest that the most phylogenetically recent part of the cerebellum, particularly crus I and II, make contributions to parallel cortico-cerebellar loops involved in executive control, salience detection, and episodic memory/self-reflection. The largest portions of the neocerebellum take part in the executive control network implicated in higher cognitive functions such as working memory.

  View details for DOI 10.1523/JNEUROSCI.1868-09.2009

  View details for Web of Science ID 000267613400030

  View details for PubMedID 19571149

  View details for PubMedCentralID PMC2742620

• Neurodegenerative Diseases Target Large-Scale Human Brain Networks NEURON Seeley, W. W., Crawford, R. K., Zhou, J., Miller, B. L., Greicius, M. D. 2009; 62 (1): 42-52

  Abstract

  During development, the healthy human brain constructs a host of large-scale, distributed, function-critical neural networks. Neurodegenerative diseases have been thought to target these systems, but this hypothesis has not been systematically tested in living humans. We used network-sensitive neuroimaging methods to show that five different neurodegenerative syndromes cause circumscribed atrophy within five distinct, healthy, human intrinsic functional connectivity networks. We further discovered a direct link between intrinsic connectivity and gray matter structure. Across healthy individuals, nodes within each functional network exhibited tightly correlated gray matter volumes. The findings suggest that human neural networks can be defined by synchronous baseline activity, a unified corticotrophic fate, and selective vulnerability to neurodegenerative illness. Future studies may clarify how these complex systems are assembled during development and undermined by disease.

  View details for DOI 10.1016/j.neuron.2009.03.024

  View details for Web of Science ID 000265346700008

  View details for PubMedID 19376066

  View details for PubMedCentralID PMC2691647

• Resting-State Functional Connectivity Reflects Structural Connectivity in the Default Mode Network CEREBRAL CORTEX Greicius, M. D., Supekar, K., Menon, V., Dougherty, R. F. 2009; 19 (1): 72-78

  Abstract

  Resting-state functional connectivity magnetic resonance imaging (fcMRI) studies constitute a growing proportion of functional brain imaging publications. This approach detects temporal correlations in spontaneous blood oxygen level-dependent (BOLD) signal oscillations while subjects rest quietly in the scanner. Although distinct resting-state networks related to vision, language, executive processing, and other sensory and cognitive domains have been identified, considerable skepticism remains as to whether resting-state functional connectivity maps reflect neural connectivity or simply track BOLD signal correlations driven by nonneural artifact. Here we combine diffusion tensor imaging (DTI) tractography with resting-state fcMRI to test the hypothesis that resting-state functional connectivity reflects structural connectivity. These 2 modalities were used to investigate connectivity within the default mode network, a set of brain regions--including medial prefrontal cortex (MPFC), medial temporal lobes (MTLs), and posterior cingulate cortex (PCC)/retropslenial cortex (RSC)--implicated in episodic memory processing. Using seed regions from the functional connectivity maps, the DTI analysis revealed robust structural connections between the MTLs and the retrosplenial cortex whereas tracts from the MPFC contacted the PCC (just rostral to the RSC). The results demonstrate that resting-state functional connectivity reflects structural connectivity and that combining modalities can enrich our understanding of these canonical brain networks.

  View details for DOI 10.1093/cercor/bhn059

  View details for Web of Science ID 000261679400007

  View details for PubMedID 18403396

  View details for PubMedCentralID PMC2605172

• Resting-state functional connectivity in neuropsychiatric disorders CURRENT OPINION IN NEUROLOGY Greicius, M. 2008; 21 (4): 424-430

  Abstract

  This review considers recent advances in the application of resting-state functional magnetic resonance imaging to the study of neuropsychiatric disorders.Resting-state functional magnetic resonance imaging is a relatively novel technique that has several potential advantages over task-activation functional magnetic resonance imaging in terms of its clinical applicability. A number of research groups have begun to investigate the use of resting-state functional magnetic resonance imaging in a variety of neuropsychiatric disorders including Alzheimer's disease, depression, and schizophrenia. Although preliminary results have been fairly consistent in some disorders (for example, Alzheimer's disease) they have been less reproducible in others (schizophrenia). Resting-state connectivity has been shown to correlate with behavioral performance and emotional measures. It's potential as a biomarker of disease and an early objective marker of treatment response is genuine but still to be realized.Resting-state functional magnetic resonance imaging has made some strides in the clinical realm but significant advances are required before it can be used in a meaningful way at the single-patient level.

  View details for Web of Science ID 000257823200006

  View details for PubMedID 18607202

• Default-mode function and task-induced deactivation have overlapping brain substrates in children NEUROIMAGE Thomason, M. E., Chang, C. E., Glover, G. H., Gabrieli, J. D., Greicius, M. D., Gotlib, I. H. 2008; 41 (4): 1493-1503

  Abstract

  The regions that comprise the functionally connected resting-state default-mode network (DMN) in adults appear to be the same as those that are characterized by task-induced decreases in blood-oxygen-level-dependent (BOLD) signal. Independent component analysis can be used to produce a picture of the DMN as an individual rests quietly in the scanner. Contrasts across conditions in which cognitive load is parametrically modulated can delineate neural structures that have decreases in activation in response to high-demand task conditions. Examination of the degree to which these networks subsume dissociable brain substrates, and of the degree to which they overlap, provides insight concerning their purpose, function, and the nature of their associations. Few studies have examined the DMN in children, and none have tested whether the neural regions that comprise the DMN during a resting condition are the same regions that show reduced activity when children engage in cognitive tasks. In this paper we describe regions that show both task-related decreases and spontaneous intrinsic activity at rest in children, and we examine the co-localization of these networks. We describe ways in which the DMN in 7-12-year-old children is both similar to and different from the DMN in adults; moreover, we document that task-induced deactivations and default-mode resting-state activity in children share common neural substrates. It appears, therefore, that even before adolescence a core aspect of task-induced deactivation involves reallocating processing resources that are active at rest. We describe how future studies assessing the development of these systems would benefit from examining these constructs as part of one continuous system.

  View details for DOI 10.1016/j.neuroimage.2008.03.029

  View details for Web of Science ID 000256620400029

  View details for PubMedID 18482851

  View details for PubMedCentralID PMC2735193

• Persistent default-mode network connectivity during light sedation HUMAN BRAIN MAPPING Greicius, M. D., Kiviniemi, V., Tervonen, O., Vainionpaa, V., Alahuhta, S., Reiss, A. L., Menon, V. 2008; 29 (7): 839-847

  Abstract

  The default-mode network (DMN) is a set of specific brain regions whose activity, predominant in the resting-state, is attenuated during cognitively demanding, externally-cued tasks. The cognitive correlates of this network have proven difficult to interrogate, but one hypothesis is that regions in the network process episodic memories and semantic knowledge integral to internally-generated mental activity. Here, we compare default-mode functional connectivity in the same group of subjects during rest and conscious sedation with midazolam, a state characterized by anterograde amnesia and a reduced level of consciousness. Although the DMN showed functional connectivity during both rest and conscious sedation, a direct comparison found that there was significantly reduced functional connectivity in the posterior cingulate cortex during conscious sedation. These results confirm that low-frequency oscillations in the DMN persist and remain highly correlated even at reduced levels of consciousness. We hypothesize that focal reductions in DMN connectivity, as shown here in the posterior cingulate cortex, may represent a stable correlate of reduced consciousness.

  View details for DOI 10.1002/hbm.20537

  View details for Web of Science ID 000256674400012

  View details for PubMedID 18219620

  View details for PubMedCentralID PMC2580760

• A cross-modal system linking primary auditory and visual cortices: Evidence from intrinsic fMRI connectivity analysis HUMAN BRAIN MAPPING Eckert, M. A., Kamdar, N. V., Chang, C. E., Beckmann, C. F., Greicius, M. D., Menon, V. 2008; 29 (7): 848-857

  Abstract

  Recent anatomical and electrophysiological evidence in primates indicates the presence of direct connections between primary auditory and primary visual cortex that constitute cross-modal systems. We examined the intrinsic functional connectivity (fcMRI) of putative primary auditory cortex in 32 young adults during resting state scanning. We found that the medial Heschl's gyrus was strongly coupled, in particular, to visual cortex along the anterior banks of the calcarine fissure. This observation was confirmed using novel group-level, tensor-based independent components analysis. fcMRI analysis revealed that although overall coupling between the auditory and visual cortex was significantly reduced when subjects performed a visual perception task, coupling between the anterior calcarine cortex and auditory cortex was not disrupted. These results suggest that primary auditory cortex has a functionally distinct relationship with the anterior visual cortex, which is known to represent the peripheral visual field. Our study provides novel, fcMRI-based, support for a neural system involving low-level auditory and visual cortices.

  View details for DOI 10.1002/hbm.20560

  View details for Web of Science ID 000256674400013

  View details for PubMedID 18412133

  View details for PubMedCentralID PMC2605422

• Network analysis of intrinsic functional brain connectivity in Alzheimer's disease PLOS COMPUTATIONAL BIOLOGY Supekar, K., Menon, V., Rubin, D., Musen, M., Greicius, M. D. 2008; 4 (6)

  Abstract

  Functional brain networks detected in task-free ("resting-state") functional magnetic resonance imaging (fMRI) have a small-world architecture that reflects a robust functional organization of the brain. Here, we examined whether this functional organization is disrupted in Alzheimer's disease (AD). Task-free fMRI data from 21 AD subjects and 18 age-matched controls were obtained. Wavelet analysis was applied to the fMRI data to compute frequency-dependent correlation matrices. Correlation matrices were thresholded to create 90-node undirected-graphs of functional brain networks. Small-world metrics (characteristic path length and clustering coefficient) were computed using graph analytical methods. In the low frequency interval 0.01 to 0.05 Hz, functional brain networks in controls showed small-world organization of brain activity, characterized by a high clustering coefficient and a low characteristic path length. In contrast, functional brain networks in AD showed loss of small-world properties, characterized by a significantly lower clustering coefficient (p<0.01), indicative of disrupted local connectivity. Clustering coefficients for the left and right hippocampus were significantly lower (p<0.01) in the AD group compared to the control group. Furthermore, the clustering coefficient distinguished AD participants from the controls with a sensitivity of 72% and specificity of 78%. Our study provides new evidence that there is disrupted organization of functional brain networks in AD. Small-world metrics can characterize the functional organization of the brain in AD, and our findings further suggest that these network measures may be useful as an imaging-based biomarker to distinguish AD from healthy aging.

  View details for DOI 10.1371/journal.pcbi.1000100

  View details for Web of Science ID 000259786700013

  View details for PubMedID 18584043

  View details for PubMedCentralID PMC2435273

• Divergent social functioning in behavioral variant frontotemporal dementia and Alzheimer disease: Reciprocal networks and neuronal evolution 5th International Meeting on Frontotemporal Dementia Conference Seeley, W. W., Allman, J. M., Carlin, D. A., Crawford, R. K., Macedo, M. N., Greicius, M. D., DeArmond, S. J., Miller, B. L. LIPPINCOTT WILLIAMS & WILKINS. 2007: S50–S57

  Abstract

  Behavioral variant frontotemporal dementia (bvFTD) disrupts our most human social and emotional functions. Early in the disease, patients show focal anterior cingulate cortex (ACC) and orbital frontoinsula (FI) degeneration, accentuated in the right hemisphere. The ACC and FI, though sometimes considered ancient in phylogeny, feature a large bipolar projection neuron, the von Economo neuron (VEN), which is found only in humans, apes, and selected whales-all large-brained mammals with complex social structures. In contrast to bvFTD, Alzheimer disease (AD) often spares social functioning, and the ACC and FI, until late in its course, damaging instead a posterior hippocampal-cingulo-temporal-parietal network involved in episodic memory retrieval. These divergent patterns of functional and regional impairment remain mysterious despite extensive molecular-level characterization of bvFTD and AD. In this report, we further develop the hypothesis that VENs drive the regional vulnerability pattern seen in bvFTD, citing recent evidence from functional imaging in healthy humans, and also structural imaging and quantitative neuropathology data from bvFTD and AD. Our most recent findings suggest that bvFTD and AD target distinct, anticorrelated intrinsic connectivity networks and that bvFTD-related VEN injury occurs throughout the ACC-FI network. We suggest that the regional and neuronal vulnerability patterns seen in bvFTD and AD underlie the divergent impact of these disorders on recently evolved social-emotional functions.

  View details for Web of Science ID 000251536500016

  View details for PubMedID 18090425

• Resting-state functional connectivity in major depression: Abnormally increased contributions from subgenual cingulate cortex and thalamus BIOLOGICAL PSYCHIATRY Greicius, M. D., Flores, B. H., Menon, V., Glover, G. H., Solvason, H. B., Kenna, H., Reiss, A. L., Schatzberg, A. F. 2007; 62 (5): 429-437

  Abstract

  Positron emission tomography (PET) studies of major depression have revealed resting-state abnormalities in the prefrontal and cingulate cortices. Recently, fMRI has been adapted to examine connectivity within a specific resting-state neural network--the default-mode network--that includes medial prefrontal and anterior cingulate cortices. The goal of this study was to examine resting-state, default-mode network functional connectivity in subjects with major depression and in healthy controls.Twenty-eight subjects with major depression and 20 healthy controls underwent 5-min fMRI scans while resting quietly. Independent component analysis was used to isolate the default-mode network in each subject. Group maps of the default-mode network were compared. A within-group analysis was performed in the depressed group to explore effects of depression refractoriness on functional connectivity.Resting-state subgenual cingulate and thalamic functional connectivity with the default-mode network were significantly greater in the depressed subjects. Within the depressed group, the length of the current depressive episode correlated positively with functional connectivity in the subgenual cingulate.This is the first study to explore default-mode functional connectivity in major depression. The findings provide cross-modality confirmation of PET studies demonstrating increased thalamic and subgenual cingulate activity in major depression. Further, the within-subject connectivity analysis employed here brings these previously isolated regions of hypermetabolism into the context of a disordered neural network. The correlation between refractoriness and subgenual cingulate functional connectivity within the network suggests that a quantitative, resting-state fMRI measure could be used to guide therapy in individual subjects.

  View details for DOI 10.1016/j.biopsych.2006.09.020

  View details for Web of Science ID 000249042800009

  View details for PubMedID 17210143

  View details for PubMedCentralID PMC2001244

• Dissociable intrinsic connectivity networks for salience processing and executive control JOURNAL OF NEUROSCIENCE Seeley, W. W., Menon, V., Schatzberg, A. F., Keller, J., Glover, G. H., Kenna, H., Reiss, A. L., Greicius, M. D. 2007; 27 (9): 2349-2356

  Abstract

  Variations in neural circuitry, inherited or acquired, may underlie important individual differences in thought, feeling, and action patterns. Here, we used task-free connectivity analyses to isolate and characterize two distinct networks typically coactivated during functional MRI tasks. We identified a "salience network," anchored by dorsal anterior cingulate (dACC) and orbital frontoinsular cortices with robust connectivity to subcortical and limbic structures, and an "executive-control network" that links dorsolateral frontal and parietal neocortices. These intrinsic connectivity networks showed dissociable correlations with functions measured outside the scanner. Prescan anxiety ratings correlated with intrinsic functional connectivity of the dACC node of the salience network, but with no region in the executive-control network, whereas executive task performance correlated with lateral parietal nodes of the executive-control network, but with no region in the salience network. Our findings suggest that task-free analysis of intrinsic connectivity networks may help elucidate the neural architectures that support fundamental aspects of human behavior.

  View details for DOI 10.1523/JNEUROSCI.5587-06.2007

  View details for Web of Science ID 000244758500023

  View details for PubMedID 17329432

  View details for PubMedCentralID PMC2680293

• Prospects for prediction - Ethics analysis of neuroimaging in Alzheimer's disease Meeting on Imaging and the Aging Brain Illes, J., Rosen, A., Greicius, M., Racine, E. BLACKWELL PUBLISHING. 2007: 278–295

  Abstract

  This article focuses on the prospects and ethics of using neuroimaging to predict Alzheimer's disease (AD). It is motivated by consideration of the historical roles of science in medicine and society, and considerations specifically contemporary of capabilities in imaging and aging, and the benefits and hope they bring. A general consensus is that combinations of imaging methods will ultimately be most fruitful in predicting disease. Their roll-out into translational practice will not be free of complexity, however, as culture and values differ in terms of what defines benefit and risk, who will benefit and who is at risk, what methods must be in place to assure the maximum safety, comfort, and protection of subjects and patients, and educational and policy needs. Proactive planning for the ethical and societal implications of predicting diseases of the aging brain is critical and will benefit all stakeholders-researchers, patients and families, health care providers, and policy makers.

  View details for DOI 10.1196/annals.1379.030

  View details for Web of Science ID 000245814800025

  View details for PubMedID 17413029

• Non-fluent progressive aphasia, depression, and OCD in a woman with progressive supranuclear palsy: Neuroanatomical and neuropathological correlations NEUROCASE Karnik, N. S., D'Apuzzo, M., Greicius, M. 2006; 12 (6): 332-338

  Abstract

  This paper details the case of a 64-year-old woman who presented to the psychiatry service with worsening mood in the context of a diagnosis of obsessive-compulsive disorder (OCD). On further examination she was found to have clinical findings consistent with frontotemporal lobar degeneration of the non-fluent progressive aphasia subtype. At post-mortem she was found to have progressive supranuclear palsy. We argue, in retrospect, that her OCD was likely prodromal to the development of her dementia. This case highlights the fact that frontotemporal lobar degeneration/progressive supranuclear palsy (FTLD/PSP) and other "tauopathies" represent a complex group of neurodegenerative disorders that may masquerade for many years as refractory psychiatric disorders.

  View details for DOI 10.1080/13554790601125957

  View details for Web of Science ID 000242985900003

  View details for PubMedID 17182396

• Default-mode activity during a passive sensory task: Uncoupled from deactivation but impacting activation JOURNAL OF COGNITIVE NEUROSCIENCE Greicius, M. D., Menon, V. 2004; 16 (9): 1484-1492

  Abstract

  Deactivation refers to increased neural activity during low-demand tasks or rest compared with high-demand tasks. Several groups have reported that a particular set of brain regions, including the posterior cingulate cortex and the medial prefrontal cortex, among others, is consistently deactivated. Taken together, these typically deactivated brain regions appear to constitute a default-mode network of brain activity that predominates in the absence of a demanding external task. Examining a passive, block-design sensory task with a standard deactivation analysis (rest epochs vs. stimulus epochs), we demonstrate that the default-mode network is undetectable in one run and only partially detectable in a second run. Using independent component analysis, however, we were able to detect the full default-mode network in both runs and to demonstrate that, in the majority of subjects, it persisted across both rest and stimulus epochs, uncoupled from the task waveform, and so mostly undetectable as deactivation. We also replicate an earlier finding that the default-mode network includes the hippocampus suggesting that episodic memory is incorporated in default-mode cognitive processing. Furthermore, we show that the more a subject's default-mode activity was correlated with the rest epochs (and "deactivated" during stimulus epochs), the greater that subject's activation to the visual and auditory stimuli. We conclude that activity in the default-mode network may persist through both experimental and rest epochs if the experiment is not sufficiently challenging. Time-series analysis of default-mode activity provides a measure of the degree to which a task engages a subject and whether it is sufficient to interrupt the processes--presumably cognitive, internally generated, and involving episodic memory--mediated by the default-mode network.

  View details for Web of Science ID 000225712000003

  View details for PubMedID 15601513

• Reduced basal forebrain and hippocampal activation during memory encoding in girls with fragile X syndrome NEUROREPORT Greicius, M. D., Boyett-Anderson, J. M., Menon, V., Reiss, A. L. 2004; 15 (10): 1579-1583

  Abstract

  Fragile X syndrome (FraX), the most common heritable cause of developmental disability, is associated with IQ, memory, and visuospatial processing deficits. The fragile X gene (FMR1) is prominently transcribed in two regions critical to memory encoding and attention: the hippocampus and the basal forebrain. To probe functional MRI activation abnormalities associated with the disorder, girls with FraX and age-matched, normally-developing girls were scanned during a test of visual memory encoding. While there were considerable similarities in activation patterns between the two groups, the girls with FraX showed significantly less activation in the hippocampus and the basal forebrain. This is the first study, to our knowledge, demonstrating functional deficits in FraX subjects in brain regions known to have the highest FMR1 transcription.

  View details for DOI 10.1097/01.wnr.0000134472.44362.be

  View details for Web of Science ID 000225140700010

  View details for PubMedID 15232287

• Default-mode network activity distinguishes Alzheimer's disease from healthy aging: Evidence from functional MRI PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Greicius, M. D., Srivastava, G., Reiss, A. L., Menon, V. 2004; 101 (13): 4637-4642

  Abstract

  Recent functional imaging studies have revealed coactivation in a distributed network of cortical regions that characterizes the resting state, or default mode, of the human brain. Among the brain regions implicated in this network, several, including the posterior cingulate cortex and inferior parietal lobes, have also shown decreased metabolism early in the course of Alzheimer's disease (AD). We reasoned that default-mode network activity might therefore be abnormal in AD. To test this hypothesis, we used independent component analysis to isolate the network in a group of 13 subjects with mild AD and in a group of 13 age-matched elderly controls as they performed a simple sensory-motor processing task. Three important findings are reported. Prominent coactivation of the hippocampus, detected in all groups, suggests that the default-mode network is closely involved with episodic memory processing. The AD group showed decreased resting-state activity in the posterior cingulate and hippocampus, suggesting that disrupted connectivity between these two regions accounts for the posterior cingulate hypometabolism commonly detected in positron emission tomography studies of early AD. Finally, a goodness-of-fit analysis applied at the individual subject level suggests that activity in the default-mode network may ultimately prove a sensitive and specific biomarker for incipient AD.

  View details for DOI 10.1073/pnas.0308627101

  View details for Web of Science ID 000220648700056

  View details for PubMedID 15070770

  View details for PubMedCentralID PMC384799

• Blockade of central cholinergic receptors impairs new learning and increases proactive interference in a word paired-associate memory task BEHAVIORAL NEUROSCIENCE Atri, A., Sherman, S., Norman, K. A., Kirchhoff, B. A., Nicolas, M. M., Greicius, M. D., Cramer, S. C., Breiter, H. C., Hasselmo, M. E., Stern, C. E. 2004; 118 (1): 223-236

  Abstract

  Experimental data and computational models suggest that blockade of muscarinic cholinergic receptors impairs paired-associate learning and increases proactive interference (E. DeRosa & M. E. Hasselmo, 2000; M. E. Hasselmo & J. M. Bower, 1993). The results presented here provide evidence in humans supporting these hypotheses. Young healthy subjects first learned baseline word pairs (A-B) and, after a delay, learned additional overlapping (A-C) and nonoverlapping (D-E) word pairs. As predicted, when compared with subjects who received the active placebo glycopyrrolate (4 microg/kg) and subjects who were not injected, those who received scopolamine (8 microg/kg) showed (a) overall impairment in new word paired-associate learning, but no impairment in cued recall of previously learned associates; and (b) greater impairment in learning overlapping (A-C) compared with nonoverlapping (D-E) paired associates.

  View details for DOI 10.1037/0735-7044.118.1.223

  View details for Web of Science ID 000188981400023

  View details for PubMedID 14979800

• Humor modulates the mesolimbic reward centers NEURON Mobbs, D., Greicius, M. D., Abdel-Azim, E., Menon, V., Reiss, A. L. 2003; 40 (5): 1041-1048

  Abstract

  Humor plays an essential role in many facets of human life including psychological, social, and somatic functioning. Recently, neuroimaging has been applied to this critical human attribute, shedding light on the affective, cognitive, and motor networks involved in humor processing. To date, however, researchers have failed to demonstrate the subcortical correlates of the most fundamental feature of humor-reward. In an effort to elucidate the neurobiological substrate that subserves the reward components of humor, we undertook a high-field (3 Tesla) event-related functional MRI study. Here we demonstrate that humor modulates activity in several cortical regions, and we present new evidence that humor engages a network of subcortical regions including the nucleus accumbens, a key component of the mesolimbic dopaminergic reward system. Further, the degree of humor intensity was positively correlated with BOLD signal intensity in these regions. Together, these findings offer new insight into the neural basis of salutary aspects of humor.

  View details for Web of Science ID 000187042200020

  View details for PubMedID 14659102

• Comparison of fMRI activation at 3 and 1.5 T during perceptual, cognitive, and affective processing NEUROIMAGE Krasnow, B., Tamm, L., Greicius, M. D., Yang, T. T., Glover, G. H., Reiss, A. L., Menon, V. 2003; 18 (4): 813-826

  Abstract

  Previous studies comparing fMRI data acquired at 1.5 T and higher field strengths have focused on examining signal increases in the visual and motor cortices. No information is, however, available on the relative gain, or the comparability of data, obtained at higher field strengths for other brain regions such as the prefrontal and other association cortices. In the present study, we investigated fMRI activation at 1.5 and 3 T during visual perception, visuospatial working memory, and affect-processing tasks. A 23% increase in striate and extrastriate activation volume was observed at 3 T compared with that for 1.5 T during the visual perception task. During the working memory task significant increases in activation volume were observed in frontal and parietal association cortices as well as subcortical structures, including the caudate, globus pallidus, putamen, and thalamus. Increases in working memory-related activation volume of 82, 73, 83, and 36% were observed in the left frontal, right frontal, left parietal, and right parietal lobes, respectively, for 3 T compared with 1.5 T. These increases were characterized by increased activation at 3 T in several prefrontal and parietal cortex regions that showed activation at 1.5 T. More importantly, at 3 T, activation was detected in several regions, such as the ventral aspects of the inferior frontal gyrus, orbitofrontal gyrus, and lingual gyrus, which did not show significant activation at 1.5 T. No difference in height or extent of activation was detected between the two scanners in the amygdala during affect processing. Signal dropout in the amygdala from susceptibility artifact was greater at 3 T, with a 12% dropout at 3 T compared with a 9% dropout at 1.5 T. The spatial smoothness of T2* images was greater at 3 T by less than 1 mm, suggesting that the greater extent of activation at 3 T beyond these spatial scales was not due primarily to increased intrinsic spatial correlations at 3 T. Rather, the increase in percentage of voxels activated reflects increased sensitivity for detection of brain activation at higher field strength. In summary, our findings suggest that functional imaging of prefrontal and other association cortices can benefit significantly from higher magnetic field strength.

  View details for DOI 10.1016/S1053-8119(03)00002-8

  View details for Web of Science ID 000182606000001

  View details for PubMedID 12725758

• Neuroimaging in developmental disorders CURRENT OPINION IN NEUROLOGY Greicius, M. D. 2003; 16 (2): 143-146

  Abstract

  This review considers the role of neuroimaging in developmental disorders by highlighting recent studies in two distinct, but overlapping, developmental disorders: autism and fragile X syndrome.After a decade of conflicting results in neuroimaging studies of autism, recent studies have provided some convergent data. One well-replicated finding is that autistic subjects have larger brains. Further, this enlargement, present as early as 3 years of age, appears to represent accelerated growth in infancy and may be followed by slowed growth in late childhood. Other findings are discussed but considered preliminary in the absence of converging evidence or replication studies. Recent work in fragile X syndrome suggests aberrant fronto-striatal and fronto-parietal networks and relates these abnormalities "forward" to behavior and "backward" to decreased protein expression.As the field of neuroimaging has matured, it has revealed its promise as a safe, reliable, in-vivo tool in the study of developmental disorders. By insisting on larger, more homogeneous patient groups and longitudinal rather than cross-sectional studies, the field is poised to fulfill its ultimate role of linking defects in molecular biology to aberrant behavior.

  View details for DOI 10.1097/01.wco.0000063763.15877.d2

  View details for Web of Science ID 000182542200004

  View details for PubMedID 12644740

• Functional connectivity in the resting brain: A network analysis of the default mode hypothesis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Greicius, M. D., Krasnow, B., Reiss, A. L., Menon, V. 2003; 100 (1): 253-258

  Abstract

  Functional imaging studies have shown that certain brain regions, including posterior cingulate cortex (PCC) and ventral anterior cingulate cortex (vACC), consistently show greater activity during resting states than during cognitive tasks. This finding led to the hypothesis that these regions constitute a network supporting a default mode of brain function. In this study, we investigate three questions pertaining to this hypothesis: Does such a resting-state network exist in the human brain? Is it modulated during simple sensory processing? How is it modulated during cognitive processing? To address these questions, we defined PCC and vACC regions that showed decreased activity during a cognitive (working memory) task, then examined their functional connectivity during rest. PCC was strongly coupled with vACC and several other brain regions implicated in the default mode network. Next, we examined the functional connectivity of PCC and vACC during a visual processing task and show that the resultant connectivity maps are virtually identical to those obtained during rest. Last, we defined three lateral prefrontal regions showing increased activity during the cognitive task and examined their resting-state connectivity. We report significant inverse correlations among all three lateral prefrontal regions and PCC, suggesting a mechanism for attenuation of default mode network activity during cognitive processing. This study constitutes, to our knowledge, the first resting-state connectivity analysis of the default mode and provides the most compelling evidence to date for the existence of a cohesive default mode network. Our findings also provide insight into how this network is modulated by task demands and what functions it might subserve.

  View details for DOI 10.1073/pnas.0135058100

  View details for Web of Science ID 000180307100046

  View details for PubMedID 12506194

  View details for PubMedCentralID PMC140943

• Regional analysis of hippocampal activation during memory encoding and retrieval: fMRI study HIPPOCAMPUS Greicius, M. D., Krasnow, B., Boyett-Anderson, J. M., Eliez, S., Schatzberg, A. F., Reiss, A. L., Menon, V. 2003; 13 (1): 164-174

  Abstract

  Investigators have recently begun to examine the differential role of subregions of the hippocampus in episodic memory. Two distinct models have gained prominence in the field. One model, outlined by Moser and Moser (Hippocampus 1998;8:608-619), based mainly on animal studies, has proposed that episodic memory is subserved by the posterior two-thirds of the hippocampus alone. A second model, derived by Lepage et al. (Hippocampus 1998;8:313-322) from their review of 52 PET studies, has suggested that the anterior hippocampus is activated by memory encoding while the posterior hippocampus is activated by memory retrieval. Functional magnetic resonance imaging (fMRI) studies have tended to show limited activation in the anteriormost regions of the hippocampus, providing support for the Moser and Moser model. A potential confounding factor in these fMRI studies, however, is that susceptibility artifact may differentially reduce signal in the anterior versus the posterior hippocampus. In the present study, we examined activation differences between hippocampal subregions during encoding and retrieval of words and interpreted our findings within the context of these two models. We also examined the extent to which susceptibility artifact affects the analysis and interpretation of hippocampal activation by demonstrating its differential effect on the anterior versus the posterior hippocampus. Both voxel-by-voxel and region-of-interest analyses were conducted, allowing us to quantify differences between the anterior and posterior aspects of the hippocampus. We detected significant hippocampal activation in both the encoding and retrieval conditions. Our data do not provide evidence for regional anatomic differences in activation between encoding and retrieval. The data do suggest that, even after accounting for susceptibility artifact, both encoding and retrieval of verbal stimuli activate the middle and posterior hippocampus more strongly than the anterior hippocampus. Finally, this study is the first to quantify the effects of susceptibility-induced signal loss on hippocampal activation and suggests that this artifact has significantly biased the interpretation of earlier fMRI studies.

  View details for DOI 10.1002/hipo.10064

  View details for Web of Science ID 000181005800014

  View details for PubMedID 12625466

• Presenile dementia syndromes: an update on taxonomy and diagnosis JOURNAL OF NEUROLOGY NEUROSURGERY AND PSYCHIATRY Greicius, M. D., Geschwind, M. D., Miller, B. L. 2002; 72 (6): 691-700

  Abstract

  The four major degenerative dementias that often begin in presenescence: are reviewed. These are Alzheimer's disease, frontotemporal dementia, dementia with Lewy bodies, and Creutzfeldt-Jakob disease. Their epidemiological, genetic, and clinical features are reviewed, and controversies in taxonomy arising from recent discoveries described. Particular attention is given to the pathological role of protein aggregation, which appears to be a factor in each disease.

  View details for Web of Science ID 000175891300005

  View details for PubMedID 12023408