Michael Eddy F Belloy

All Publications

• 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

• Decoding the heterogeneity of Alzheimer's disease diagnosis and progression using multilayer networks. Molecular psychiatry Avelar-Pereira, B., Belloy, M. E., O'Hara, R., Hosseini, S. M. 2022

  Abstract

  Alzheimer's disease (AD) is a multifactorial and heterogeneous disorder, which makes early detection a challenge. Studies have attempted to combine biomarkers to improve AD detection and predict progression. However, most of the existing work reports results in parallel or compares normalized findings but does not analyze data simultaneously. We tested a multi-dimensional network framework, applied to 490 subjects (cognitively normal [CN] = 147; mild cognitive impairment [MCI] = 287; AD = 56) from ADNI, to create a single model capable of capturing the heterogeneity and progression of AD. First, we constructed subject similarity networks for structural magnetic resonance imaging, amyloid-β positron emission tomography, cerebrospinal fluid, cognition, and genetics data and then applied multilayer community detection to find groups with shared similarities across modalities. Individuals were also followed-up longitudinally, with AD subjects having, on average, 4.5 years of follow-up. Our findings show that multilayer community detection allows for accurate identification of present and future AD (≈90%) and is also able to identify cases that were misdiagnosed clinically. From all MCI participants who developed AD or reverted to CN, the multilayer model correctly identified 90.8% and 88.5% of cases respectively. We observed similar subtypes across the full sample and when examining multimodal data from subjects with no AD pathology (i.e., amyloid negative). Finally, these results were also validated using an independent testing set. In summary, the multilayer framework is successful in detecting AD and provides unique insight into the heterogeneity of the disease by identifying subtypes that share similar multidisciplinary profiles of neurological, cognitive, pathological, and genetics information.

  View details for DOI 10.1038/s41380-022-01886-z

  View details for PubMedID 36539525

• 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

• 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

• Deep neural networks with controlled variable selection for the identification of putative causal genetic variants NATURE MACHINE INTELLIGENCE Kassani, P. H., Lu, F., Le Guen, Y., Belloy, M. E., He, Z. 2022

  View details for DOI 10.1038/s42256-022-00525-0

  View details for Web of Science ID 000854675000002

• 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

• 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

• 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

• APOE*4-stratified genome-wide association study of Alzheimer's disease in over 350,000 individuals. Alzheimer's & dementia : the journal of the Alzheimer's Association Belloy, M. E., Eger, S. J., Guen, Y. L., Kennedy, G., He, Z., Napolioni, V., Greicius, M. D. 1800; 17 Suppl 3: e055905

  Abstract

  BACKGROUND: APOE*4 is the strongest genetic risk factor for late-onset Alzheimer's disease (AD) and is highly pleiotropic, such that it may be considered as a biological factor that can affect overall genetic risk for AD. To advance our understanding of the genetic architecture of AD, we sought to perform the largest APOE*4-stratified genome-wide association study (GWAS) of AD.METHOD: Twenty-five publicly available AD GWAS datasets provided case-control diagnoses for phase-1 samples (imputed to the HRC r1.1 reference panel). The UK Biobank provided subjects with family history of AD status, transformed into an AD phenotype as described previously (Jansen et al., 2019) for phase-2 samples. Linear mixed model regressions were performed on case-control status (LMM-BOLT v.2.3.4), adjusting for age (age-at-onset in cases; age-at-last-exam in controls), sex, APOE*4 and APOE*2 dosage, the first 12 genetic principal components, array/batch, cohort in phase-1, and assessment center in phase-2. In phase-3, phase-1 and phase-2 findings were combined using multivariate genome-wide meta-analysis (Jansen et al., 2019). APOE*4+ heterogeneity tests were evaluated per phase and meta-analyzed in phase-3.RESULT: Participant demographics are in Table 1. Combining results from both APOE*4-stratified analyses, 106 lead variants across 98 loci passed suggestive significance (p<10-5 ; Figure 1). Although most variants reached only suggestive significance, 28 loci were previously reported at genome-wide significance in large-scale GWAS of AD (Kunkle et al., 2019, Jansen et al., 2019, Bellenguez et al., 2020), supporting that we identified potentially relevant AD loci. APOE*4-stratified effects were observed for 28 variants/loci covered across both phase-1 and phase-2 (NAPOE4+ =19; NAPOE4- =9; Table 2), and 25 variants/loci seen only in phase-2 (NAPOE4+ =17; NAPOE4- =8; Table 3). Notably, a genome-wide significant APOE*4+ heterogeneity effect was observed for the USP17L13 locus (a regulator of deubiquitination), while PPP1R12A, BRINP1, PCBD1, and SESN2 loci passed suggestive significance.CONCLUSION: Our findings revealed novel AD risk loci/genes and characterized which of these associated with AD risk differentially across APOE*4 status. This contributes highly to personalized genetic medicine and paves the way towards new potential AD drug targets. Ongoing work is adding samples for phase-1 analyses (imputing data to TOPMed) and pursuing both multi-omics and AD endophenotype validation efforts for variant prioritization.

  View details for DOI 10.1002/alz.055905

  View details for PubMedID 35108901

• 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

• 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

• 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

• Resting Brain Fluctuations Are Intrinsically Coupled to Visual Response Dynamics. Cerebral cortex (New York, N.Y. : 1991) Belloy, M. E., Billings, J., Abbas, A., Kashyap, A., Pan, W. J., Hinz, R., Vanreusel, V., Van Audekerke, J., Van der Linden, A., Keilholz, S. D., Verhoye, M., Keliris, G. A. 2020

  Abstract

  How do intrinsic brain dynamics interact with processing of external sensory stimuli? We sought new insights using functional magnetic resonance imaging to track spatiotemporal activity patterns at the whole brain level in lightly anesthetized mice, during both resting conditions and visual stimulation trials. Our results provide evidence that quasiperiodic patterns (QPPs) are the most prominent component of mouse resting brain dynamics. These QPPs captured the temporal alignment of anticorrelation between the default mode (DMN)- and task-positive (TPN)-like networks, with global brain fluctuations, and activity in neuromodulatory nuclei of the reticular formation. Specifically, the phase of QPPs prior to stimulation could significantly stratify subsequent visual response magnitude, suggesting QPPs relate to brain state fluctuations. This is the first observation in mice that dynamics of the DMN- and TPN-like networks, and particularly their anticorrelation, capture a brain state dynamic that affects sensory processing. Interestingly, QPPs also displayed transient onset response properties during visual stimulation, which covaried with deactivations in the reticular formation. We conclude that QPPs appear to capture a brain state fluctuation that may be orchestrated through neuromodulation. Our findings provide new frontiers to understand the neural processes that shape functional brain states and modulate sensory input processing.

  View details for DOI 10.1093/cercor/bhaa305

  View details for PubMedID 33108464

• 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

• 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

• Bottom-up sensory processing can induce negative BOLD responses and reduce functional connectivity in nodes of the default mode-like network in rats. NeuroImage Hinz, R., Peeters, L. M., Shah, D., Missault, S., Belloy, M., Vanreusel, V., Malekzadeh, M., Verhoye, M., Van der Linden, A., Keliris, G. A. 2019; 197: 167-176

  Abstract

  The default mode network is a large-scale brain network that is active during rest and internally focused states and deactivates as well as desynchronizes during externally oriented (top-down) attention demanding cognitive tasks. However, it is not sufficiently understood if salient stimuli, able to trigger bottom-up attentional processes, could also result in similar reduction of activity and functional connectivity in the DMN. In this study, we investigated whether bottom-up sensory processing could influence the default mode-like network (DMLN) in rats. DMLN activity was examined using block-design visual functional magnetic resonance imaging (fMRI) while its synchronization was investigated by comparing functional connectivity during a resting versus a continuously stimulated brain state by unpredicted light flashes. We demonstrated that the BOLD response in DMLN regions was decreased during visual stimulus blocks and increased during blanks. Furthermore, decreased inter-network functional connectivity between the DMLN and visual networks as well as decreased intra-network functional connectivity within the DMLN was observed during the continuous visual stimulation. These results suggest that triggering of bottom-up attention mechanisms in sedated rats can lead to a cascade similar to top-down orienting of attention in humans and is able to deactivate and desynchronize the DMLN.

  View details for DOI 10.1016/j.neuroimage.2019.04.065

  View details for PubMedID 31029872

• Quasi-periodic patterns contribute to functional connectivity in the brain NEUROIMAGE Abbas, A., Belloy, M., Kashyap, A., Billings, J., Nezafati, M., Schumacher, E. H., Keilholz, S. 2019; 191: 193–204

  Abstract

  Functional connectivity is widely used to study the coordination of activity between brain regions over time. Functional connectivity in the default mode and task positive networks is particularly important for normal brain function. However, the processes that give rise to functional connectivity in the brain are not fully understood. It has been postulated that low-frequency neural activity plays a key role in establishing the functional architecture of the brain. Quasi-periodic patterns (QPPs) are a reliably observable form of low-frequency neural activity that involve the default mode and task positive networks. Here, QPPs from resting-state and working memory task-performing individuals were acquired. The spatiotemporal pattern, strength, and frequency of the QPPs between the two groups were compared and the contribution of QPPs to functional connectivity in the brain was measured. In task-performing individuals, the spatiotemporal pattern of the QPP changes, particularly in task-relevant regions, and the QPP tends to occur with greater strength and frequency. Differences in the QPPs between the two groups could partially account for the variance in functional connectivity between resting-state and task-performing individuals. The QPPs contribute strongly to connectivity in the default mode and task positive networks and to the strength of anti-correlation seen between the two networks. Many of the connections affected by QPPs are also disrupted during several neurological disorders. These findings contribute to understanding the dynamic neural processes that give rise to functional connectivity in the brain and how they may be disrupted during disease.

  View details for DOI 10.1016/j.neuroimage.2019.01.076

  View details for Web of Science ID 000462145700017

  View details for PubMedID 30753928

  View details for PubMedCentralID PMC6440826

• Molecular Imaging of Immune Cell Dynamics During De- and Remyelination in the Cuprizone Model of Multiple Sclerosis by [F-18]DPA-714 PET and MRI THERANOSTICS Zinnhardt, B., Belloy, M., Fricke, I. B., Orije, J., Guglielmetti, C., Hermann, S., Wagner, S., Schaefers, M., Van der Linden, A., Jacobs, A. H. 2019; 9 (6): 1523–37

  View details for DOI 10.7150/thno.32461

  View details for Web of Science ID 000460134200001

• 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

• Dynamic resting state fMRI analysis in mice reveals a set of Quasi-Periodic Patterns and illustrates their relationship with the global signal NEUROIMAGE Belloy, M. E., Naeyaert, M., Abbas, A., Shah, D., Vanreusel, V., Van Audekerke, J., Keilholz, S. D., Keliris, G. A., Van der Linden, A., Verhoye, M. 2018; 180: 463–84

  Abstract

  Time-resolved 'dynamic' over whole-period 'static' analysis of low frequency (LF) blood-oxygen level dependent (BOLD) fluctuations provides many additional insights into the macroscale organization and dynamics of neural activity. Although there has been considerable advancement in the development of mouse resting state fMRI (rsfMRI), very little remains known about its dynamic repertoire. Here, we report for the first time the detection of a set of recurring spatiotemporal Quasi-Periodic Patterns (QPPs) in mice, which show spatial similarity with known resting state networks. Furthermore, we establish a close relationship between several of these patterns and the global signal. We acquired high temporal rsfMRI scans under conditions of low (LA) and high (HA) medetomidine-isoflurane anesthesia. We then employed the algorithm developed by Majeed et al. (2011), previously applied in rats and humans, which detects and averages recurring spatiotemporal patterns in the LF BOLD signal. One type of observed patterns in mice was highly similar to those originally observed in rats, displaying propagation from lateral to medial cortical regions, which suggestively pertain to a mouse Task-Positive like network (TPN) and Default Mode like network (DMN). Other QPPs showed more widespread or striatal involvement and were no longer detected after global signal regression (GSR). This was further supported by diminished detection of subcortical dynamics after GSR, with cortical dynamics predominating. Observed QPPs were both qualitatively and quantitatively determined to be consistent across both anesthesia conditions, with GSR producing the same outcome. Under LA, QPPs were consistently detected at both group and single subject level. Under HA, consistency and pattern occurrence rate decreased, whilst cortical contribution to the patterns diminished. These findings confirm the robustness of QPPs across species and demonstrate a new approach to study mouse LF BOLD spatiotemporal dynamics and mechanisms underlying functional connectivity. The observed impact of GSR on QPPs might help better comprehend its controversial role in conventional resting state studies. Finally, consistent detection of QPPs at single subject level under LA promises a step forward towards more reliable mouse rsfMRI and further confirms the importance of selecting an optimal anesthesia regime.

  View details for DOI 10.1016/j.neuroimage.2018.01.075

  View details for Web of Science ID 000443271100012

  View details for PubMedID 29454935

  View details for PubMedCentralID PMC6093802

• Quasi-Periodic Patterns of Neural Activity improve Classification of Alzheimer's Disease in Mice SCIENTIFIC REPORTS Belloy, M. E., Shah, D., Abbas, A., Kashyap, A., Rossner, S., Van der Linden, A., Keilholz, S. D., Keliris, G. A., Verhoye, M. 2018; 8: 10024

  Abstract

  Resting state (rs)fMRI allows measurement of brain functional connectivity and has identified default mode (DMN) and task positive (TPN) network disruptions as promising biomarkers for Alzheimer's disease (AD). Quasi-periodic patterns (QPPs) of neural activity describe recurring spatiotemporal patterns that display DMN with TPN anti-correlation. We reasoned that QPPs could provide new insights into AD network dysfunction and improve disease diagnosis. We therefore used rsfMRI to investigate QPPs in old TG2576 mice, a model of amyloidosis, and age-matched controls. Multiple QPPs were determined and compared across groups. Using linear regression, we removed their contribution from the functional scans and assessed how they reflected functional connectivity. Lastly, we used elastic net regression to determine if QPPs improved disease classification. We present three prominent findings: (1) Compared to controls, TG2576 mice were marked by opposing neural dynamics in which DMN areas were anti-correlated and displayed diminished anti-correlation with the TPN. (2) QPPs reflected lowered DMN functional connectivity in TG2576 mice and revealed significantly decreased DMN-TPN anti-correlations. (3) QPP-derived measures significantly improved classification compared to conventional functional connectivity measures. Altogether, our findings provide insight into the neural dynamics of aberrant network connectivity in AD and indicate that QPPs might serve as a translational diagnostic tool.

  View details for DOI 10.1038/s41598-018-28237-9

  View details for Web of Science ID 000437097000041

  View details for PubMedID 29968786

  View details for PubMedCentralID PMC6030071