Integrative functional genomic analysis of human brain development and neuropsychiatric risks
Open accessAbstract
INTRODUCTION: The brain is responsible for cognition, behavior, and much of what makes us uniquely human. The development of the brain is a highly complex process, and this process is reliant on precise regulation of molecular and cellular events grounded in the spatiotemporal regulation of the transcriptome. Disruption of this regulation can lead to neuropsychiatric disorders. RATIONALE: The regulatory, epigenomic, and transcriptomic features of the human brain have not been comprehensively compiled across time, regions, or cell types. Understanding the etiology of neuropsychiatric disorders requires knowledge not just of endpoint differences between healthy and diseased brains but also of the developmental and cellular contexts in which these differences arise. Moreover, an emerging body of research indicates that many aspects of the development and physiology of the human brain are not well recapitulated in model organisms, and therefore it is necessary that neuropsychiatric disorders be understood in the broader context of the developing and adult human brain. RESULTS: Here we describe the generation and analysis of a variety of genomic data modalities at the tissue and single-cell levels, including transcriptome, DNA methylation, and histone modifications across multiple brain regions ranging in age from embryonic development through adulthood. We observed a widespread transcriptomic transition beginning during late fetal development and consisting of sharply decreased regional differences. This reduction coincided with increases in the transcriptional signatures of mature neurons and the expression of genes associated with dendrite development, synapse development, and neuronal activity, all of which were temporally synchronous across neocortical areas, as well as myelination and oligodendrocytes, which were asynchronous. Moreover, genes including MEF2C , SATB2 , and TCF4 , with genetic associations to multiple brain-related traits and disorders, converged in a small number of modules exhibiting spatial or spatiotemporal specificity. CONCLUSION: We generated and applied our dataset to document transcriptomic and epigenetic changes across human development and then related those changes to major neuropsychiatric disorders. These data allowed us to identify genes, cell types, gene coexpression modules, and spatiotemporal loci where disease risk might converge, demonstrating the utility of the dataset and providing new insights into human development and disease. Spatiotemporal dynamics of human brain development and neuropsychiatric risks.: Human brain development begins during embryonic development and continues through adulthood (top). Integrating data modalities (bottom left) revealed age- and cell type–specific properties and global patterns of transcriptional dynamics, including a late fetal transition (bottom middle). We related the variation in gene expression (brown, high; purple, low) to regulatory elements in the fetal and adult brains, cell type–specific signatures, and genetic loci associated with neuropsychiatric disorders (bottom right; gray circles indicate enrichment for corresponding features among module genes). Relationships depicted in this panel do not correspond to specific observations. CBC, cerebellar cortex; STR, striatum; HIP, hippocampus; MD, mediodorsal nucleus of thalamus; AMY, amygdala.
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Integrative analyses demonstrate the usefulness of functional genomics for unraveling molecular mechanisms in the brain.
“In summary, our integrative analyses demonstrate the usefulness of functional genomics for unraveling molecular mechanisms in the brain (21, 61), and the results of these analyses suggest directions for further research into the etiology of brain disorders.”
From Comprehensive functional genomic resource and integrative model for the human brain (2018) · cites this paper as [61]
The higher structural similarity of NeuN− cells with adult brain than fetal brain is indicative of gliogenesis in the postnatal brain.
“We found that NeuN− cells showed higher structural similarity with the adult brain than the fetal brain, indicative of gliogenesis in the postnatal brain20.”
From Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders (2021) · cites this paper as [20]
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Self-citation
- Authors
- Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., Sousa, A. M. M., Werling, D. M., Kitchen, R. R., Kang, H. J., Pletikos, M., Choi, J., Muchnik, S., Xu, X., Wang, D., Lorente-Galdos, B., Liu, S., Giusti-Rodríguez, P., Won, H., de Leeuw, C. A., Pardiñas, A. F., BrainSpan Consortium, PsychENCODE Consortium, Subgroup, P. D., Hu, M., Jin, F., Li, Y., Owen, M. J., O’Donovan, M. C., Walters, J. T. R., Posthuma, D., Reimers, M. A., Levitt, P., Weinberger, D. R., Hyde, T. M., Kleinman, J. E., Geschwind, D. H., Hawrylycz, M. J., State, M. W., Sanders, S. J., Sullivan, P. F., Gerstein, M. B., Lein, E. S., Knowles, J. A., Sestan, N., Willsey, A. J., Oldre, A., Szafer, A., Camarena, A., Cherskov, A., Charney, A. W., Abyzov, A., Kozlenkov, A., Safi, A., Jones, A. R., Ashley-Koch, A. E., Ebbert, A., Price, A. J., Sekijima, A., Kefi, A., Bernard, A., Amiri, A., Sboner, A., Clark, A., Jaffe, A. E., Tebbenkamp, A. T. N., Sodt, A. J., Guillozet-Bongaarts, A. L., Nairn, A. C., Carey, A., Huttner, A., Chervenak, A., Szekely, A., Shieh, A. W., Harmanci, A., Lipska, B. K., Carlyle, B. C., Gregor, B. W., Kassim, B. S., Sheppard, B., Bichsel, C., Hahn, C.-G., Lee, C.-K., Chen, C., Kuan, C. L., Dang, C., Lau, C., Cuhaciyan, C., Armoskus, C., Mason, C. E., Liu, C., Slaughterbeck, C. R., Bennet, C., Pinto, D., Polioudakis, D., Franjic, D., Miller, D. J., Bertagnolli, D., Lewis, D. A., Feng, D., Sandman, D., Clarke, D., Williams, D., DelValle, D., Fitzgerald, D., Shen, E. H., Flatow, E., Zharovsky, E., Burke, E. E., Olson, E., Fulfs, E., Mattei, E., Hadjimichael, E., Deelman, E., Navarro, F. C. P., Wu, F., Lee, F., Cheng, F., Goes, F. S., Vaccarino, F. M., Liu, F., Hoffman, G. E., Gürsoy, G., Gee, G., Mehta, G., Coppola, G., Giase, G., Sedmak, G., Johnson, G. D., Wray, G. A., Crawford, G. E., Gu, G., van Bakel, H., Witt, H., Yoon, H. J., Pratt, H., Zhao, H., Glass, I. A., Huey, J., Arnold, J., Noonan, J. P., Bendl, J., Jochim, J. M., Goldy, J., Herstein, J., Wiseman, J. R., Miller, J. A., Mariani, J., Stoll, J., Moore, J., Szatkiewicz, J., Leng, J., Zhang, J., Parente, J., Rozowsky, J., Fullard, J. F., Hohmann, J. G., Morris, J., Phillips, J. W., Warrell, J., Shin, J. H., An, J.-Y., Belmont, J., Nyhus, J., Pendergraft, J., Bryois, J., Roll, K., Grennan, K. S., Aiona, K., White, K. P., Aldinger, K. A., Smith, K. A., Girdhar, K., Brouner, K., Mangravite, L. M., Brown, L., Collado-Torres, L., Cheng, L., Gourley, L., Song, L., Ubieta, L. D. L. T., Habegger, L., Ng, L., Hauberg, M. E., Onorati, M., Webster, M. J., Kundakovic, M., Skarica, M., Reimers, M., Johnson, M. B., Chen, M. M., Garrett, M. E., Sarreal, M., Reding, M., Gu, M., Peters, M. A., Fisher, M., Gandal, M. J., Purcaro, M., Smith, M., Brown, M., Shibata, M., Brown, M., Xu, M., Yang, M., Ray, M., Shapovalova, N. V., Francoeur, N., Sjoquist, N., Mastan, N., Kaur, N., Parikshak, N., Mosqueda, N. F., Ngo, N.-K., Dee, N., Ivanov, N. A., Devillers, O., Roussos, P., Parker, P. D., Manser, P., Wohnoutka, P., Farnham, P. J., Zandi, P., Emani, P. S., Dalley, R. A., Mayani, R., Tao, R., Gittin, R., Straub, R. E., Lifton, R. P., Jacobov, R., Howard, R. E., Park, R. B., Dai, R., Abramowicz, S., Akbarian, S., Schreiner, S., Ma, S., Parry, S. E., Shapouri, S., Weissman, S., Caldejon, S., Mane, S., Ding, S.-L., Scuderi, S., Dracheva, S., Butler, S., Lisgo, S. N., Rhie, S. K., Lindsay, S., Datta, S., Souaiaia, T., Roychowdhury, T., Gomez, T., Naluai-Cecchini, T., Beach, T. G., Goodman, T., Gao, T., Dolbeare, T. A., Fliss, T., Reddy, T. E., Chen, T., Hyde, T. M., Brunetti, T., Lemon, T. A., Desta, T., Borrman, T., Haroutunian, V., Spitsyna, V. N., Swarup, V., Shi, X., Jiang, Y., Xia, Y., Chen, Y.-H., Jiang, Y., Wang, Y., Chae, Y., Yang, Y. T., Kim, Y., Riley, Z. L., Krsnik, Z., Deng, Z., Weng, Z., Lin, Z., & Li, Z.
- Affiliations
- Yale University (US)
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA.
- SUNY Downstate Health Sciences University (US)
- Allen Institute for Brain Science (US)
- National Research Foundation of Korea (KR)
- University of California, San Francisco (US)
- Boston University (US)
- Stony Brook University (US)
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA.
- University of North Carolina at Chapel Hill (US)
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, Netherlands.
- Cardiff University (GB)
- Cleveland Clinic (US)
- University of Southern California (US)
- Lieber Institute for Brain Development (US)
- University of California, Los Angeles (US)
- Vrije Universiteit Amsterdam (NL)
- Case Western Reserve University (US)
- Michigan State University (US)
- Corresponding author
- Li, Mingfeng
- Santpere, Gabriel
- Evgrafov, Oleg V.
- Gulden, Forrest O.
- Pochareddy, Sirisha
- Sunkin, Susan M.
- Li, Zhen
- Shin, Yurae
- Gerstein, Mark B.
- Lein, Ed S.
- Knowles, James A.
- Li, Zhuo
- ORCID
- Li, Mingfeng
- Santpere, Gabriel
- Imamura Kawasawa, Yuka
- Evgrafov, Oleg V.
- Gulden, Forrest O.
- Pochareddy, Sirisha
- Sunkin, Susan M.
- Li, Zhen
- Shin, Yurae
- Zhu, Ying
- Sousa, André M. M.
- Werling, Donna M.
- Kitchen, Robert R.
- Kang, Hyo Jung
- Pletikos, Mihovil
- Choi, Jinmyung
- Muchnik, Sydney
- Xu, Xuming
- Wang, Daifeng
- Liu, Shuang
- Won, Hyejung
- Pardiñas, Antonio F.
- Hu, Ming
- Jin, Fulai
- Owen, Michael J.
- O’Donovan, Michael C.
- Walters, James T. R.
- Posthuma, Danielle
- Reimers, Mark A.
- Levitt, Pat
- Weinberger, Daniel R.
- Hyde, Thomas M.
- Kleinman, Joel E.
- Geschwind, Daniel H.
- Hawrylycz, Michael J.
- State, Matthew W.
- Sanders, Stephan J.
- Sullivan, Patrick F.
- Gerstein, Mark B.
- Lein, Ed S.
- Knowles, James A.
- Sestan, Nenad
- Willsey, A. Jeremy
- Oldre, Aaron
- Szafer, Aaron
- Camarena, Adrian
- Cherskov, Adriana
- Charney, Alexander W.
- Abyzov, Alexej
- Kozlenkov, Alexey
- Safi, Alexias
- Price, Amanda J.
- Kefi, Amira
- Bernard, Amy
- Amiri, Anahita
- Sboner, Andrea
- Jaffe, Andrew E.
- Tebbenkamp, Andrew T. N.
- Nairn, Angus C.
- Huttner, Anita
- Szekely, Anna
- Shieh, Annie W.
- Harmanci, Arif
- Carlyle, Becky C.
- Sheppard, Brooke
- Lee, Chang-Kyu
- Chen, Chao
- Mason, Christopher E.
- Liu, Chunyu
- Slaughterbeck, Cliff R.
- Pinto, Dalila
- Franjic, Daniel
- Miller, Daniel J.
- Bertagnolli, Darren
- Lewis, David A.
- Feng, David
- Clarke, Declan
- Fitzgerald, Dominic
- Zharovsky, Elizabeth
- Olson, Eric
- Mattei, Eugenio
- Hadjimichael, Evi
- Deelman, Ewa
- Wu, Feinan
- Lee, Felix
- Cheng, Feng
- Goes, Fernando S.
- Vaccarino, Flora M.
- Liu, Fuchen
- Hoffman, Gabriel E.
- Gürsoy, Gamze
- Coppola, Gianfilippo
- Giase, Gina
- Sedmak, Goran
- Johnson, Graham D.
- Wray, Gregory A.
- Crawford, Gregory E.
- Witt, Heather
- Pratt, Henry
- Zhao, Hongyu
- Glass, Ian A.
- Huey, Jack
- Noonan, James P.
- Bendl, Jaroslav
- Goldy, Jeff
- Wiseman, Jennifer R.
- Miller, Jeremy A.
- Mariani, Jessica
- Szatkiewicz, Jin
- Leng, Jing
- Zhang, Jing
- Rozowsky, Joel
- Fullard, John F.
- Hohmann, John G.
- Morris, John
- Phillips, John W.
- Warrell, Jonathan
- Shin, Joo Heon
- An, Joon-Yong
- Nyhus, Julie
- Pendergraft, Julie
- Bryois, Julien
- White, Kevin P.
- Aldinger, Kimberly A.
- Girdhar, Kiran
- Mangravite, Lara M.
- Cheng, Lijun
- Song, Lingyun
- Ng, Lydia
- Hauberg, Mads E.
- Onorati, Marco
- Webster, Maree J.
- Johnson, Matthew B.
- Chen, Maxine M.
- Reding, Melissa
- Gu, Mengting
- Peters, Mette A.
- Fisher, Michael
- Gandal, Michael J.
- Purcaro, Michael
- Brown, Miguel
- Shibata, Mikihito
- Xu, Min
- Yang, Mo
- Shapovalova, Nadiya V.
- Francoeur, Nancy
- Sjoquist, Nathan
- Mastan, Naveed
- Kaur, Navjot
- Parikshak, Neelroop
- Dee, Nick
- Ivanov, Nikolay A.
- Roussos, Panos
- Parker, Patrick D.
- Wohnoutka, Paul
- Farnham, Peggy J.
- Zandi, Peter
- Emani, Prashant S.
- Dalley, Rachel A.
- Mayani, Rajiv
- Tao, Ran
- Straub, Richard E.
- Lifton, Richard P.
- Park, Royce B.
- Dai, Rujia
- Akbarian, Schahram
- Schreiner, Shannon
- Ma, Shaojie
- Shapouri, Sheila
- Caldejon, Shiella
- Mane, Shrikant
- Ding, Song-Lin
- Scuderi, Soraya
- Dracheva, Stella
- Lisgo, Steven N.
- Rhie, Suhn Kyong
- Lindsay, Susan
- Souaiaia, Tade
- Roychowdhury, Tanmoy
- Gao, Tianliuyun
- Dolbeare, Tim A.
- Fliss, Tim
- Reddy, Timothy E.
- Chen, Ting
- Brunetti, Tonya
- Desta, Tsega
- Borrman, Tyler
- Haroutunian, Vahram
- Spitsyna, Valeria N.
- Swarup, Vivek
- Shi, Xu
- Jiang, Yan
- Xia, Yan
- Jiang, Yi
- Wang, Yongjun
- Yang, Yucheng T.
- Kim, Yunjung
- Riley, Zack L.
- Deng, Zemin
- Weng, Zhiping
- Lin, Zhixiang
- Li, Zhuo
- Venue
- Science
- Published
- 2018-12-14
- Volume
- 362
- Issue
- 6420
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC6413317
- OpenAlex
- W2904647285
- Cited by
- 810
- References
- 82
- Citations by year
- 2026: 83 · 2025: 89 · 2024: 120 · 2023: 110 · 2022: 117 · 2021: 110 · 2020: 102 · 2019: 68 · 2018: 8 · 2017: 1
- FWCI
- 46.77
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (acceptedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- CINECA IRIS Institutial research information system (University of Pisa) (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- VU Research Portal (submittedVersion, other-oa)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- Funders
- National Institute of Mental Health (MH103339, MH089929, MH106934)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Single-cell and spatial transcriptomics
- Keywords
- human brain development, neuropsychiatric disorders, transcriptome, DNA methylation, histone modifications, epigenomics, single-cell transcriptomics, spatiotemporal gene expression, neuronal maturation, myelination, oligodendrocytes, MEF2C, SATB2, TCF4, gene co-expression modules, disease risk
- MeSH terms
- Mental Disorders, Brain, Humans, Nervous System Diseases, Gene Expression Regulation, Developmental, Epigenesis, Genetic, Gene Regulatory Networks, Neurogenesis, Epigenomics, Single-Cell Analysis, Transcriptome
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Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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