Inma Cobos is a physician scientist recently recruited to Stanford in the Department of Pathology. She is a neuropathologist and neuroscientist with expertise in neurodegeneration.

Inma received her medical and doctoral degrees from the University of Murcia in Spain and completed post-doctoral training in Developmental Neurobiology at the University of California, San Francisco. She then pursued a clinical residency and fellowship in Anatomic Pathology and Neuropathology at Massachusetts General Hospital, Harvard Medical School. Before joining Stanford, she was an Assistant Professor in the Department of Pathology and Neuropathology at the UCLA David Geffen School of Medicine.

Her research program combines her background in diagnostic neuropathology, knowledge of developmental neuroscience, and state-of-the-art cellular and molecular technologies to advance the understanding of Alzheimer’s disease and related dementias. She is currently applying single-cell methods to human brain to dissect the contributions of distinct cell types to Alzheimer’s disease pathogenesis and investigate the mechanisms of tau-mediated neurodegeneration in human brain. Her work is supported by the NIH National Institute of Aging (R01), the Alzheimer’s Association, and BrightFocus. She recently received the Ben Barres Early Career Acceleration Award from the Chan Zuckerberg Initiative (CZI).

Clinical Focus

  • Neuropathology
  • Anatomic and Clinical Pathology

Academic Appointments

Honors & Awards

  • Ben Barres Early Career Acceleration Award, Chan Zuckerberg Initiative (2018)
  • Research Career Development Award, Stop Cancer (2016)
  • NAAR Postdoctoral Fellowship, National Alliance for Autism Research/Autism Speaks (2004–2006)
  • NARSAD Young Investigator Award, National Alliance for Research on Schizophrenia and Depression (2003–2005)
  • Postdoctoral Fellowship, Spanish Ministry of Education and Science (2001-2003)
  • Doctoral Extraordinary Prize, University of Murcia, Spain (2001)
  • Neuroscience Master’s Student Fellowship, International University of Andalusia, Spain (1997)
  • Predoctoral Fellowship, Government of Murcia, Spain (1996–2000)

Professional Education

  • Board Certification: American Board of Pathology, Neuropathology (2015)
  • Board Certification: American Board of Pathology, Anatomic Pathology (2015)
  • Fellowship: Massachusetts General Hospital Dept of Pathology (2015) MA
  • Residency: Massachusetts General Hospital Dept of Pathology (2013) MA
  • PhD, University of Murcia School of Medicine, Spain (2000)
  • Medical Education: University of Murcia School of Medicine (1996) Spain

Current Research and Scholarly Interests

Our lab uses cellular and molecular methods, single-cell technology, and quantitative histology to study human neurodegenerative diseases. Current projects include:

- Using single-cell RNA-sequencing to understand selective vulnerability and disease progression in human Alzheimer’s disease brain

- Investigating mechanisms of tau-related neurodegeneration in human brain

- Studying the neocortical and limbic systems in Diffuse Lewy Body Disease (DLBD) at the single cell level

Stanford Advisees

All Publications

  • Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer's disease. Neuron Otero-Garcia, M., Mahajani, S. U., Wakhloo, D., Tang, W., Xue, Y., Morabito, S., Pan, J., Oberhauser, J., Madira, A. E., Shakouri, T., Deng, Y., Allison, T., He, Z., Lowry, W. E., Kawaguchi, R., Swarup, V., Cobos, I. 2022


    Tau aggregation in neurofibrillary tangles (NFTs) is closely associated with neurodegeneration and cognitive decline in Alzheimer's disease (AD). However, the molecular signatures that distinguish between aggregation-prone and aggregation-resistant cell states are unknown. We developed methods for the high-throughput isolation and transcriptome profiling of single somas with NFTs from the human AD brain, quantified the susceptibility of 20 neocortical subtypes for NFT formation and death, and identified both shared and cell-type-specific signatures. NFT-bearing neurons shared a marked upregulation of synaptic transmission-related genes, including a core set of 63 genes enriched for synaptic vesicle cycling. Oxidative phosphorylation and mitochondrial dysfunction were highly cell-type dependent. Apoptosis was only modestly enriched, and the susceptibilities of NFT-bearing and NFT-free neurons for death were highly similar. Our analysis suggests that NFTs represent cell-type-specific responses to stress and synaptic dysfunction. We provide a resource for biomarker discovery and the investigation of tau-dependent and tau-independent mechanisms of neurodegeneration.

    View details for DOI 10.1016/j.neuron.2022.06.021

    View details for PubMedID 35882228

  • 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


    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

  • Human Astrocytes Exhibit Tumor Microenvironment-, Age-, and Sex-Related Transcriptomic Signatures. The Journal of neuroscience : the official journal of the Society for Neuroscience Krawczyk, M. C., Haney, J. R., Pan, L., Caneda, C., Khankan, R. R., Reyes, S. D., Chang, J. W., Morselli, M., Vinters, H. V., Wang, A. C., Cobos, I., Gandal, M. J., Bergsneider, M., Kim, W., Liau, L. M., Yong, W., Jalali, A., Deneen, B., Grant, G. A., Mathern, G. W., Fallah, A., Zhang, Y. 1800


    Astrocytes are critical for the development and function of synapses. There are notable species differences between human astrocytes and commonly used animal models. Yet, it is unclear whether astrocytic genes involved in synaptic function are stable or exhibit dynamic changes associated with disease states and age in humans, which is a barrier in understanding human astrocyte biology and its potential involvement in neurological diseases. To better understand the properties of human astrocytes, we acutely purified astrocytes from the cerebral cortices of over 40 humans across various ages, sexes, and disease states. We performed RNA sequencing to generate transcriptomic profiles of these astrocytes and identified genes associated with these biological variables. We found that human astrocytes in tumor-surrounding regions downregulate genes involved in synaptic function and sensing of signals in the microenvironment, suggesting involvement of peri-tumor astrocytes in tumor-associated neural circuit dysfunction. In aging, we also found downregulation of synaptic regulators and upregulation of markers of cytokine signaling, while in maturation we identified changes in ionic transport with implications for calcium signaling. In addition, we identified subtle sexual dimorphism in human cortical astrocytes, which has implications for observed sex differences across many neurological disorders. Overall, genes involved in synaptic function exhibit dynamic changes in the peritumor microenvironment and aging. This data provides powerful new insights into human astrocyte biology in several biologically relevant states, that will aid in generating novel testable hypotheses about homeostatic and reactive astrocytes in humans.SIGNIFICANCE STATEMENTAstrocytes are an abundant class of cells playing integral roles at synapses. Astrocyte dysfunction is implicated in a variety of human neurological diseases. Yet our knowledge of astrocytes is largely based on mouse studies. Direct knowledge of human astrocyte biology remains limited. Here, we present transcriptomic profiles of human cortical astrocytes, and we identified molecular differences associated with age, sex, and disease state. We found that peritumor and aging astrocytes downregulate genes involved in astrocyte-synapse interactions. These data provide necessary insight into human astrocyte biology that will improve our understanding of human disease.

    View details for DOI 10.1523/JNEUROSCI.0407-21.2021

    View details for PubMedID 34987109

  • Defining the nature of human pluripotent stem cell-derived interneurons via single-cell analysis. Stem cell reports Allison, T., Langerman, J., Sabri, S., Otero-Garcia, M., Lund, A., Huang, J., Wei, X., Samarasinghe, R. A., Polioudakis, D., Mody, I., Cobos, I., Novitch, B. G., Geschwind, D. H., Plath, K., Lowry, W. E. 2021


    The specification of inhibitory neurons has been described for the mouse and human brain, and many studies have shown that pluripotent stem cells (PSCs) can be used to create interneurons invitro. It is unclear whether invitro methods to produce human interneurons generate all the subtypes found in brain, and how similar invitro and invivo interneurons are. We applied single-nuclei and single-cell transcriptomics to model interneuron development from human cortex and interneurons derived from PSCs. We provide a direct comparison of various invitro interneuron derivation methods to determine the homogeneity achieved. We find that PSC-derived interneurons capture stages of development prior to mid-gestation, and represent a minority of potential subtypes found in brain. Comparison with those found in fetal or adult brain highlighted decreased expression of synapse-related genes. These analyses highlight the potential to tailor the method of generation to drive formation of particular subtypes.

    View details for DOI 10.1016/j.stemcr.2021.08.006

    View details for PubMedID 34506726

  • Nav1.1-Overexpressing Interneuron Transplants Restore Brain Rhythms and Cognition in a Mouse Model of Alzheimer's Disease. Neuron Martinez-Losa, M., Tracy, T. E., Ma, K., Verret, L., Clemente-Perez, A., Khan, A. S., Cobos, I., Ho, K., Gan, L., Mucke, L., Alvarez-Dolado, M., Palop, J. J. 2018; 98 (1): 75-89.e5


    Inhibitory interneurons regulate the oscillatory rhythms and network synchrony that are required for cognitive functions and disrupted in Alzheimer's disease (AD). Network dysrhythmias in AD and multiple neuropsychiatric disorders are associated with hypofunction of Nav1.1, a voltage-gated sodium channel subunit predominantly expressed in interneurons. We show that Nav1.1-overexpressing, but not wild-type, interneuron transplants derived from the embryonic medial ganglionic eminence (MGE) enhance behavior-dependent gamma oscillatory activity, reduce network hypersynchrony, and improve cognitive functions in human amyloid precursor protein (hAPP)-transgenic mice, which simulate key aspects of AD. Increased Nav1.1 levels accelerated action potential kinetics of transplanted fast-spiking and non-fast-spiking interneurons. Nav1.1-deficient interneuron transplants were sufficient to cause behavioral abnormalities in wild-type mice. We conclude that the efficacy of interneuron transplantation and the function of transplanted cells in an AD-relevant context depend on their Nav1.1 levels. Disease-specific molecular optimization of cell transplants may be required to ensure therapeutic benefits in different conditions.

    View details for DOI 10.1016/j.neuron.2018.02.029

    View details for PubMedID 29551491

    View details for PubMedCentralID PMC5886814

  • Inhibitory interneuron deficit links altered network activity and cognitive dysfunction in Alzheimer model. Cell Verret, L., Mann, E. O., Hang, G. B., Barth, A. M., Cobos, I., Ho, K., Devidze, N., Masliah, E., Kreitzer, A. C., Mody, I., Mucke, L., Palop, J. J. 2012; 149 (3): 708-21


    Alzheimer's disease (AD) results in cognitive decline and altered network activity, but the mechanisms are unknown. We studied human amyloid precursor protein (hAPP) transgenic mice, which simulate key aspects of AD. Electroencephalographic recordings in hAPP mice revealed spontaneous epileptiform discharges, indicating network hypersynchrony, primarily during reduced gamma oscillatory activity. Because this oscillatory rhythm is generated by inhibitory parvalbumin (PV) cells, network dysfunction in hAPP mice might arise from impaired PV cells. Supporting this hypothesis, hAPP mice and AD patients had decreased levels of the interneuron-specific and PV cell-predominant voltage-gated sodium channel subunit Nav1.1. Restoring Nav1.1 levels in hAPP mice by Nav1.1-BAC expression increased inhibitory synaptic activity and gamma oscillations and reduced hypersynchrony, memory deficits, and premature mortality. We conclude that reduced Nav1.1 levels and PV cell dysfunction critically contribute to abnormalities in oscillatory rhythms, network synchrony, and memory in hAPP mice and possibly in AD.

    View details for DOI 10.1016/j.cell.2012.02.046

    View details for PubMedID 22541439

    View details for PubMedCentralID PMC3375906

  • Dlx transcription factors promote migration through repression of axon and dendrite growth NEURON Cobos, I., Borello, U., Rubenstein, J. R. 2007; 54 (6): 873–88


    In the mouse telencephalon, Dlx homeobox transcription factors are essential for the tangential migration of subpallial-derived GABAergic interneurons to neocortex. However, the mechanisms underlying this process are poorly understood. Here, we demonstrate that Dlx1/2 has a central role in restraining neurite growth of subpallial-derived immature interneurons at a stage when they migrate tangentially to cortex. In Dlx1-/-;Dlx2-/- mutants, neurite length is increased and cells fail to migrate. In Dlx1-/-;Dlx2+/- mutants, while the tangential migration of immature interneurons appears normal, they develop dendritic and axonal processes with increased length and decreased branching, and have deficits in their neocortical laminar positions. Thus, Dlx1/2 is required for coordinating programs of neurite maturation and migration. In this regard, we provide genetic evidence that in immature interneurons Dlx1/2 repression of the p21-activated serine/threonine kinase PAK3, a downstream effector of the Rho family of GTPases, is critical in restraining neurite growth and promoting tangential migration.

    View details for DOI 10.1016/j.neuron.2007.05.024

    View details for Web of Science ID 000247645600008

    View details for PubMedID 17582329

    View details for PubMedCentralID PMC4921237

  • Mice lacking Dlx1 show subtype-specific loss of interneurons, reduced inhibition and epilepsy. Nature neuroscience Cobos, I., Calcagnotto, M. E., Vilaythong, A. J., Thwin, M. T., Noebels, J. L., Baraban, S. C., Rubenstein, J. L. 2005; 8 (8): 1059-68


    Dlx homeodomain transcription factors are essential during embryonic development for the production of forebrain GABAergic interneurons. Here we show that Dlx1 is also required for regulating the functional longevity of cortical and hippocampal interneurons in the adult brain. We demonstrate preferential Dlx1 expression in a subset of cortical and hippocampal interneurons which, in postnatal Dlx1 mutants, show a time-dependent reduction in number. This reduction preferentially affects calretinin(+) (bipolar cells) and somatostatin(+) subtypes (for example, bitufted cells), whereas parvalbumin(+) subpopulations (basket cells and chandelier cells) seem to be unaffected. Cell transplantation analysis demonstrates that interneuron loss reflects cell-autonomous functions of Dlx1. The decrease in the number of interneurons was associated with a reduction of GABA-mediated inhibitory postsynaptic current in neocortex and hippocampus in vitro and cortical dysrhythmia in vivo. Dlx1 mutant mice show generalized electrographic seizures and histological evidence of seizure-induced reorganization, linking the Dlx1 mutation to delayed-onset epilepsy associated with interneuron loss.

    View details for DOI 10.1038/nn1499

    View details for PubMedID 16007083

  • Origins of cortical interneuron subtypes. The Journal of neuroscience : the official journal of the Society for Neuroscience Xu, Q., Cobos, I., De La Cruz, E., Rubenstein, J. L., Anderson, S. A. 2004; 24 (11): 2612-22


    Cerebral cortical functions are conducted by two general classes of neurons: glutamatergic projection neurons and GABAergic interneurons. Distinct interneuron subtypes serve distinct roles in modulating cortical activity and can be differentially affected in cortical diseases, but little is known about the mechanisms for generating their diversity. Recent evidence suggests that many cortical interneurons originate within the subcortical telencephalon and then migrate tangentially into the overlying cortex. To test the hypothesis that distinct interneuron subtypes are derived from distinct telencephalic subdivisions, we have used an in vitro assay to assess the developmental potential of subregions of the telencephalic proliferative zone (PZ) to give rise to neurochemically defined interneuron subgroups. PZ cells from GFP+ donor mouse embryos were transplanted onto neonatal cortical feeder cells and assessed for their ability to generate specific interneuron subtypes. Our results suggest that the parvalbumin- and the somatostatin-expressing interneuron subgroups originate primarily within the medial ganglionic eminence (MGE) of the subcortical telencephalon, whereas the calretinin-expressing interneurons appear to derive mainly from the caudal ganglionic eminence (CGE). These results are supported by findings from primary cultures of cortex from Nkx2.1 mutants, in which normal MGE fails to form but in which the CGE is less affected. In these cultures, parvalbumin- and somatostatin-expressing cells are absent, although calretinin-expressing interneurons are present. Interestingly, calretinin-expressing bipolar interneurons were nearly absent from cortical cultures of Dlx1/2 mutants. By establishing spatial differences in the origins of interneuron subtypes, these studies lay the groundwork for elucidating the molecular bases for their distinct differentiation pathways.

    View details for DOI 10.1523/JNEUROSCI.5667-03.2004

    View details for PubMedID 15028753

  • Enhancing mitosis quantification and detection in meningiomas with computational digital pathology. Acta neuropathologica communications Gu, H., Yang, C., Al-Kharouf, I., Magaki, S., Lakis, N., Williams, C. K., Alrosan, S. M., Onstott, E. K., Yan, W., Khanlou, N., Cobos, I., Zhang, X. R., Zarrin-Khameh, N., Vinters, H. V., Chen, X. A., Haeri, M. 2024; 12 (1): 7


    Mitosis is a critical criterion for meningioma grading. However, pathologists' assessment of mitoses is subject to significant inter-observer variation due to challenges in locating mitosis hotspots and accurately detecting mitotic figures. To address this issue, we leverage digital pathology and propose a computational strategy to enhance pathologists' mitosis assessment. The strategy has two components: (1) A depth-first search algorithm that quantifies the mathematically maximum mitotic count in 10 consecutive high-power fields, which can enhance the preciseness, especially in cases with borderline mitotic count. (2) Implementing a collaborative sphere to group a set of pathologists to detect mitoses under each high-power field, which can mitigate subjective random errors in mitosis detection originating from individual detection errors. By depth-first search algorithm (1) , we analyzed 19 meningioma slides and discovered that the proposed algorithm upgraded two borderline cases verified at consensus conferences. This improvement is attributed to the algorithm's ability to quantify the mitotic count more comprehensively compared to other conventional methods of counting mitoses. In implementing a collaborative sphere (2) , we evaluated the correctness of mitosis detection from grouped pathologists and/or pathology residents, where each member of the group annotated a set of 48 high-power field images for mitotic figures independently. We report that groups with sizes of three can achieve an average precision of 0.897 and sensitivity of 0.699 in mitosis detection, which is higher than an average pathologist in this study (precision: 0.750, sensitivity: 0.667). The proposed computational strategy can be integrated with artificial intelligence workflow, which envisions the future of achieving a rapid and robust mitosis assessment by interactive assisting algorithms that can ultimately benefit patient management.

    View details for DOI 10.1186/s40478-023-01707-6

    View details for PubMedID 38212848

    View details for PubMedCentralID 8328013

  • Nuclear RNA catabolism controls endogenous retroviruses, gene expression asymmetry, and dedifferentiation. Molecular cell Torre, D., Fstkchyan, Y. S., Ho, J. S., Cheon, Y., Patel, R. S., Degrace, E. J., Mzoughi, S., Schwarz, M., Mohammed, K., Seo, J. S., Romero-Bueno, R., Demircioglu, D., Hasson, D., Tang, W., Mahajani, S. U., Campisi, L., Zheng, S., Song, W. S., Wang, Y. C., Shah, H., Francoeur, N., Soto, J., Salfati, Z., Weirauch, M. T., Warburton, P., Beaumont, K., Smith, M. L., Mulder, L., Villalta, S. A., Kessenbrock, K., Jang, C., Lee, D., De Rubeis, S., Cobos, I., Tam, O., Hammell, M. G., Seldin, M., Shi, Y., Basu, U., Sebastiano, V., Byun, M., Sebra, R., Rosenberg, B. R., Benner, C., Guccione, E., Marazzi, I. 2023


    Endogenous retroviruses (ERVs) are remnants of ancient parasitic infections and comprise sizable portions of most genomes. Although epigenetic mechanisms silence most ERVs by generating a repressive environment that prevents their expression (heterochromatin), little is known about mechanisms silencing ERVs residing in open regions of the genome (euchromatin). This is particularly important during embryonic development, where induction and repression of distinct classes of ERVs occur in short temporal windows. Here, we demonstrate that transcription-associated RNA degradation by the nuclear RNA exosome and Integrator is a regulatory mechanism that controls the productive transcription of most genes and many ERVs involved in preimplantation development. Disrupting nuclear RNA catabolism promotes dedifferentiation to a totipotent-like state characterized by defects in RNAPII elongation and decreased expression of long genes (gene-length asymmetry). Our results indicate that RNA catabolism is a core regulatory module of gene networks that safeguards RNAPII activity, ERV expression, cell identity, and developmental potency.

    View details for DOI 10.1016/j.molcel.2023.10.036

    View details for PubMedID 37995687

  • Lifelong restructuring of 3D genome architecture in cerebellar granule cells. Science (New York, N.Y.) Tan, L., Shi, J., Moghadami, S., Parasar, B., Wright, C. P., Seo, Y., Vallejo, K., Cobos, I., Duncan, L., Chen, R., Deisseroth, K. 2023; 381 (6662): 1112-1119


    The cerebellum contains most of the neurons in the human brain and exhibits distinctive modes of development and aging. In this work, by developing our single-cell three-dimensional (3D) genome assay-diploid chromosome conformation capture, or Dip-C-into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we resolved the first 3D genome structures of single cerebellar cells, created life-spanning 3D genome atlases for both humans and mice, and jointly measured transcriptome and chromatin accessibility during development. We found that although the transcriptome and chromatin accessibility of cerebellar granule neurons mature in early postnatal life, 3D genome architecture gradually remodels throughout life, establishing ultra-long-range intrachromosomal contacts and specific interchromosomal contacts that are rarely seen in neurons. These results reveal unexpected evolutionarily conserved molecular processes that underlie distinctive features of neural development and aging across the mammalian life span.

    View details for DOI 10.1126/science.adh3253

    View details for PubMedID 37676945

  • Deregulation of ER-mitochondria contact formation and mitochondrial calcium homeostasis mediated by VDAC in fragile X syndrome. Developmental cell Geng, J., Khaket, T. P., Pan, J., Li, W., Zhang, Y., Ping, Y., Cobos Sillero, M. I., Lu, B. 2023; 58 (7): 597-615.e10


    Loss of fragile X messenger ribonucleoprotein (FMRP) causes fragile X syndrome (FXS), the most prevalent form of inherited intellectual disability. Here, we show that FMRP interacts with the voltage-dependent anion channel (VDAC) to regulate the formation and function of endoplasmic reticulum (ER)-mitochondria contact sites (ERMCSs), structures that are critical for mitochondrial calcium (mito-Ca2+) homeostasis. FMRP-deficient cells feature excessive ERMCS formation and ER-to-mitochondria Ca2+ transfer. Genetic and pharmacological inhibition of VDAC or other ERMCS components restored synaptic structure, function, and plasticity and rescued locomotion and cognitive deficits of the Drosophila dFmr1 mutant. Expressing FMRP C-terminal domain (FMRP-C), which confers FMRP-VDAC interaction, rescued the ERMCS formation and mito-Ca2+ homeostasis defects in FXS patient iPSC-derived neurons and locomotion and cognitive deficits in Fmr1 knockout mice. These results identify altered ERMCS formation and mito-Ca2+ homeostasis as contributors to FXS and offer potential therapeutic targets.

    View details for DOI 10.1016/j.devcel.2023.03.002

    View details for PubMedID 37040696

  • Sex-Specific Oligodendroglia Response in Alzheimer's Disease Bharani, K., Dharshini, A., Oberhauser, J., Cobos, I. ELSEVIER SCIENCE INC. 2023: S1459
  • Cerebellar Granule Cells Develop Non-neuronal 3D Genome Architecture over the Lifespan. bioRxiv : the preprint server for biology Tan, L., Shi, J., Moghadami, S., Wright, C. P., Parasar, B., Seo, Y., Vallejo, K., Cobos, I., Duncan, L., Chen, R., Deisseroth, K. 2023


    The cerebellum contains most of the neurons in the human brain, and exhibits unique modes of development, malformation, and aging. For example, granule cells-the most abundant neuron type-develop unusually late and exhibit unique nuclear morphology. Here, by developing our high-resolution single-cell 3D genome assay Dip-C into population-scale (Pop-C) and virus-enriched (vDip-C) modes, we were able to resolve the first 3D genome structures of single cerebellar cells, create life-spanning 3D genome atlases for both human and mouse, and jointly measure transcriptome and chromatin accessibility during development. We found that while the transcriptome and chromatin accessibility of human granule cells exhibit a characteristic maturation pattern within the first year of postnatal life, 3D genome architecture gradually remodels throughout life into a non-neuronal state with ultra-long-range intra-chromosomal contacts and specific inter-chromosomal contacts. This 3D genome remodeling is conserved in mice, and robust to heterozygous deletion of chromatin remodeling disease-associated genes ( Chd8 or Arid1b ). Together these results reveal unexpected and evolutionarily-conserved molecular processes underlying the unique development and aging of the mammalian cerebellum.

    View details for DOI 10.1101/2023.02.25.530020

    View details for PubMedID 36865235

  • Swollen axons impair neuronal circuits NATURE Cobos, I., Palop, J. J. 2022; 612 (7939): 218-220
  • Swollen axons impair neuronal circuits NATURE Cobos, I., Palop, J. J. 2022: 218-220

    View details for DOI 10.1038/d41586-022-03800-7

    View details for Web of Science ID 000925198400005

    View details for PubMedID 36450951

  • Whole-Transcriptome Profiling and circRNA-miRNA-mRNA Regulatory Networks in B-Cell Development. Frontiers in immunology Pan, J., Hu, S., Ren, X., Hu, H., Deng, X., Yu, B., Cobos, I., Chen, X., Zhang, W. 2022; 13: 812924


    The generation and differentiation of B lymphocytes (B cells) is a flexible process with many critical regulatory factors. Previous studies indicated that non-coding RNAs play multiple roles in the development of lymphocytes. However, little has been known about the circular RNA (circRNA) profiles and their competing endogenous RNA (ceRNA) networks in B-cell development and differentiation. Here, four B-cell subsets were purified from single-cell suspensions of mouse bone marrow. Then RNA sequencing (RNA-Seq) was used to display expression profiles of circRNAs, miRNAs and mRNAs during B-cell differentiation. 175, 203, 219 and 207 circRNAs were specifically expressed in pro-B cells, pre-B cells, immature B cells and mature B cells, respectively. The circRNA-associated ceRNA networks constructed in two sequential stages of B-cell differentiation revealed the potential mechanism of circRNAs in these processes. This study is the first to explore circRNA profiles and circRNA-miRNA-mRNA networks in different B-cell developmental stages of mouse bone marrow, which contribute to further research on their mechanism in B-cell development and differentiation.

    View details for DOI 10.3389/fimmu.2022.812924

    View details for PubMedID 35386709

    View details for PubMedCentralID PMC8978327

  • Dysregulation of brain and choroid plexus cell types in severe COVID-19 (vol 595, pg 565, 2021) NATURE Yang, A. C., Kern, F., Losada, P. M., Agam, M. R., Maat, C. A., Schmartz, G. P., Fehlmann, T., Stein, J. A., Schaum, N., Lee, D. P., Calcuttawala, K., Vest, R. T., Berdnik, D., Lu, N., Hahn, O., Gate, D., McNerney, M., Channappa, D., Cobos, I., Ludwig, N., Schulz-Schaeffer, W. J., Keller, A., Wyss-Coray, T. 2021

    View details for DOI 10.1038/s41586-021-04080-3

    View details for Web of Science ID 000704968600001

    View details for PubMedID 34625744

    View details for PubMedCentralID PMC8500262

  • Dysregulation of brain and choroid plexus cell types in severe COVID-19. Nature Yang, A. C., Kern, F., Losada, P. M., Agam, M. R., Maat, C. A., Schmartz, G. P., Fehlmann, T., Stein, J. A., Schaum, N., Lee, D. P., Calcuttawala, K., Vest, R. T., Berdnik, D., Lu, N., Hahn, O., Gate, D., McNerney, M. W., Channappa, D., Cobos, I., Ludwig, N., Schulz-Schaeffer, W. J., Keller, A., Wyss-Coray, T. 2021


    Though SARS-CoV-2 primarily targets the respiratory system, patients and survivors can suffer neurological symptoms1-3. Yet, an unbiased understanding of the cellular and molecular processes affected in the brains of COVID-19 patients is still missing. Here, we profile 65,309 single-nucleus transcriptomes from 30 frontal cortex and choroid plexus samples across 14 control (including 1 terminal influenza) and 8 COVID-19 patients. While a systematic analysis yields no molecular traces of SARS-CoV-2 in the brain, we observe broad cellular perturbations which predict that choroid plexus barrier cells sense and relay peripheral inflammation into the brain and show that peripheral T cells infiltrate the parenchyma. We discover COVID-19 disease-associated microglia and astrocyte subpopulations that share features with pathological cell states reported in human neurodegenerative disease4-6. Synaptic signaling of upper-layer excitatory neurons-evolutionarily expanded in humans7 and linked to cognitive function8-are preferentially affected in COVID-19. Across cell types, COVID-19 perturbations overlap with those in chronic brain disorders and reside in genetic variants associated with cognition, schizophrenia, and depression. Our findings and public dataset provide a molecular framework to understand COVID-19 related neurological disease observed now and which may emerge later.

    View details for DOI 10.1038/s41586-021-03710-0

    View details for PubMedID 34153974

  • The CD22-IGF2R interaction is a therapeutic target for microglial lysosome dysfunction in Niemann-Pick type C. Science translational medicine Pluvinage, J. V., Sun, J., Claes, C., Flynn, R. A., Haney, M. S., Iram, T., Meng, X., Lindemann, R., Riley, N. M., Danhash, E., Chadarevian, J. P., Tapp, E., Gate, D., Kondapavulur, S., Cobos, I., Chetty, S., Pașca, A. M., Pașca, S. P., Berry-Kravis, E., Bertozzi, C. R., Blurton-Jones, M., Wyss-Coray, T. 2021; 13 (622): eabg2919


    [Figure: see text].

    View details for DOI 10.1126/scitranslmed.abg2919

    View details for PubMedID 34851695

  • Genome-wide association study and functional validation implicates JADE1 in tauopathy. Acta neuropathologica Farrell, K., Kim, S., Han, N., Iida, M. A., Gonzalez, E. M., Otero-Garcia, M., Walker, J. M., Richardson, T. E., Renton, A. E., Andrews, S. J., Fulton-Howard, B., Humphrey, J., Vialle, R. A., Bowles, K. R., de Paiva Lopes, K., Whitney, K., Dangoor, D. K., Walsh, H., Marcora, E., Hefti, M. M., Casella, A., Sissoko, C. T., Kapoor, M., Novikova, G., Udine, E., Wong, G., Tang, W., Bhangale, T., Hunkapiller, J., Ayalon, G., Graham, R. R., Cherry, J. D., Cortes, E. P., Borukov, V. Y., McKee, A. C., Stein, T. D., Vonsattel, J. P., Teich, A. F., Gearing, M., Glass, J., Troncoso, J. C., Frosch, M. P., Hyman, B. T., Dickson, D. W., Murray, M. E., Attems, J., Flanagan, M. E., Mao, Q., Mesulam, M. M., Weintraub, S., Woltjer, R. L., Pham, T., Kofler, J., Schneider, J. A., Yu, L., Purohit, D. P., Haroutunian, V., Hof, P. R., Gandy, S., Sano, M., Beach, T. G., Poon, W., Kawas, C. H., Corrada, M. M., Rissman, R. A., Metcalf, J., Shuldberg, S., Salehi, B., Nelson, P. T., Trojanowski, J. Q., Lee, E. B., Wolk, D. A., McMillan, C. T., Keene, C. D., Latimer, C. S., Montine, T. J., Kovacs, G. G., Lutz, M. I., Fischer, P., Perrin, R. J., Cairns, N. J., Franklin, E. E., Cohen, H. T., Raj, T., Cobos, I., Frost, B., Goate, A., White Iii, C. L., Crary, J. F. 2021


    Primary age-related tauopathy (PART) is a neurodegenerative pathology with features distinct from but also overlapping with Alzheimer disease (AD). While both exhibit Alzheimer-type temporal lobe neurofibrillary degeneration alongside amnestic cognitive impairment, PART develops independently of amyloid-β (Aβ) plaques. The pathogenesis of PART is not known, but evidence suggests an association with genes that promote tau pathology and others that protect from Aβ toxicity. Here, we performed a genetic association study in an autopsy cohort of individuals with PART (n = 647) using Braak neurofibrillary tangle stage as a quantitative trait. We found some significant associations with candidate loci associated with AD (SLC24A4, MS4A6A, HS3ST1) and progressive supranuclear palsy (MAPT and EIF2AK3). Genome-wide association analysis revealed a novel significant association with a single nucleotide polymorphism on chromosome 4 (rs56405341) in a locus containing three genes, including JADE1 which was significantly upregulated in tangle-bearing neurons by single-soma RNA-seq. Immunohistochemical studies using antisera targeting JADE1 protein revealed localization within tau aggregates in autopsy brains with four microtubule-binding domain repeats (4R) isoforms and mixed 3R/4R, but not with 3R exclusively. Co-immunoprecipitation in post-mortem human PART brain tissue revealed a specific binding of JADE1 protein to four repeat tau lacking N-terminal inserts (0N4R). Finally, knockdown of the Drosophila JADE1 homolog rhinoceros (rno) enhanced tau-induced toxicity and apoptosis in vivo in a humanized 0N4R mutant tau knock-in model, as quantified by rough eye phenotype and terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) in the fly brain. Together, these findings indicate that PART has a genetic architecture that partially overlaps with AD and other tauopathies and suggests a novel role for JADE1 as a modifier of neurofibrillary degeneration.

    View details for DOI 10.1007/s00401-021-02379-z

    View details for PubMedID 34719765

  • Hepatic arginase deficiency fosters dysmyelination during postnatal CNS development. JCI insight Liu, X., Haney, J. R., Cantero, G., Lambert, J. R., Otero-Garcia, M., Truong, B., Gropman, A., Cobos, I., Cederbaum, S. D., Lipshutz, G. S. 2019; 4 (17)


    Deficiency of arginase is associated with hyperargininemia, and prominent features include spastic diplegia/tetraplegia, clonus, and hyperreflexia; loss of ambulation, intellectual disability and progressive neurological decline are other signs. To gain greater insight into the unique neuromotor features, we performed gene expression profiling of the motor cortex of a murine model of the disorder. Coexpression network analysis suggested an abnormality with myelination, which was supported by limited existing human data. Utilizing electron microscopy, marked dysmyelination was detected in 2-week-old homozygous Arg1-KO mice. The corticospinal tract was found to be adversely affected, supporting dysmyelination as the cause of the unique neuromotor features and implicating oligodendrocyte impairment in a deficiency of hepatic Arg1. Following neonatal hepatic gene therapy to express Arg1, the subcortical white matter, pyramidal tract, and corticospinal tract all showed a remarkable recovery in terms of myelinated axon density and ultrastructural integrity with active wrapping of axons by nearby oligodendrocyte processes. These findings support the following conclusions: arginase deficiency is a leukodystrophy affecting the brain and spinal cord while sparing the peripheral nervous system, and neonatal AAV hepatic gene therapy can rescue the defects associated with myelinated axons, strongly implicating the functional recovery of oligodendrocytes after restoration of hepatic arginase activity.

    View details for DOI 10.1172/jci.insight.130260

    View details for PubMedID 31484827

  • Dlx1 and Dlx2 Promote Interneuron GABA Synthesis, Synaptogenesis, and Dendritogenesis. Cerebral cortex (New York, N.Y. : 1991) Pla, R., Stanco, A., Howard, M. A., Rubin, A. N., Vogt, D., Mortimer, N., Cobos, I., Potter, G. B., Lindtner, S., Price, J. D., Nord, A. S., Visel, A., Schreiner, C. E., Baraban, S. C., Rowitch, D. H., Rubenstein, J. L. 2018; 28 (11): 3797-3815


    The postnatal functions of the Dlx1&2 transcription factors in cortical interneurons (CINs) are unknown. Here, using conditional Dlx1, Dlx2, and Dlx1&2 knockouts (CKOs), we defined their roles in specific CINs. The CKOs had dendritic, synaptic, and survival defects, affecting even PV+ CINs. We provide evidence that DLX2 directly drives Gad1, Gad2, and Vgat expression, and show that mutants had reduced mIPSC amplitude. In addition, the mutants formed fewer GABAergic synapses on excitatory neurons and had reduced mIPSC frequency. Furthermore, Dlx1/2 CKO had hypoplastic dendrites, fewer excitatory synapses, and reduced excitatory input. We provide evidence that some of these phenotypes were due to reduced expression of GRIN2B (a subunit of the NMDA receptor), a high confidence Autism gene. Thus, Dlx1&2 coordinate key components of CIN postnatal development by promoting their excitability, inhibitory output, and survival.

    View details for DOI 10.1093/cercor/bhx241

    View details for PubMedID 29028947

    View details for PubMedCentralID PMC6188538

  • GABAergic Interneuron Differentiation in the Basal Forebrain Is Mediated through Direct Regulation of Glutamic Acid Decarboxylase Isoforms by Dlx Homeobox Transcription Factors. The Journal of neuroscience : the official journal of the Society for Neuroscience Le, T. N., Zhou, Q. P., Cobos, I., Zhang, S., Zagozewski, J., Japoni, S., Vriend, J., Parkinson, T., Du, G., Rubenstein, J. L., Eisenstat, D. D. 2017; 37 (36): 8816-8829


    GABA is the key inhibitory neurotransmitter in the cortex but regulation of its synthesis during forebrain development is poorly understood. In the telencephalon, members of the distal-less (Dlx) homeobox gene family are expressed in, and regulate the development of, the basal ganglia primodia from which many GABAergic neurons originate and migrate to other forebrain regions. The Dlx1/Dlx2 double knock-out mice die at birth with abnormal cortical development, including loss of tangential migration of GABAergic inhibitory interneurons to the neocortex (Anderson et al., 1997a). We have discovered that specific promoter regulatory elements of glutamic acid decarboxylase isoforms (Gad1 and Gad2), which regulate GABA synthesis from the excitatory neurotransmitter glutamate, are direct transcriptional targets of both DLX1 and DLX2 homeoproteins in vivo Further gain- and loss-of-function studies in vitro and in vivo demonstrated that both DLX1 and DLX2 are necessary and sufficient for Gad gene expression. DLX1 and/or DLX2 activated the transcription of both Gad genes, and defects in Dlx function disrupted the differentiation of GABAergic interneurons with global reduction in GABA levels in the forebrains of the Dlx1/Dlx2 double knock-out mouse in vivo Identification of Gad genes as direct Dlx transcriptional targets is significant; it extends our understanding of Dlx gene function in the developing forebrain beyond the regulation of tangential interneuron migration to the differentiation of GABAergic interneurons arising from the basal telencephalon, and may help to unravel the pathogenesis of several developmental brain disorders.SIGNIFICANCE STATEMENT GABA is the major inhibitory neurotransmitter in the brain. We show that Dlx1/Dlx2 homeobox genes regulate GABA synthesis during forebrain development through direct activation of glutamic acid decarboxylase enzyme isoforms that convert glutamate to GABA. This discovery helps explain how Dlx mutations result in abnormal forebrain development, due to defective differentiation, in addition to the loss of tangential migration of GABAergic inhibitory interneurons to the neocortex. Reduced numbers or function of cortical GABAergic neurons may lead to hyperactivity states such as seizures (Cobos et al., 2005) or contribute to the pathogenesis of some autism spectrum disorders. GABAergic dysfunction in the basal ganglia could disrupt the learning and development of complex motor and cognitive behaviors (Rubenstein and Merzenich, 2003).

    View details for DOI 10.1523/JNEUROSCI.2125-16.2017

    View details for PubMedID 28821666

    View details for PubMedCentralID PMC6596671

  • A 63-Year-Old Man With Progressive Visual Symptoms. JAMA neurology Mitchell, S. B., Lucente, D., Larvie, M., Cobos, M. I., Frosch, M., Dickerson, B. C. 2017; 74 (1): 114-118


    A 63-year-old man presented with a 4-year history of insidious onset and gradual progression of visual symptoms including right homonymous hemianopsia, alexia, and simultanagnosia with preserved memory. Magnetic resonance imaging, perfusion single-photon emission computed tomography, and fluorodeoxyglucose positron emission tomographic scans revealed strikingly asymmetric left parieto-occipital abnormality. Neuropsychological testing was performed. The differential diagnosis, pathologic findings, genetic testing results, and diagnosis are discussed.

    View details for DOI 10.1001/jamaneurol.2016.2210

    View details for PubMedID 27842190

  • CASE RECORDS of the MASSACHUSETTS GENERAL HOSPITAL. Case 23-2015. A 51-Year-Old Woman with Headache, Cognitive Impairment, and Weakness. The New England journal of medicine Batchelor, T. T., Chen, Y. B., Rapalino, O., Cobos, I. 2015; 373 (4): 367-77

    View details for DOI 10.1056/NEJMcpc1406415

    View details for PubMedID 26200983

  • Human von Economo neurons express transcription factors associated with Layer V subcerebral projection neurons. Cerebral cortex (New York, N.Y. : 1991) Cobos, I., Seeley, W. W. 2015; 25 (1): 213-20


    The von Economo neurons (VENs) are large bipolar Layer V projection neurons found chiefly in the anterior cingulate and frontoinsular cortices. Although VENs have been linked to prevalent illnesses such as frontotemporal dementia, autism, and schizophrenia, little is known about VEN identity, including their major projection targets. Here, we undertook a developmental transcription factor expression study, focusing on markers associated with specific classes of Layer V projection neurons. Using mRNA in situ hybridization, we found that VENs prominently express FEZF2 and CTIP2, transcription factors that regulate the fate and differentiation of subcerebral projection neurons, in humans aged 3 months to 65 years. In contrast, few VENs expressed markers associated with callosal or corticothalamic projections. These findings suggest that VENs may represent a specialized Layer V projection neuron for linking cortical autonomic control sites to brainstem or spinal cord regions.

    View details for DOI 10.1093/cercor/bht219

    View details for PubMedID 23960210

    View details for PubMedCentralID PMC4318933

  • Influence of a Subtype of Inhibitory Interneuron on Stimulus-Specific Responses in Visual Cortex CEREBRAL CORTEX Mao, R., Schummers, J., Knoblich, U., Lacey, C. J., Van Wart, A., Cobos, I., Kim, C., Huguenard, J. R., Rubenstein, J. L., Sur, M. 2012; 22 (3): 493-508


    Inhibition modulates receptive field properties and integrative responses of neurons in cortical circuits. The contribution of specific interneuron classes to cortical circuits and emergent responses is unknown. Here, we examined neuronal responses in primary visual cortex (V1) of adult Dlx1(-/-) mice, which have a selective reduction in cortical dendrite-targeting interneurons (DTIs) that express calretinin, neuropeptide Y, and somatostatin. The V1 neurons examined in Dlx1(-/-) mice have reduced orientation selectivity and altered firing rates, with elevated late responses, suggesting that local inhibition at dendrites has a specific role in modulating neuronal computations. We did not detect overt changes in the physiological properties of thalamic relay neurons and features of thalamocortical projections, such as retinotopic maps and eye-specific inputs, in the mutant mice, suggesting that the defects are cortical in origin. These experimental results are well explained by a computational model that integrates broad tuning from dendrite-targeting and narrower tuning from soma-targeting interneuron subclasses. Our findings suggest a key role for DTIs in the fine-tuning of stimulus-specific cortical responses.

    View details for DOI 10.1093/cercor/bhr057

    View details for Web of Science ID 000300495800001

    View details for PubMedID 21666125

    View details for PubMedCentralID PMC3278313

  • Step-by-step in situ hybridization method for localizing gene expression changes in the brain. Methods in molecular biology (Clifton, N.J.) Palop, J. J., Roberson, E. D., Cobos, I. 2011; 670: 207-30


    RNA in situ hybridization is a powerful technique for examining gene expression in specific cell populations. This method is particularly useful in the central nervous system with its high cellular diversity and dynamic gene expression regulation associated with development, plasticity, neuronal activity, aging, and disease. Standard quantitative techniques such as Western blotting and real-time PCR allow the detection of altered gene or protein expression but provide no information about their cellular source or possible alterations in expression patterns. Here, we describe a step-by-step RNA in situ hybridization method on adult and embryonic brain sections for quantitative neuroscience. We include fully detailed protocols for RNase-free material preparation, perfusion, fixation, sectioning, selection of expressed sequence tag cDNA clones, linearization of cDNA, synthesis of digoxigenin-labeled RNA probes (riboprobes), in situ hybridization on floating and mounted sections, nonradioactive immunohistochemical detection of riboprobes for light and fluorescence microscopy, and double labeling. We also include useful information about quality-control steps, key online sites, commercially available products, stock solutions, and storage. Finally, we provide examples of the utility of this approach in understanding the neuropathogenesis of Alzheimer's disease. With virtually all genomic coding sequences cloned or being cloned into cDNA plasmids, this technique has become highly accessible to explore gene expression profiles at the cellular and brain region level.

    View details for DOI 10.1007/978-1-60761-744-0_15

    View details for PubMedID 20967593

  • A mutation in the pericentrin gene causes abnormal interneuron migration to the olfactory bulb in mice. Developmental biology Endoh-Yamagami, S., Karkar, K. M., May, S. R., Cobos, I., Thwin, M. T., Long, J. E., Ashique, A. M., Zarbalis, K., Rubenstein, J. L., Peterson, A. S. 2010; 340 (1): 41-53


    Precise control of neuronal migration is essential for proper function of the brain. Taking a forward genetic screen, we isolated a mutant mouse with defects in interneuron migration. By genetic mapping, we identified a frame shift mutation in the pericentrin (Pcnt) gene. The Pcnt gene encodes a large centrosomal coiled-coil protein that has been implicated in schizophrenia. Recently, frame shift and premature termination mutations in the pericentrin (PCNT) gene were identified in individuals with Seckel syndrome and microcephalic osteodysplastic primordial dwarfism (MOPD II), both of which are characterized by greatly reduced body and brain sizes. The mouse Pcnt mutant shares features with the human syndromes in its overall growth retardation and reduced brain size. We found that dorsal lateral ganglionic eminence (dLGE)-derived olfactory bulb interneurons are severely affected and distributed abnormally in the rostral forebrain in the mutant. Furthermore, mutant interneurons exhibit abnormal migration behavior and RNA interference knockdown of Pcnt impairs cell migration along the rostal migratory stream (RMS) into the olfactory bulb. These findings indicate that pericentrin is required for proper migration of olfactory bulb interneurons and provide a developmental basis for association of pericentrin function with interneuron defects in human schizophrenia.

    View details for DOI 10.1016/j.ydbio.2010.01.017

    View details for PubMedID 20096683

  • Dlx1&2 and Mash1 transcription factors control MGE and CGE patterning and differentiation through parallel and overlapping pathways. Cerebral cortex (New York, N.Y. : 1991) Long, J. E., Cobos, I., Potter, G. B., Rubenstein, J. L. 2009; 19 Suppl 1: i96-106


    Here we define the expression of approximately 100 transcription factors (TFs) in progenitors and neurons of the developing mouse medial and caudal ganglionic eminences, anlage of the basal ganglia and pallial interneurons. We have begun to elucidate the transcriptional hierarchy of these genes with respect to the Dlx homeodomain genes, which are essential for differentiation of most gamma-aminobutyric acidergic projection neurons of the basal ganglia. This analysis identified Dlx-dependent and Dlx-independent pathways. The Dlx-independent pathway depends in part on the function of the Mash1 basic helix-loop-helix (b-HLH) TF. These analyses define core transcriptional components that differentially specify the identity and differentiation of the globus pallidus, basal telencephalon, and pallial interneurons.

    View details for DOI 10.1093/cercor/bhp045

    View details for PubMedID 19386638

    View details for PubMedCentralID PMC2693539

  • Dlx1&2 and Mash1 transcription factors control striatal patterning and differentiation through parallel and overlapping pathways. The Journal of comparative neurology Long, J. E., Swan, C., Liang, W. S., Cobos, I., Potter, G. B., Rubenstein, J. L. 2009; 512 (4): 556-72


    Here we define the expression of approximately 100 transcription factors in progenitors and neurons of the developing basal ganglia. We have begun to elucidate the transcriptional hierarchy of these genes with respect to the Dlx homeodomain genes, which are essential for differentiation of most GABAergic projection neurons of the basal ganglia. This analysis identified Dlx-dependent and Dlx-independent pathways. The Dlx-independent pathway depends in part on the function of the Mash1 b-HLH transcription factor. These analyses define core transcriptional components that differentially specify the identity and differentiation of the striatum, nucleus accumbens, and septum.

    View details for DOI 10.1002/cne.21854

    View details for PubMedID 19030180

    View details for PubMedCentralID PMC2761428

  • FGF15 promotes neurogenesis and opposes FGF8 function during neocortical development. Neural development Borello, U., Cobos, I., Long, J. E., McWhirter, J. R., Murre, C., Rubenstein, J. L. 2008; 3: 17


    Growth, differentiation and regional specification of telencephalic domains, such as the cerebral cortex, are regulated by the interplay of secreted proteins produced by patterning centers and signal transduction systems deployed in the surrounding neuroepithelium. Among other signaling molecules, members of the fibroblast growth factor (FGF) family have a prominent role in regulating growth, differentiation and regional specification. In the mouse telencephalon the rostral patterning center expresses members of the Fgf family (Fgf8, Fgf15, Fgf17, Fgf18). FGF8 and FGF17 signaling have major roles in specification and morphogenesis of the rostroventral telencephalon, whereas the functions of FGF15 and FGF18 in the rostral patterning center have not been established.Using Fgf15-/- mutant mice, we provide evidence that FGF15 suppresses proliferation, and that it promotes differentiation, expression of CoupTF1 and caudoventral fate; thus, reducing Fgf15 and Fgf8 dosage have opposite effects. Furthermore, we show that FGF15 and FGF8 differentially phosphorylate ERK (p42/44), AKT and S6 in cultures of embryonic cortex. Finally, we show that FGF15 inhibits proliferation in cortical cultures.FGF15 and FGF8 have distinct signaling properties, and opposite effects on neocortical patterning and differentiation; FGF15 promotes CoupTF1 expression, represses proliferation and promotes neural differentiation.

    View details for DOI 10.1186/1749-8104-3-17

    View details for PubMedID 18625063

    View details for PubMedCentralID PMC2492847

  • Transcriptional regulation of cortical interneuron development. The Journal of neuroscience : the official journal of the Society for Neuroscience Butt, S. J., Cobos, I., Golden, J., Kessaris, N., Pachnis, V., Anderson, S. 2007; 27 (44): 11847-50

    View details for DOI 10.1523/JNEUROSCI.3525-07.2007

    View details for PubMedID 17978022

  • Chicken lateral septal organ and other circumventricular organs form in a striatal subdomain abutting the molecular striatopallidal border. The Journal of comparative neurology Bardet, S. M., Cobos, I., Puelles, E., Martínez-De-La-Torre, M., Puelles, L. 2006; 499 (5): 745-67


    The avian lateral septal organ (LSO) is a telencephalic circumventricular specialization with liquor-contacting neurons (Kuenzel and van Tienhoven [1982] J. Comp. Neurol. 206:293-313). We studied the topological position of the chicken LSO relative to molecular borders defined previously within the telencephalic subpallium (Puelles et al. [2000] J. Comp. Neurol. 424:409-438). Differential expression of Dlx5 and Nkx2.1 homeobox genes, or the Shh gene encoding a secreted morphogen, allows distinction of striatal, pallidal, and preoptic subpallial sectors. The chicken LSO complex was characterized chemoarchitectonically from embryonic to posthatching stages, by using immunohistochemistry for calbindin, tyrosine hydroxylase, NKX2.1, and BEN proteins and in situ hybridization for Nkx2.1, Nkx2.2, Nkx6.1, Shh, and Dlx5 mRNA. Medial and lateral parts of LSO appear, respectively, at the striatal part of the septum and adjacent bottom of the lateral ventricle (accumbens), in lateral continuity with another circumventricular organ that forms along a thin subregion of the entire striatum, abutting the molecular striatopallidal boundary; we called this the "striatopallidal organ" (SPO). The SPO displays associated distal periventricular cells, which are lacking in the LSO. Moreover, the SPO is continuous caudomedially with a thin, linear ependymal specialization found around the extended amygdala and preoptic areas. This differs from SPO and LSO in some molecular aspects. We tentatively identified this structure as being composed of an "extended amygdala organ" (EAO) and a "preoptohypothalamic organ" (PHO). The position of LSO, SPO, EAO, and PHO within a linear Dlx5-expressing ventricular domain that surrounds the Nkx2.1-expressing pallidopreoptic domain provides an unexpected insight into possible common and differential causal mechanisms underlying their formation.

    View details for DOI 10.1002/cne.21121

    View details for PubMedID 17048229

  • Cellular patterns of transcription factor expression in developing cortical interneurons. Cerebral cortex (New York, N.Y. : 1991) Cobos, I., Long, J. E., Thwin, M. T., Rubenstein, J. L. 2006; 16 Suppl 1: i82-8


    Most gamma-aminobutyric acidergic interneurons in the neocortex and hippocampus are derived from subpallial progenitors in the medial ganglionic eminence and migrate tangentially to the pallium, where they differentiate into a diverse set of neuronal subtypes. Toward elucidating the mechanisms underlying the generation of interneuron diversity, we have studied in mice the expression patterns in differentiating and mature neocortical interneurons of 8 transcription factors, including 6 homeobox (Dlx1, Dlx2, Dlx5, Arx, Lhx6, Cux2), 1 basic helix-loop-helix, (NPAS1), and 1 bZIP (MafB). Their patterns of expression change during interneuron differentiation and show distinct distributions within interneuron subpopulations in adult neocortex. This study is a first step to define the combinatorial codes of transcription factors that participate in regulating the specification and function of cortical interneuron subtypes.

    View details for DOI 10.1093/cercor/bhk003

    View details for PubMedID 16766712

  • Severe hearing loss in Dlxl mutant mice. Hearing research Polley, D. B., Cobos, I., Merzenich, M. M., Rubenstein, J. L. 2006; 214 (1-2): 84-8


    The Dlx homeobox gene family participates in regulating middle and inner ear development. A significant role for Dlxl, in particular,has been demonstrated in the development of the middle ear ossicles, but the functional consequences of Dlx.l gene mutation on hearing thresholds has not been assessed. The present study characterizes auditory brainstem responses to click and tonal stimuli in a non-lethal variant of a Dlxl gene knockout. We found that peripheral hearing thresholds for click and tonal stimuli were significantly elevated in homozygous Dlxl knockout (Dlxl-/ ) compared to both heterozygous (Dlxl+/ ) and wild type (Dlxl+/+) mice. Thus, abnormal mor-phogenesis of the incus and stapes that has been documented previously with histological measures is now known to result in a severe peripheral hearing deficit.

    View details for DOI 10.1016/j.heares.2006.02.008

    View details for PubMedID 16632068

  • The vertebrate ortholog of Aristaless is regulated by Dlx genes in the developing forebrain. The Journal of comparative neurology Cobos, I., Broccoli, V., Rubenstein, J. L. 2005; 483 (3): 292-303


    The Dlx transcription factors have a central role in controlling the development of gamma-aminobutyric acid (GABA)-ergic neurons in the forebrain. However, little is known about how they control the properties of GABAergic neurons. One candidate is the Aristaless (Arx) homeobox gene, which lies genetically downstream of the fly Dlx gene (Distal-less, Dll). The expression of Arx in the mouse forebrain includes Dlx-expressing territories, such us the ventral thalamus, parts of the hypothalamus, and the ganglionic eminences and their derivatives in the subpallial telencephalon, and is expressed, as with the Dlx genes, in cortical GABAergic neurons. By using gain-of-function and loss-of-function assays in mouse and chicken embryos, we show that the Dlx genes have a conserved role in regulating the expression of Arx in the forebrain of vertebrates. Ectopic expression of Dlx genes with electroporation in brain slices from mouse embryos and in the neural tube of chick embryos shows that Dlx genes are sufficient to induce Arx ectopically. Moreover, we provide evidence that the Dlx genes exert a functionally relevant role in regulating Arx in vivo, as shown by the severe reduction in the expression of Arx in Dlx1/2 double-knockout mice. Therefore, our results suggest evolutionarily conserved functions of Dlx genes in regulating Arx expression between Drosophila and vertebrates.

    View details for DOI 10.1002/cne.20405

    View details for PubMedID 15682394

  • Graded phenotypic response to partial and complete deficiency of a brain-specific transcript variant of the winged helix transcription factor RFX4. Development (Cambridge, England) Blackshear, P. J., Graves, J. P., Stumpo, D. J., Cobos, I., Rubenstein, J. L., Zeldin, D. C. 2003; 130 (19): 4539-52


    One line of mice harboring a cardiac-specific epoxygenase transgene developed head swelling and rapid neurological decline in young adulthood, and had marked hydrocephalus of the lateral and third ventricles. The transgene was found to be inserted into an intron in the mouse Rfx4 locus. This insertion apparently prevented expression of a novel variant transcript of RFX4 (RFX4_v3), a member of the regulatory factor X family of winged helix transcription factors. Interruption of two alleles resulted in profound failure of dorsal midline brain structure formation and perinatal death, presumably by interfering with expression of downstream genes. Interruption of a single allele prevented formation of the subcommissural organ, a structure important for cerebrospinal fluid flow through the aqueduct of Sylvius, and resulted in congenital hydrocephalus. These data implicate the RFX4_v3 variant transcript as being crucial for early brain development, as well as for the genesis of the subcommissural organ. These findings may be relevant to human congenital hydrocephalus, a birth defect that affects approximately 0.6 per 1000 newborns.

    View details for DOI 10.1242/dev.00661

    View details for PubMedID 12925582

  • Fate map of the avian anterior forebrain at the four-somite stage, based on the analysis of quail-chick chimeras. Developmental biology Cobos, I., Shimamura, K., Rubenstein, J. L., Martínez, S., Puelles, L. 2001; 239 (1): 46-67


    To better understand the topological organization of the primordia within the anterior forebrain, we made a fate map of the rostral neural plate in the chick. Homotopic grafts at the four-somite stage were allowed to survive for up to 9 days to enable an analysis of definitive brain structures. In some cases, the topography of the grafted neuroepithelia was compared with gene expression patterns. The midpoint of the anterior neural ridge maps upon the anterior commissure in the closed neural tube, continuing concentrically into the preoptic area and optic field. Non-neural epithelium just in front of this median ridge gives rise to the adenohypophysis. Areas for the presumptive pallial commissure, septum, and prosencephalic choroidal tissue lie progressively more posteriorly along the ridge, peripheral to the telencephalic entopeduncular and striatopallidal primordia (the subpallium), and the pallium (olfactory bulb, dorsal ventricular ridge, and cortical domains). Subpallial structures lie topologically anterior to the pallial formations, and both are concentric to the septum. Within the pallium, the major cortical domains (Wulst and caudolateral, parahippocampal, and hippocampal cortices) appear posterior to the dorsal ventricular ridge. The amygdaloid region appears concentrically across both the subpallial and pallial regions. This fate map shows that the arrangement of the prospective primordia in the neural plate is basically a flattened representation of topological relationships present in the mature brain, though marked phenomena of differential growth and selective tangential migration of some cell populations complicate the histogenetic constitution of the mature telencephalon.

    View details for DOI 10.1006/dbio.2001.0423

    View details for PubMedID 11784018

  • The avian telencephalic subpallium originates inhibitory neurons that invade tangentially the pallium (dorsal ventricular ridge and cortical areas). Developmental biology Cobos, I., Puelles, L., Martínez, S. 2001; 239 (1): 30-45


    Recent data on the development of the mammalian neocortex support that the majority of its inhibitory GABAergic interneurons originate within the subpallium (ganglionic eminences). Support for such tangential migration into the pallium has come from experiments using fluorescent tracers or lineage analysis with retrovirus, and the phenotypes of mutant mice with different abnormalities in the developing subpallium. In the present study, we describe tangential migration of subpallial-derived neurons in the developing chick telencephalon. Using quail-chick grafts, we precisely identified the neuroepithelial origin, time-course, and pathways of migration, as well as the identity and relative distribution of the diverse tangentially migrated neurons. The analysis of selective grafts of the pallidal and striatal primordia allowed us to determine the relative contribution of each primordium to the population of migrating neurons. Moreover, we found that, like in mammals, the vast majority of the GABAergic and calbindin-immunoreactive neurons within the pallium (dorsal ventricular ridge and cortical areas) have an extracortical, subpallial origin. Our results suggest that the telencephalon of birds and mammals share developmental mechanisms for the origin and migration of their cortical interneurons, which probably first evolved at an earlier stage in the radiation of vertebrates than was thought before.

    View details for DOI 10.1006/dbio.2001.0422

    View details for PubMedID 11784017

  • Monofocal origin of telencephalic oligodendrocytes in the anterior entopeduncular area of the chick embryo. Development (Cambridge, England) Olivier, C., Cobos, I., Perez Villegas, E. M., Spassky, N., Zalc, B., Martinez, S., Thomas, J. L. 2001; 128 (10): 1757-69


    Oligodendrocytes are the myelin-forming cells in the central nervous system. In the brain, oligodendrocyte precursors arise in multiple restricted foci, distributed along the caudorostral axis of the ventricular neuroepithelium. In chick embryonic hind-, mid- and caudal forebrain, oligodendrocytes have a basoventral origin, while in the rostral fore-brain oligodendrocytes emerge from alar territories (Perez Villegas, E. M., Olivier, C., Spassky, N., Poncet, C., Cochard, P., Zalc, B., Thomas, J. L. and Martinez, S. (1999) Dev. Biol. 216, 98-113). To investigate the respective territories colonized by oligodendrocyte progenitor cells that originate from either the basoventral or alar foci, we have created a series of quail-chick chimeras. Homotopic chimeras demonstrate clearly that, during embryonic development, oligodendrocyte progenitors that emerge from the alar anterior entopeduncular area migrate tangentially to invade the entire telencephalon, whereas those from the basal rhombomeric foci show a restricted rostrocaudal distribution and colonize only their rhombomere of origin. Heterotopic chimeras indicate that differences in the migratory properties of oligodendroglial cells do not depend on their basoventral or alar ventricular origin. Irrespective of their origin (basal or alar), oligodendrocytes migrate only short distances in the hindbrain and long distances in the prosencephalon. Furthermore, we provide evidence that, in the developing chick brain, all telencephalic oligodendrocytes originate from the anterior entopeduncular area and that the prominent role of anterior entopeduncular area in telencephalic oligodendrogenesis is conserved between birds and mammals.

    View details for PubMedID 11311157

  • The early steps of oligodendrogenesis: insights from the study of the plp lineage in the brain of chicks and rodents. Developmental neuroscience Spassky, N., Olivier, C., Cobos, I., LeBras, B., Goujet-Zalc, C., Martínez, S., Zalc, B., Thomas, J. L. 2001; 23 (4-5): 318-26


    Oligodendrocytes are the myelin-forming cells of the central nervous system. Over the last decade, their development in the embryonic brain and spinal cord has been documented following the discovery of early oligodendroglial markers. These early expressed oligodendroglial genes nevertheless show differences in their spatiotemporal pattern of expression and it is not yet clear if their expression is linked in a linear way. This review highlights the common themes underlying the spatiotemporal aspects of oligodendrogenesis in chick and rodent brain and discusses some recent advances in the knowledge of the cell lineage expressing plp, one of the early oligodendroglial genes. We suggest a model of oligodendroglial commitment whereby definitive oligodendroglial progenitor formation is preceded by a primitive neuroglial progenitor stage and whereby different oligodendrocyte lineages might segregate from either plp-positive or plp-negative primitive progenitor cells.

    View details for DOI 10.1159/000048715

    View details for PubMedID 11756747

  • Spatiotemporal development of oligodendrocytes in the embryonic brain. Journal of neuroscience research Thomas, J. L., Spassky, N., Perez Villegas, E. M., Olivier, C., Cobos, I., Goujet-Zalc, C., Martínez, S., Zalc, B. 2000; 59 (4): 471-6


    In the central nervous system (CNS), oligodendrocytes have long been considered to be the last cell type to be generated during development. In rodents, the progenitor cells that give rise to oligodendrocytes have been reported to originate in the subventricular zone. Here, we review recent data demonstrating the existence of oligodendrocyte precursor cells in the ventricular layer of the neural tube that emerge prior to the progenitor stage. Oligodendrocyte precursors arise in restricted foci that are distributed along the rostrocaudal axis of the neural tube, for the most part ventrally. The generation of oligodendrocyte precursor cells occurs either simultaneously with, or follows closely upon the emergence of the first neurons. Experiments with quail-chick chimeras provide evidence that oligodendrocyte progenitors derived from ventricular precursors migrate either tangentially or radially to colonize extensive or segmentally restricted territories of the brain. The choice depends on their site of origin. Finally, we discuss the possibility that oligodendrocytes could be a mosaic population that originates from at least two types of precursor cells.

    View details for DOI 10.1002/(SICI)1097-4547(20000215)59:4<471::AID-JNR1>3.0.CO;2-3

    View details for PubMedID 10679785

  • FGF8 induces formation of an ectopic isthmic organizer and isthmocerebellar development via a repressive effect on Otx2 expression. Development (Cambridge, England) Martinez, S., Crossley, P. H., Cobos, I., Rubenstein, J. L., Martin, G. R. 1999; 126 (6): 1189-200


    Beads containing recombinant FGF8 (FGF8-beads) were implanted in the prospective caudal diencephalon or midbrain of chick embryos at stages 9-12. This induced the neuroepithelium rostral and caudal to the FGF8-bead to form two ectopic, mirror-image midbrains. Furthermore, cells in direct contact with the bead formed an outgrowth that protruded laterally from the neural tube. Tissue within such lateral outgrowths developed proximally into isthmic nuclei and distally into a cerebellum-like structure. These morphogenetic effects were apparently due to FGF8-mediated changes in gene expression in the vicinity of the bead, including a repressive effect on Otx2 and an inductive effect on En1, Fgf8 and Wnt1 expression. The ectopic Fgf8 and Wnt1 expression domains formed nearly complete concentric rings around the FGF8-bead, with the Wnt1 ring outermost. These observations suggest that FGF8 induces the formation of a ring-like ectopic signaling center (organizer) in the lateral wall of the brain, similar to the one that normally encircles the neural tube at the isthmic constriction, which is located at the boundary between the prospective midbrain and hindbrain. This ectopic isthmic organizer apparently sends long-range patterning signals both rostrally and caudally, resulting in the development of the two ectopic midbrains. Interestingly, our data suggest that these inductive signals spread readily in a caudal direction, but are inhibited from spreading rostrally across diencephalic neuromere boundaries. These results provide insights into the mechanism by which FGF8 induces an ectopic organizer and suggest that a negative feedback loop between Fgf8 and Otx2 plays a key role in patterning the midbrain and anterior hindbrain.

    View details for PubMedID 10021338

  • Calretinin in pretecto- and olivocerebellar projections in the chick: immunohistochemical and experimental study. The Journal of comparative neurology De Castro, F., Cobos, I., Puelles, L., Martinez, S. 1998; 397 (2): 149-62


    Calretinin (CaR) is a calcium-binding protein that is distributed extensively in the central nervous system. It is localized in the cell bodies and neurites of specific neuronal populations and serves, therefore, as a reliable anatomical marker. Some components of the pretectocerebellar projection, which connects specific pretectal nuclei to caudal cerebellar folia, are concerned with the cerebellar control of visual reflexes. We investigated the distribution of pretectocerebellar-projecting neurons in relation to cells that show CaR immunoreactivity. Cells that project to the cerebellar cortex in the diencephalic primary visual nuclei and in other grisea, like the nucleus spiriformis medialis and the nucleus dorsofrontalis, colocalized with those that appeared to be immunolabeled intensely with anti-CaR antiserum. To explore the hypothesis of a common developmental origin of these pretectal cerebellopetal neurons, we also investigated the development of CaR-immunopositive cells in the chick pretectum and the arrival of their fibers in the cerebellum, from 10 days of incubation (stage 36) to posthatching stages. Finally, we analyzed the source of CaR+ climbing fibers and found a subpopulation of CaR+ cells in the inferior olivary nucleus. On the whole, these results suggest that there is a common developmental origin of pretectal cerebellopetal neurons, some of which share the property of CaR expression. The functional significance of this correlation needs to be investigated.

    View details for PubMedID 9658281