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1. Single-cell genomics and regulatory networks for 388 human brains.

Author

Emani, Prashant, Liu, Jason, Clarke, Declan, Jensen, Matthew, Warrell, Jonathan, Gupta, Chirag, Meng, Ran, Lee, Che Yu, Xu, Siwei, Dursun, Cagatay, Lou, Shaoke, Chen, Yuhang, Chu, Zhiyuan, Galeev, Timur, Hwang, Ahyeon, Li, Yunyang, Ni, Pengyu, Zhou, Xiao, Bakken, Trygve, Bendl, Jaroslav, Bicks, Lucy, Chatterjee, Tanima, Cheng, Lijun, Cheng, Yuyan, Dai, Yi, Duan, Ziheng, Flaherty, Mary, Fullard, John, Gancz, Michael, Garrido-Martín, Diego, Gaynor-Gillett, Sophia, Grundman, Jennifer, Hawken, Natalie, Henry, Ella, Hoffman, Gabriel, Huang, Ao, Jiang, Yunzhe, Jin, Ting, Jorstad, Nikolas, Kawaguchi, Riki, Khullar, Saniya, Liu, Jianyin, Liu, Junhao, Liu, Shuang, Ma, Shaojie, Margolis, Michael, Mazariegos, Samantha, Moore, Jill, Moran, Jennifer, Nguyen, Eric, Phalke, Nishigandha, Pjanic, Milos, Pratt, Henry, Quintero, Diana, Rajagopalan, Ananya, Riesenmy, Tiernon, Shedd, Nicole, Shi, Manman, Spector, Megan, Terwilliger, Rosemarie, Travaglini, Kyle, Wamsley, Brie, Wang, Gaoyuan, Xia, Yan, Xiao, Shaohua, Yang, Andrew, Zheng, Suchen, Gandal, Michael, Lee, Donghoon, Lein, Ed, Roussos, Panos, Sestan, Nenad, Weng, Zhiping, White, Kevin, Won, Hyejung, Girgenti, Matthew, Zhang, Jing, Wang, Daifeng, Geschwind, Daniel, and Gerstein, Mark

Subjects
Humans, Aging, Brain, Cell Communication, Chromatin, Gene Regulatory Networks, Genomics, Mental Disorders, Prefrontal Cortex, Quantitative Trait Loci, Single-Cell Analysis
Abstract

Single-cell genomics is a powerful tool for studying heterogeneous tissues such as the brain. Yet little is understood about how genetic variants influence cell-level gene expression. Addressing this, we uniformly processed single-nuclei, multiomics datasets into a resource comprising >2.8 million nuclei from the prefrontal cortex across 388 individuals. For 28 cell types, we assessed population-level variation in expression and chromatin across gene families and drug targets. We identified >550,000 cell type-specific regulatory elements and >1.4 million single-cell expression quantitative trait loci, which we used to build cell-type regulatory and cell-to-cell communication networks. These networks manifest cellular changes in aging and neuropsychiatric disorders. We further constructed an integrative model accurately imputing single-cell expression and simulating perturbations; the model prioritized ~250 disease-risk genes and drug targets with associated cell types.

Published
2024

2. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain

Author

Wen, Cindy, Margolis, Michael, Dai, Rujia, Zhang, Pan, Przytycki, Pawel F, Vo, Daniel D, Bhattacharya, Arjun, Matoba, Nana, Tang, Miao, Jiao, Chuan, Kim, Minsoo, Tsai, Ellen, Hoh, Celine, Aygün, Nil, Walker, Rebecca L, Chatzinakos, Christos, Clarke, Declan, Pratt, Henry, Peters, Mette A, Gerstein, Mark, Daskalakis, Nikolaos P, Weng, Zhiping, Jaffe, Andrew E, Kleinman, Joel E, Hyde, Thomas M, Weinberger, Daniel R, Bray, Nicholas J, Sestan, Nenad, Geschwind, Daniel H, Roeder, Kathryn, Gusev, Alexander, Pasaniuc, Bogdan, Stein, Jason L, Love, Michael I, Pollard, Katherine S, Liu, Chunyu, Gandal, Michael J, Akbarian, Schahram, Abyzov, Alexej, Ahituv, Nadav, Arasappan, Dhivya, Almagro Armenteros, Jose Juan, Beliveau, Brian J, Bendl, Jaroslav, Berretta, Sabina, Bharadwaj, Rahul A, Bicks, Lucy, Brennand, Kristen, Capauto, Davide, Champagne, Frances A, Chatterjee, Tanima, Chatzinakos, Chris, Chen, Yuhang, Chen, H Isaac, Cheng, Yuyan, Cheng, Lijun, Chess, Andrew, Chien, Jo-fan, Chu, Zhiyuan, Clement, Ashley, Collado-Torres, Leonardo, Cooper, Gregory M, Crawford, Gregory E, Davila-Velderrain, Jose, Deep-Soboslay, Amy, Deng, Chengyu, DiPietro, Christopher P, Dracheva, Stella, Drusinsky, Shiron, Duan, Ziheng, Duong, Duc, Dursun, Cagatay, Eagles, Nicholas J, Edelstein, Jonathan, Emani, Prashant S, Fullard, John F, Galani, Kiki, Galeev, Timur, Gaynor, Sophia, Girdhar, Kiran, Goes, Fernando S, Greenleaf, William, Grundman, Jennifer, Guo, Hanmin, Guo, Qiuyu, Gupta, Chirag, Hadas, Yoav, Hallmayer, Joachim, Han, Xikun, Haroutunian, Vahram, Hawken, Natalie, He, Chuan, Henry, Ella, Hicks, Stephanie C, Ho, Marcus, Ho, Li-Lun, Hoffman, Gabriel E, Huang, Yiling, Huuki-Myers, Louise A, and Hwang, Ahyeon

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Biological Psychology, Psychology, Mental Illness, Mental Health, Human Genome, Neurosciences, Brain Disorders, Mental health, Humans, Alternative Splicing, Atlases as Topic, Autism Spectrum Disorder, Brain, Gene Expression Regulation, Developmental, Gene Regulatory Networks, Genome-Wide Association Study, Protein Isoforms, Quantitative Trait Loci, Schizophrenia, Transcriptome, Mental Disorders, PsychENCODE Consortium†, PsychENCODE Consortium, General Science & Technology
Abstract

Neuropsychiatric genome-wide association studies (GWASs), including those for autism spectrum disorder and schizophrenia, show strong enrichment for regulatory elements in the developing brain. However, prioritizing risk genes and mechanisms is challenging without a unified regulatory atlas. Across 672 diverse developing human brains, we identified 15,752 genes harboring gene, isoform, and/or splicing quantitative trait loci, mapping 3739 to cellular contexts. Gene expression heritability drops during development, likely reflecting both increasing cellular heterogeneity and the intrinsic properties of neuronal maturation. Isoform-level regulation, particularly in the second trimester, mediated the largest proportion of GWAS heritability. Through colocalization, we prioritized mechanisms for about 60% of GWAS loci across five disorders, exceeding adult brain findings. Finally, we contextualized results within gene and isoform coexpression networks, revealing the comprehensive landscape of transcriptome regulation in development and disease.

Published
2024

3. Massively parallel characterization of regulatory elements in the developing human cortex

Author

Deng, Chengyu, Whalen, Sean, Steyert, Marilyn, Ziffra, Ryan, Przytycki, Pawel F, Inoue, Fumitaka, Pereira, Daniela A, Capauto, Davide, Norton, Scott, Vaccarino, Flora M, Pollen, Alex A, Nowakowski, Tomasz J, Ahituv, Nadav, Pollard, Katherine S, Akbarian, Schahram, Abyzov, Alexej, Arasappan, Dhivya, Almagro Armenteros, Jose Juan, Beliveau, Brian J, Bendl, Jaroslav, Berretta, Sabina, Bharadwaj, Rahul A, Bhattacharya, Arjun, Bicks, Lucy, Brennand, Kristen, Champagne, Frances A, Chatterjee, Tanima, Chatzinakos, Chris, Chen, Yuhang, Chen, H Isaac, Cheng, Yuyan, Cheng, Lijun, Chess, Andrew, Chien, Jo-fan, Chu, Zhiyuan, Clarke, Declan, Clement, Ashley, Collado-Torres, Leonardo, Cooper, Gregory M, Crawford, Gregory E, Dai, Rujia, Daskalakis, Nikolaos P, Davila-Velderrain, Jose, Deep-Soboslay, Amy, DiPietro, Christopher P, Dracheva, Stella, Drusinsky, Shiron, Duan, Ziheng, Duong, Duc, Dursun, Cagatay, Eagles, Nicholas J, Edelstein, Jonathan, Emani, Prashant S, Fullard, John F, Galani, Kiki, Galeev, Timur, Gandal, Michael J, Gaynor, Sophia, Gerstein, Mark, Geschwind, Daniel H, Girdhar, Kiran, Goes, Fernando S, Greenleaf, William, Grundman, Jennifer, Guo, Hanmin, Guo, Qiuyu, Gupta, Chirag, Hadas, Yoav, Hallmayer, Joachim, Han, Xikun, Haroutunian, Vahram, Hawken, Natalie, He, Chuan, Henry, Ella, Hicks, Stephanie C, Ho, Marcus, Ho, Li-Lun, Hoffman, Gabriel E, Huang, Yiling, Huuki-Myers, Louise A, Hwang, Ahyeon, Hyde, Thomas M, Iatrou, Artemis, Jajoo, Aarti, Jensen, Matthew, Jiang, Lihua, Jin, Peng, Jin, Ting, Jops, Connor, Jourdon, Alexandre, Kawaguchi, Riki, Kellis, Manolis, Khullar, Saniya, Kleinman, Joel E, Kleopoulos, Steven P, and Kozlenkov, Alex

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Stem Cell Research - Embryonic - Human, Stem Cell Research, Human Genome, Genetics, Neurosciences, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Neurological, Humans, Cerebral Cortex, Chromatin, Deep Learning, Enhancer Elements, Genetic, Gene Expression Regulation, Developmental, Neurogenesis, Neurons, Organoids, Regulatory Sequences, Nucleic Acid, Promoter Regions, Genetic, Regulatory Elements, Transcriptional, PsychENCODE Consortium‡, PsychENCODE Consortium, General Science & Technology
Abstract

Nucleotide changes in gene regulatory elements are important determinants of neuronal development and diseases. Using massively parallel reporter assays in primary human cells from mid-gestation cortex and cerebral organoids, we interrogated the cis-regulatory activity of 102,767 open chromatin regions, including thousands of sequences with cell type-specific accessibility and variants associated with brain gene regulation. In primary cells, we identified 46,802 active enhancer sequences and 164 variants that alter enhancer activity. Activity was comparable in organoids and primary cells, suggesting that organoids provide an adequate model for the developing cortex. Using deep learning we decoded the sequence basis and upstream regulators of enhancer activity. This work establishes a comprehensive catalog of functional gene regulatory elements and variants in human neuronal development.

Published
2024

6. Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains.

Author

Demontis, Ditte, Walters, G, Athanasiadis, Georgios, Walters, Raymond, Therrien, Karen, Nielsen, Trine, Farajzadeh, Leila, Voloudakis, Georgios, Bendl, Jaroslav, Zeng, Biau, Zhang, Wen, Grove, Jakob, Als, Thomas, Duan, Jinjie, Satterstrom, F, Bybjerg-Grauholm, Jonas, Bækved-Hansen, Marie, Gudmundsson, Olafur, Magnusson, Sigurdur, Baldursson, Gisli, Davidsdottir, Katrin, Haraldsdottir, Gyda, Agerbo, Esben, Hoffman, Gabriel, Dalsgaard, Søren, Martin, Joanna, Ribasés, Marta, Boomsma, Dorret, Soler Artigas, Maria, Roth Mota, Nina, Howrigan, Daniel, Medland, Sarah, Zayats, Tetyana, Rajagopal, Veera, Nordentoft, Merete, Mors, Ole, Hougaard, David, Mortensen, Preben, Daly, Mark, Faraone, Stephen, Stefansson, Hreinn, Roussos, Panos, Franke, Barbara, Werge, Thomas, Neale, Benjamin, Stefansson, Kari, and Børglum, Anders

Subjects
Humans, Genome-Wide Association Study, Attention Deficit Disorder with Hyperactivity, Brain, Cognition, Genetic Predisposition to Disease
Abstract

Attention-deficit hyperactivity disorder (ADHD) is a prevalent neurodevelopmental disorder with a major genetic component. Here, we present a genome-wide association study meta-analysis of ADHD comprising 38,691 individuals with ADHD and 186,843 controls. We identified 27 genome-wide significant loci, highlighting 76 potential risk genes enriched among genes expressed particularly in early brain development. Overall, ADHD genetic risk was associated with several brain-specific neuronal subtypes and midbrain dopaminergic neurons. In exome-sequencing data from 17,896 individuals, we identified an increased load of rare protein-truncating variants in ADHD for a set of risk genes enriched with probable causal common variants, potentially implicating SORCS3 in ADHD by both common and rare variants. Bivariate Gaussian mixture modeling estimated that 84-98% of ADHD-influencing variants are shared with other psychiatric disorders. In addition, common-variant ADHD risk was associated with impaired complex cognition such as verbal reasoning and a range of executive functions, including attention.

Published
2023

11. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae

Author

Thompson, Ryan C., Simons, Nicole W., Wilkins, Lillian, Cheng, Esther, Del Valle, Diane Marie, Hoffman, Gabriel E., Cervia, Carlo, Fennessy, Brian, Mouskas, Konstantinos, Francoeur, Nancy J., Johnson, Jessica S., Lepow, Lauren, Le Berichel, Jessica, Chang, Christie, Beckmann, Aviva G., Wang, Ying-chih, Nie, Kai, Zaki, Nicholas, Tuballes, Kevin, Barcessat, Vanessa, Cedillo, Mario A., Yuan, Dan, Huckins, Laura, Roussos, Panos, Marron, Thomas U., Glicksberg, Benjamin S., Nadkarni, Girish, Heath, James R., Gonzalez-Kozlova, Edgar, Boyman, Onur, Kim-Schulze, Seunghee, Sebra, Robert, Merad, Miriam, Gnjatic, Sacha, Schadt, Eric E., Charney, Alexander W., and Beckmann, Noam D.

Published
2023
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13. Analysis of Genetically Regulated Gene Expression Identifies a Prefrontal PTSD Gene, SNRNP35, Specific to Military Cohorts

Author

Huckins, Laura M, Chatzinakos, Chris, Breen, Michael S, Hartmann, Jakob, Klengel, Torsten, da Silva Almeida, Ana C, Dobbyn, Amanda, Girdhar, Kiran, Hoffman, Gabriel E, Klengel, Claudia, Logue, Mark W, Lori, Adriana, Maihofer, Adam X, Morrison, Filomene G, Nguyen, Hoang T, Park, Yongjin, Ruderfer, Douglas, Sloofman, Laura G, van Rooij, Sanne JH, Consortium, PTSD Working Group of Psychiatric Genomics, Baker, Dewleen G, Chen, Chia-Yen, Cox, Nancy, Duncan, Laramie E, Geyer, Mark A, Glatt, Stephen J, Im, Hae Kyung, Risbrough, Victoria B, Smoller, Jordan W, Stein, Dan J, Yehuda, Rachel, Liberzon, Israel, Koenen, Karestan C, Jovanovic, Tanja, Kellis, Manolis, Miller, Mark W, Bacanu, Silviu-Alin, Nievergelt, Caroline M, Buxbaum, Joseph D, Sklar, Pamela, Ressler, Kerry J, Stahl, Eli A, and Daskalakis, Nikolaos P

Subjects
Genetics, Brain Disorders, Post-Traumatic Stress Disorder (PTSD), Mental Health, Neurosciences, 1.1 Normal biological development and functioning, Underpinning research, Neurological, Animals, Case-Control Studies, Cohort Studies, Dexamethasone, Down-Regulation, Gene Expression Regulation, Gene Regulatory Networks, Genetic Predisposition to Disease, Humans, Leukocytes, Male, Mice, Mice, Inbred C57BL, Military Personnel, Prefrontal Cortex, RNA Interference, RNA, Small Interfering, Repressor Proteins, Ribonucleoproteins, Small Nuclear, Stress Disorders, Post-Traumatic, PTSD Working Group of Psychiatric Genomics Consortium, GWAS, PTSD, blood, civilian, glucocorticoid, military, prefrontal cortex, sex, splicing, transcriptomic imputation, genetics, Transcriptomic Imputation, trauma, Biochemistry and Cell Biology, Medical Physiology
Abstract

To reveal post-traumatic stress disorder (PTSD) genetic risk influences on tissue-specific gene expression, we use brain and non-brain transcriptomic imputation. We impute genetically regulated gene expression (GReX) in 29,539 PTSD cases and 166,145 controls from 70 ancestry-specific cohorts and identify 18 significant GReX-PTSD associations corresponding to specific tissue-gene pairs. The results suggest substantial genetic heterogeneity based on ancestry, cohort type (military versus civilian), and sex. Two study-wide significant PTSD associations are identified in European and military European cohorts; ZNF140 is predicted to be upregulated in whole blood, and SNRNP35 is predicted to be downregulated in dorsolateral prefrontal cortex, respectively. In peripheral leukocytes from 175 marines, the observed PTSD differential gene expression correlates with the predicted differences for these individuals, and deployment stress produces glucocorticoid-regulated expression changes that include downregulation of both ZNF140 and SNRNP35. SNRNP35 knockdown in cells validates its functional role in U12-intron splicing. Finally, exogenous glucocorticoids in mice downregulate prefrontal Snrnp35 expression.

Published
2020

14. Identification of shared and differentiating genetic architecture for autism spectrum disorder, attention-deficit hyperactivity disorder and case subgroups

Author

Mattheisen, Manuel, Grove, Jakob, Als, Thomas D., Martin, Joanna, Voloudakis, Georgios, Meier, Sandra, Demontis, Ditte, Bendl, Jaroslav, Walters, Raymond, Carey, Caitlin E., Rosengren, Anders, Strom, Nora I., Hauberg, Mads Engel, Zeng, Biao, Hoffman, Gabriel, Zhang, Wen, Bybjerg-Grauholm, Jonas, Bækvad-Hansen, Marie, Agerbo, Esben, Cormand, Bru, Nordentoft, Merete, Werge, Thomas, Mors, Ole, Hougaard, David M., Buxbaum, Joseph D., Faraone, Stephen V., Franke, Barbara, Dalsgaard, Søren, Mortensen, Preben B., Robinson, Elise B., Roussos, Panos, Neale, Benjamin M., Daly, Mark J., and Børglum, Anders D.

Published
2022
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16. The three-dimensional landscape of cortical chromatin accessibility in Alzheimer’s disease

Author

Bendl, Jaroslav, Hauberg, Mads E., Girdhar, Kiran, Im, Eunju, Vicari, James M., Rahman, Samir, Fernando, Michael B., Townsley, Kayla G., Dong, Pengfei, Misir, Ruth, Kleopoulos, Steven P., Reach, Sarah M., Apontes, Pasha, Zeng, Biao, Zhang, Wen, Voloudakis, Georgios, Brennand, Kristen J., Nixon, Ralph A., Haroutunian, Vahram, Hoffman, Gabriel E., Fullard, John F., and Roussos, Panos

Published
2022
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18. Genetic regulation of cell type–specific chromatin accessibility shapes brain disease etiology

Author

Zeng, Biao, primary, Bendl, Jaroslav, additional, Deng, Chengyu, additional, Lee, Donghoon, additional, Misir, Ruth, additional, Reach, Sarah M., additional, Kleopoulos, Steven P., additional, Auluck, Pavan, additional, Marenco, Stefano, additional, Lewis, David A., additional, Haroutunian, Vahram, additional, Ahituv, Nadav, additional, Fullard, John F., additional, Hoffman, Gabriel E., additional, and Roussos, Panos, additional

Published
2024
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19. Transcriptomic sex differences in postmortem brain samples from patients with psychiatric disorders

Author

Xia, Yan, primary, Xia, Cuihua, additional, Jiang, Yi, additional, Chen, Yu, additional, Zhou, Jiaqi, additional, Dai, Rujia, additional, Han, Cong, additional, Mao, Zhongzheng, additional, Consortium, PsychENCODE, additional, Liu, Chunyu, additional, Chen, Chao, additional, Akbarian, Schahram, additional, Abyzov, Alexej, additional, Ahituv, Nadav, additional, Arasappan, Dhivya, additional, Almagro Armenteros, Jose Juan, additional, Beliveau, Brian J., additional, Bendl, Jaroslav, additional, Berretta, Sabina, additional, Bharadwaj, Rahul A., additional, Bhattacharya, Arjun, additional, Bicks, Lucy, additional, Brennand, Kristen, additional, Capauto, Davide, additional, Champagne, Frances A., additional, Chatterjee, Tanima, additional, Chatzinakos, Chris, additional, Chen, Yuhang, additional, Chen, H. Isaac, additional, Cheng, Yuyan, additional, Cheng, Lijun, additional, Chess, Andrew, additional, Chien, Jo-fan, additional, Chu, Zhiyuan, additional, Clarke, Declan, additional, Clement, Ashley, additional, Collado-Torres, Leonardo, additional, Cooper, Gregory M., additional, Crawford, Gregory E., additional, Daskalakis, Nikolaos P., additional, Davila-Velderrain, Jose, additional, Deep-Soboslay, Amy, additional, Deng, Chengyu, additional, DiPietro, Christopher P., additional, Dracheva, Stella, additional, Drusinsky, Shiron, additional, Duan, Ziheng, additional, Duong, Duc, additional, Dursun, Cagatay, additional, Eagles, Nicholas J., additional, Edelstein, Jonathan, additional, Emani, Prashant S., additional, Fullard, John F., additional, Galani, Kiki, additional, Galeev, Timur, additional, Gandal, Michael J., additional, Gaynor, Sophia, additional, Gerstein, Mark, additional, Geschwind, Daniel H., additional, Girdhar, Kiran, additional, Goes, Fernando S., additional, Greenleaf, William, additional, Grundman, Jennifer, additional, Guo, Hanmin, additional, Guo, Qiuyu, additional, Gupta, Chirag, additional, Hadas, Yoav, additional, Hallmayer, Joachim, additional, Han, Xikun, additional, Haroutunian, Vahram, additional, Hawken, Natalie, additional, He, Chuan, additional, Henry, Ella, additional, Hicks, Stephanie C., additional, Ho, Marcus, additional, Ho, Li-Lun, additional, Hoffman, Gabriel E., additional, Huang, Yiling, additional, Huuki-Myers, Louise A., additional, Hwang, Ahyeon, additional, Hyde, Thomas M., additional, Iatrou, Artemis, additional, Inoue, Fumitaka, additional, Jajoo, Aarti, additional, Jensen, Matthew, additional, Jiang, Lihua, additional, Jin, Peng, additional, Jin, Ting, additional, Jops, Connor, additional, Jourdon, Alexandre, additional, Kawaguchi, Riki, additional, Kellis, Manolis, additional, Khullar, Saniya, additional, Kleinman, Joel E., additional, Kleopoulos, Steven P., additional, Kozlenkov, Alex, additional, Kriegstein, Arnold, additional, Kundaje, Anshul, additional, Kundu, Soumya, additional, Lee, Cheyu, additional, Lee, Donghoon, additional, Li, Junhao, additional, Li, Mingfeng, additional, Lin, Xiao, additional, Liu, Shuang, additional, Liu, Jason, additional, Liu, Jianyin, additional, Lou, Shaoke, additional, Loupe, Jacob M., additional, Lu, Dan, additional, Ma, Shaojie, additional, Ma, Liang, additional, Margolis, Michael, additional, Mariani, Jessica, additional, Martinowich, Keri, additional, Maynard, Kristen R., additional, Mazariegos, Samantha, additional, Meng, Ran, additional, Myers, Richard M., additional, Micallef, Courtney, additional, Mikhailova, Tatiana, additional, Ming, Guo-li, additional, Mohammadi, Shahin, additional, Monte, Emma, additional, Montgomery, Kelsey S., additional, Moore, Jill E., additional, Moran, Jennifer R., additional, Mukamel, Eran A., additional, Nairn, Angus C., additional, Nemeroff, Charles B., additional, Ni, Pengyu, additional, Norton, Scott, additional, Nowakowski, Tomasz, additional, Omberg, Larsson, additional, Page, Stephanie C., additional, Park, Saejeong, additional, Patowary, Ashok, additional, Pattni, Reenal, additional, Pertea, Geo, additional, Peters, Mette A., additional, Phalke, Nishigandha, additional, Pinto, Dalila, additional, Pjanic, Milos, additional, Pochareddy, Sirisha, additional, Pollard, Katherine S., additional, Pollen, Alex, additional, Pratt, Henry, additional, Przytycki, Pawel F., additional, Purmann, Carolin, additional, Qin, Zhaohui S., additional, Qu, Ping-Ping, additional, Quintero, Diana, additional, Raj, Towfique, additional, Rajagopalan, Ananya S., additional, Reach, Sarah, additional, Reimonn, Thomas, additional, Ressler, Kerry J., additional, Ross, Deanna, additional, Roussos, Panos, additional, Rozowsky, Joel, additional, Ruth, Misir, additional, Ruzicka, W. Brad, additional, Sanders, Stephan J., additional, Schneider, Juliane M., additional, Scuderi, Soraya, additional, Sebra, Robert, additional, Sestan, Nenad, additional, Seyfried, Nicholas, additional, Shao, Zhiping, additional, Shedd, Nicole, additional, Shieh, Annie W., additional, Shin, Joo Heon, additional, Skarica, Mario, additional, Snijders, Clara, additional, Song, Hongjun, additional, State, Matthew W., additional, Stein, Jason, additional, Steyert, Marilyn, additional, Subburaju, Sivan, additional, Sudhof, Thomas, additional, Snyder, Michael, additional, Tao, Ran, additional, Therrien, Karen, additional, Tsai, Li-Huei, additional, Urban, Alexander E., additional, Vaccarino, Flora M., additional, van Bake, Harm, additional, Vo, Daniel, additional, Voloudakis, Georgios, additional, Wamsley, Brie, additional, Wang, Tao, additional, Wang, Sidney H., additional, Wang, Daifeng, additional, Wang, Yifan, additional, Warrell, Jonathan, additional, Wei, Yu, additional, Weimer, Annika K., additional, Weinberger, Daniel R., additional, Wen, Cindy, additional, Weng, Zhiping, additional, Whalen, Sean, additional, White, Kevin P., additional, Willsey, A. Jeremy, additional, Won, Hyejung, additional, Wong, Wing, additional, Wu, Hao, additional, Wu, Feinan, additional, Wuchty, Stefan, additional, Wylie, Dennis, additional, Xu, Siwei, additional, Yap, Chloe X., additional, Zeng, Biao, additional, Zhang, Pan, additional, Zhang, Chunling, additional, Zhang, Bin, additional, Zhang, Jing, additional, Zhang, Yanqiong, additional, Zhou, Xiao, additional, Ziffra, Ryan, additional, Zeier, Zane R., additional, and Zintel, Trisha M., additional

Published
2024
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20. Publisher Correction: Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

Author

Huckins, Laura M, Dobbyn, Amanda, Ruderfer, Douglas M, Hoffman, Gabriel, Wang, Weiqing, Pardiñas, Antonio F, Rajagopal, Veera M, Als, Thomas D, T. Nguyen, Hoang, Girdhar, Kiran, Boocock, James, Roussos, Panos, Fromer, Menachem, Kramer, Robin, Domenici, Enrico, Gamazon, Eric R, Purcell, Shaun, Demontis, Ditte, Børglum, Anders D, Walters, James TR, O’Donovan, Michael C, Sullivan, Patrick, Owen, Michael J, Devlin, Bernie, Sieberts, Solveig K, Cox, Nancy J, Im, Hae Kyung, Sklar, Pamela, and Stahl, Eli A

Subjects
Genetics, Neurosciences, Human Genome, Serious Mental Illness, Schizophrenia, Brain Disorders, Mental Health, Biotechnology, Mental health, CommonMind Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, iPSYCH-GEMS Schizophrenia Working Group, Biological Sciences, Medical and Health Sciences, Developmental Biology
Abstract

In the HTML version of the article originally published, the author group 'The Schizophrenia Working Group of the Psychiatric Genomics Consortium' was displayed incorrectly. The error has been corrected in the HTML version of the article.

Published
2019

21. Gene expression imputation across multiple brain regions provides insights into schizophrenia risk

Author

Huckins, Laura M, Dobbyn, Amanda, Ruderfer, Douglas M, Hoffman, Gabriel, Wang, Weiqing, Pardiñas, Antonio F, Rajagopal, Veera M, Als, Thomas D, T. Nguyen, Hoang, Girdhar, Kiran, Boocock, James, Roussos, Panos, Fromer, Menachem, Kramer, Robin, Domenici, Enrico, Gamazon, Eric R, Purcell, Shaun, Demontis, Ditte, Børglum, Anders D, Walters, James TR, O’Donovan, Michael C, Sullivan, Patrick, Owen, Michael J, Devlin, Bernie, Sieberts, Solveig K, Cox, Nancy J, Im, Hae Kyung, Sklar, Pamela, and Stahl, Eli A

Subjects
Biological Sciences, Genetics, Mental Health, Brain Disorders, Human Genome, Schizophrenia, 2.1 Biological and endogenous factors, Aetiology, Mental health, Brain, Case-Control Studies, Gene Expression, Genetic Predisposition to Disease, Genome-Wide Association Study, Genotype, Humans, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Risk, Transcriptome, CommonMind Consortium, Schizophrenia Working Group of the Psychiatric Genomics Consortium, iPSYCH-GEMS Schizophrenia Working Group, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Transcriptomic imputation approaches combine eQTL reference panels with large-scale genotype data in order to test associations between disease and gene expression. These genic associations could elucidate signals in complex genome-wide association study (GWAS) loci and may disentangle the role of different tissues in disease development. We used the largest eQTL reference panel for the dorso-lateral prefrontal cortex (DLPFC) to create a set of gene expression predictors and demonstrate their utility. We applied DLPFC and 12 GTEx-brain predictors to 40,299 schizophrenia cases and 65,264 matched controls for a large transcriptomic imputation study of schizophrenia. We identified 413 genic associations across 13 brain regions. Stepwise conditioning identified 67 non-MHC genes, of which 14 did not fall within previous GWAS loci. We identified 36 significantly enriched pathways, including hexosaminidase-A deficiency, and multiple porphyric disorder pathways. We investigated developmental expression patterns among the 67 non-MHC genes and identified specific groups of pre- and postnatal expression.

Published
2019

22. Transcriptome and epigenome landscape of human cortical development modeled in organoids

Author

Amiri, Anahita, Coppola, Gianfilippo, Scuderi, Soraya, Wu, Feinan, Roychowdhury, Tanmoy, Liu, Fuchen, Pochareddy, Sirisha, Shin, Yurae, Safi, Alexias, Song, Lingyun, Zhu, Ying, Sousa, André MM, Gerstein, Mark, Crawford, Gregory E, Sestan, Nenad, Abyzov, Alexej, Vaccarino, Flora M, Akbarian, Schahram, An, Joon-Yong, Armoskus, Christoper, Ashley-Koch, Allison E, Beach, Thomas G, Belmont, Judson, Bendl, Jaroslav, Borrman, Tyler, Brown, Leanne, Brown, Miguel, Brown, Mimi, Brunetti, Tonya, Bryois, Julien, Burke, Emily E, Camarena, Adrian, Carlyle, Becky C, Chae, Yooree, Charney, Alexander W, Chen, Chao, Cheng, Lijun, Cherskov, Adriana, Choi, Jinmyung, Clarke, Declan, Collado-Torres, Leonardo, Dai, Rujia, De La Torre Ubieta, Luis, DelValle, Diane, Devillers, Olivia, Dracheva, Stella, Emani, Prashant S, Evgrafov, Oleg V, Farnham, Peggy J, Fitzgerald, Dominic, Flatow, Elie, Francoeur, Nancy, Fullard, John F, Gandal, Michael J, Gao, Tianliuyun, Garrett, Melanie E, Geschwind, Daniel H, Giase, Gina, Girdhar, Kiran, Giusti-Rodriguez, Paola, Goes, Fernando S, Goodman, Thomas, Grennan, Kay S, Gu, Mengting, Gürsoy, Gamze, Hadjimichael, Evi, Hahn, Chang-Gyu, Haroutunian, Vahram, Hauberg, Mads E, Hoffman, Gabriel E, Huey, Jack, Hyde, Thomas M, Ivanov, Nikolay A, Jacobov, Rivka, Jaffe, Andrew E, Jiang, Yan, Jiang, Yi, Johnson, Graham D, Kassim, Bibi S, Kefi, Amira, Kim, Yunjung, Kitchen, Robert R, Kleiman, Joel E, Knowles, James A, Kozlenkov, Alexey, Li, Mingfeng, Li, Zhen, Lipska, Barbara K, Liu, Chunyu, Liu, Shuang, Mangravite, Lara M, Mariani, Jessica, Mattei, Eugenio, Miller, Daniel J, Moore, Jill, Nairn, Angus C, Navarro, Fabio CP, Park, Royce B, Peters, Mette A, and Pinto, Dalila

Subjects
Stem Cell Research - Nonembryonic - Human, Stem Cell Research - Embryonic - Human, Stem Cell Research - Induced Pluripotent Stem Cell - Human, Stem Cell Research, Genetics, Stem Cell Research - Induced Pluripotent Stem Cell, Human Genome, Intellectual and Developmental Disabilities (IDD), Autism, Brain Disorders, Biotechnology, Clinical Research, Mental Health, Pediatric, Neurosciences, 2.1 Biological and endogenous factors, Underpinning research, Aetiology, 1.1 Normal biological development and functioning, Neurological, Cerebral Cortex, Enhancer Elements, Genetic, Epigenesis, Genetic, Gene Expression Regulation, Developmental, Humans, Induced Pluripotent Stem Cells, Models, Neurological, Neurogenesis, Organoids, Transcriptome, PsychENCODE Consortium, General Science & Technology
Abstract

Genes implicated in neuropsychiatric disorders are active in human fetal brain, yet difficult to study in a longitudinal fashion. We demonstrate that organoids from human pluripotent cells model cerebral cortical development on the molecular level before 16 weeks postconception. A multiomics analysis revealed differentially active genes and enhancers, with the greatest changes occurring at the transition from stem cells to progenitors. Networks of converging gene and enhancer modules were assembled into six and four global patterns of expression and activity across time. A pattern with progressive down-regulation was enriched with human-gained enhancers, suggesting their importance in early human brain development. A few convergent gene and enhancer modules were enriched in autism-associated genes and genomic variants in autistic children. The organoid model helps identify functional elements that may drive disease onset.

Published
2018

23. Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk

Author

Rajarajan, Prashanth, Borrman, Tyler, Liao, Will, Schrode, Nadine, Flaherty, Erin, Casiño, Charlize, Powell, Samuel, Yashaswini, Chittampalli, LaMarca, Elizabeth A, Kassim, Bibi, Javidfar, Behnam, Espeso-Gil, Sergio, Li, Aiqun, Won, Hyejung, Geschwind, Daniel H, Ho, Seok-Man, MacDonald, Matthew, Hoffman, Gabriel E, Roussos, Panos, Zhang, Bin, Hahn, Chang-Gyu, Weng, Zhiping, Brennand, Kristen J, and Akbarian, Schahram

Subjects
Human Genome, Prevention, Brain Disorders, Neurosciences, Schizophrenia, Stem Cell Research, Genetics, Mental Health, Underpinning research, 2.1 Biological and endogenous factors, Aetiology, 1.1 Normal biological development and functioning, Neurological, Mental health, Brain, Cells, Cultured, Chromatin, Chromatin Assembly and Disassembly, Chromosomes, Human, Connectome, Epigenesis, Genetic, Gene Expression Regulation, Developmental, Genetic Predisposition to Disease, Genome, Human, Genome-Wide Association Study, Humans, Male, Neural Stem Cells, Neurogenesis, Neuroglia, Neurons, Nucleic Acid Conformation, Protein Interaction Maps, Proteomics, Risk, Transcription, Genetic, Transcriptome, General Science & Technology
Abstract

To explore the developmental reorganization of the three-dimensional genome of the brain in the context of neuropsychiatric disease, we monitored chromosomal conformations in differentiating neural progenitor cells. Neuronal and glial differentiation was associated with widespread developmental remodeling of the chromosomal contact map and included interactions anchored in common variant sequences that confer heritable risk for schizophrenia. We describe cell type-specific chromosomal connectomes composed of schizophrenia risk variants and their distal targets, which altogether show enrichment for genes that regulate neuronal connectivity and chromatin remodeling, and evidence for coordinated transcriptional regulation and proteomic interaction of the participating genes. Developmentally regulated chromosomal conformation changes at schizophrenia-relevant sequences disproportionally occurred in neurons, highlighting the existence of cell type-specific disease risk vulnerabilities in spatial genome organization.

Published
2018

24. Comprehensive functional genomic resource and integrative model for the human brain

Author

Wang, Daifeng, Liu, Shuang, Warrell, Jonathan, Won, Hyejung, Shi, Xu, Navarro, Fabio CP, Clarke, Declan, Gu, Mengting, Emani, Prashant, Yang, Yucheng T, Xu, Min, Gandal, Michael J, Lou, Shaoke, Zhang, Jing, Park, Jonathan J, Yan, Chengfei, Rhie, Suhn Kyong, Manakongtreecheep, Kasidet, Zhou, Holly, Nathan, Aparna, Peters, Mette, Mattei, Eugenio, Fitzgerald, Dominic, Brunetti, Tonya, Moore, Jill, Jiang, Yan, Girdhar, Kiran, Hoffman, Gabriel E, Kalayci, Selim, Gümüş, Zeynep H, Crawford, Gregory E, Roussos, Panos, Akbarian, Schahram, Jaffe, Andrew E, White, Kevin P, Weng, Zhiping, Sestan, Nenad, Geschwind, Daniel H, Knowles, James A, Gerstein, Mark B, Ashley-Koch, Allison E, Garrett, Melanie E, Song, Lingyun, Safi, Alexias, Johnson, Graham D, Wray, Gregory A, Reddy, Timothy E, Goes, Fernando S, Zandi, Peter, Bryois, Julien, Price, Amanda J, Ivanov, Nikolay A, Collado-Torres, Leonardo, Hyde, Thomas M, Burke, Emily E, Kleiman, Joel E, Tao, Ran, Shin, Joo Heon, Kundakovic, Marija, Brown, Leanne, Kassim, Bibi S, Park, Royce B, Wiseman, Jennifer R, Zharovsky, Elizabeth, Jacobov, Rivka, Devillers, Olivia, Flatow, Elie, Lipska, Barbara K, Lewis, David A, Haroutunian, Vahram, Hahn, Chang-Gyu, Charney, Alexander W, Dracheva, Stella, Kozlenkov, Alexey, Belmont, Judson, DelValle, Diane, Francoeur, Nancy, Hadjimichael, Evi, Pinto, Dalila, van Bakel, Harm, Fullard, John F, Bendl, Jaroslav, Hauberg, Mads E, Mangravite, Lara M, Peters, Mette A, Chae, Yooree, Peng, Junmin, Niu, Mingming, Wang, Xusheng, Webster, Maree J, Beach, Thomas G, Chen, Chao, and Jiang, Yi

Subjects
Human Genome, Biotechnology, Schizophrenia, Mental Health, Brain Disorders, Genetics, Neurosciences, 1.1 Normal biological development and functioning, 2.1 Biological and endogenous factors, Underpinning research, Aetiology, Mental health, Brain, Datasets as Topic, Deep Learning, Enhancer Elements, Genetic, Epigenesis, Genetic, Epigenomics, Gene Expression Regulation, Gene Regulatory Networks, Genome-Wide Association Study, Humans, Mental Disorders, Quantitative Trait Loci, Single-Cell Analysis, Transcriptome, PsychENCODE Consortium, General Science & Technology
Abstract

Despite progress in defining genetic risk for psychiatric disorders, their molecular mechanisms remain elusive. Addressing this, the PsychENCODE Consortium has generated a comprehensive online resource for the adult brain across 1866 individuals. The PsychENCODE resource contains ~79,000 brain-active enhancers, sets of Hi-C linkages, and topologically associating domains; single-cell expression profiles for many cell types; expression quantitative-trait loci (QTLs); and further QTLs associated with chromatin, splicing, and cell-type proportions. Integration shows that varying cell-type proportions largely account for the cross-population variation in expression (with >88% reconstruction accuracy). It also allows building of a gene regulatory network, linking genome-wide association study variants to genes (e.g., 321 for schizophrenia). We embed this network into an interpretable deep-learning model, which improves disease prediction by ~6-fold versus polygenic risk scores and identifies key genes and pathways in psychiatric disorders.

Published
2018

25. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

Author

Gandal, Michael J, Zhang, Pan, Hadjimichael, Evi, Walker, Rebecca L, Chen, Chao, Liu, Shuang, Won, Hyejung, van Bakel, Harm, Varghese, Merina, Wang, Yongjun, Shieh, Annie W, Haney, Jillian, Parhami, Sepideh, Belmont, Judson, Kim, Minsoo, Moran Losada, Patricia, Khan, Zenab, Mleczko, Justyna, Xia, Yan, Dai, Rujia, Wang, Daifeng, Yang, Yucheng T, Xu, Min, Fish, Kenneth, Hof, Patrick R, Warrell, Jonathan, Fitzgerald, Dominic, White, Kevin, Jaffe, Andrew E, Peters, Mette A, Gerstein, Mark, Liu, Chunyu, Iakoucheva, Lilia M, Pinto, Dalila, Geschwind, Daniel H, Ashley-Koch, Allison E, Crawford, Gregory E, Garrett, Melanie E, Song, Lingyun, Safi, Alexias, Johnson, Graham D, Wray, Gregory A, Reddy, Timothy E, Goes, Fernando S, Zandi, Peter, Bryois, Julien, Price, Amanda J, Ivanov, Nikolay A, Collado-Torres, Leonardo, Hyde, Thomas M, Burke, Emily E, Kleiman, Joel E, Tao, Ran, Shin, Joo Heon, Akbarian, Schahram, Girdhar, Kiran, Jiang, Yan, Kundakovic, Marija, Brown, Leanne, Kassim, Bibi S, Park, Royce B, Wiseman, Jennifer R, Zharovsky, Elizabeth, Jacobov, Rivka, Devillers, Olivia, Flatow, Elie, Hoffman, Gabriel E, Lipska, Barbara K, Lewis, David A, Haroutunian, Vahram, Hahn, Chang-Gyu, Charney, Alexander W, Dracheva, Stella, Kozlenkov, Alexey, DelValle, Diane, Francoeur, Nancy, Roussos, Panos, Fullard, John F, Bendl, Jaroslav, Hauberg, Mads E, Mangravite, Lara M, Chae, Yooree, Peng, Junmin, Niu, Mingming, Wang, Xusheng, Webster, Maree J, Beach, Thomas G, Jiang, Yi, and Grennan, Kay S

Subjects
Pharmacology and Pharmaceutical Sciences, Biological Sciences, Biomedical and Clinical Sciences, Genetics, Neurosciences, Intellectual and Developmental Disabilities (IDD), Brain Disorders, Mental Illness, Bipolar Disorder, Mental Health, Schizophrenia, Biotechnology, Serious Mental Illness, Autism, Human Genome, Aetiology, 2.1 Biological and endogenous factors, Mental health, Good Health and Well Being, Autism Spectrum Disorder, Brain, Genetic Predisposition to Disease, Humans, Protein Isoforms, RNA Splicing, Sequence Analysis, RNA, Transcriptome, PsychENCODE Consortium, General Science & Technology
Abstract

Most genetic risk for psychiatric disease lies in regulatory regions, implicating pathogenic dysregulation of gene expression and splicing. However, comprehensive assessments of transcriptomic organization in diseased brains are limited. In this work, we integrated genotypes and RNA sequencing in brain samples from 1695 individuals with autism spectrum disorder (ASD), schizophrenia, and bipolar disorder, as well as controls. More than 25% of the transcriptome exhibits differential splicing or expression, with isoform-level changes capturing the largest disease effects and genetic enrichments. Coexpression networks isolate disease-specific neuronal alterations, as well as microglial, astrocyte, and interferon-response modules defining previously unidentified neural-immune mechanisms. We integrated genetic and genomic data to perform a transcriptome-wide association study, prioritizing disease loci likely mediated by cis effects on brain expression. This transcriptome-wide characterization of the molecular pathology across three major psychiatric disorders provides a comprehensive resource for mechanistic insight and therapeutic development.

Published
2018

26. Chromatin domain alterations linked to 3D genome organization in a large cohort of schizophrenia and bipolar disorder brains

Author

Girdhar, Kiran, Hoffman, Gabriel E., Bendl, Jaroslav, Rahman, Samir, Dong, Pengfei, Liao, Will, Hauberg, Mads E., Sloofman, Laura, Brown, Leanne, Devillers, Olivia, Kassim, Bibi S., Wiseman, Jennifer R., Park, Royce, Zharovsky, Elizabeth, Jacobov, Rivky, Flatow, Elie, Kozlenkov, Alexey, Gilgenast, Thomas, Johnson, Jessica S., Couto, Lizette, Peters, Mette A., Phillips-Cremins, Jennifer E., Hahn, Chang-Gyu, Gur, Raquel E., Tamminga, Carol A., Lewis, David A., Haroutunian, Vahram, Dracheva, Stella, Lipska, Barbara K., Marenco, Stefano, Kundakovic, Marija, Fullard, John F., Jiang, Yan, Roussos, Panos, and Akbarian, Schahram

Published
2022
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28. A translational genomics approach identifies IL10RB as the top candidate gene target for COVID-19 susceptibility

Author

Voloudakis, Georgios, Vicari, James M., Venkatesh, Sanan, Hoffman, Gabriel E., Dobrindt, Kristina, Zhang, Wen, Beckmann, Noam D., Higgins, Christina A., Argyriou, Stathis, Jiang, Shan, Hoagland, Daisy, Gao, Lina, Corvelo, André, Cho, Kelly, Lee, Kyung Min, Bian, Jiantao, Lee, Jennifer S., Iyengar, Sudha K., Luoh, Shiuh-Wen, Akbarian, Schahram, Striker, Robert, Assimes, Themistocles L., Schadt, Eric E., Lynch, Julie A., Merad, Miriam, tenOever, Benjamin R., Charney, Alexander W., Brennand, Kristen J., Fullard, John F., and Roussos, Panos

Published
2022
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29. Hippocampal CA1 Pyramidal Neurons Display Sublayer and Circuitry Dependent Degenerative Expression Profiles in Aged Female Down Syndrome Mice.

Author

Alldred, Melissa J., Pidikiti, Harshitha, Ibrahim, Kryillos W., Lee, Sang Han, Heguy, Adriana, Hoffman, Gabriel E., Mufson, Elliott J., Stutzmann, Grace E., and Ginsberg, Stephen D.

Subjects
ALZHEIMER'S disease, INNERVATION, TEMPORAL lobe, DOWN syndrome, RNA sequencing, PYRAMIDAL neurons
Abstract

Background: Individuals with Down syndrome (DS) have intellectual disability and develop Alzheimer's disease (AD) pathology during midlife, particularly in the hippocampal component of the medial temporal lobe memory circuit. However, molecular and cellular mechanisms underlying selective vulnerability of hippocampal CA1 neurons remains a major knowledge gap during DS/AD onset. This is compounded by evidence showing spatial (e.g., deep versus superficial) localization of pyramidal neurons (PNs) has profound effects on activity and innervation within the CA1 region. Objective: We investigated whether there is a spatial profiling difference in CA1 PNs in an aged female DS/AD mouse model. We posit dysfunction may be dependent on spatial localization and innervation patterns within discrete CA1 subfields. Methods: Laser capture microdissection was performed on trisomic CA1 PNs in an established mouse model of DS/AD compared to disomic controls, isolating the entire CA1 pyramidal neuron layer and sublayer microisolations of deep and superficial PNs from the distal CA1 (CA1a) region. Results: RNA sequencing and bioinformatic inquiry revealed dysregulation of CA1 PNs based on spatial location and innervation patterns. The entire CA1 region displayed the most differentially expressed genes (DEGs) in trisomic mice reflecting innate DS vulnerability, while trisomic CA1a deep PNs exhibited fewer but more physiologically relevant DEGs, as evidenced by bioinformatic inquiry. Conclusions: CA1a deep neurons displayed numerous DEGs linked to cognitive functions whereas CA1a superficial neurons, with approximately equal numbers of DEGs, were not linked to pathways of dysregulation, suggesting the spatial location of vulnerable CA1 PNs plays an important role in circuit dissolution. [ABSTRACT FROM AUTHOR]

Published
2024
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30. Author Correction: Genome-wide analyses of ADHD identify 27 risk loci, refine the genetic architecture and implicate several cognitive domains

Author

Demontis, Ditte, Walters, G. Bragi, Athanasiadis, Georgios, Walters, Raymond, Therrien, Karen, Nielsen, Trine Tollerup, Farajzadeh, Leila, Voloudakis, Georgios, Bendl, Jaroslav, Zeng, Biau, Zhang, Wen, Grove, Jakob, Als, Thomas D., Duan, Jinjie, Satterstrom, F. Kyle, Bybjerg-Grauholm, Jonas, Bækved-Hansen, Marie, Gudmundsson, Olafur O., Magnusson, Sigurdur H., Baldursson, Gisli, Davidsdottir, Katrin, Haraldsdottir, Gyda S., Agerbo, Esben, Hoffman, Gabriel E., Dalsgaard, Søren, Martin, Jonna, Ribasés, Marta, Boomsma, Dorret I., Soler Artigas, Maria, Roth Mota, Nina, Howrigan, Daniel, Medland, Sarah E., Zayats, Tetyana, Rajagopal, Veera M., Nordentoft, Merete, Mors, Ole, Hougaard, David M., Mortensen, Preben Bo, Daly, Mark J., Faraone, Stephen V., Stefansson, Hreinn, Roussos, Panos, Franke, Barbara, Werge, Thomas, Neale, Benjamin M., Stefansson, Kari, and Børglum, Anders D.

Published
2023
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32. Alzheimer's disease transcriptional landscape in ex-vivo human microglia

Author

Roussos, Panos, primary, Kosoy, Roman, additional, Fullard, John, additional, Bendl, Jaroslav, additional, Kleopoulos, Steven, additional, Shao, Zhiping, additional, Argyriou, Stathis, additional, Mathur, Deepika, additional, Vicari, James, additional, Ma, Yixuan, additional, Humphrey, Jack, additional, Brophy, Erica, additional, Raj, Towfique, additional, Katsel, Pavel, additional, Voloudakis, Georgios, additional, Lee, Donghoon, additional, Bennett, David, additional, Haroutunian, Vahram, additional, and Hoffman, Gabriel, additional

Published
2024
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35. Transcriptomic profiling of prefrontal cortex reveals shared mechanisms underlying Alzheimer’s and Parkinson’s Diseases

Author

Bendl, Jaroslav, primary, Hoffman, Gabriel E, additional, Lee, Donghoon, additional, M, Prashant N, additional, Bennett, David A. A, additional, Davis, David A., additional, Scott, William K., additional, Berretta, Sabina, additional, Haroutunian, Vahram, additional, Fullard, John F, additional, and Roussos, Panos, additional

Published
2023
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36. Unraveling the transcriptomic landscape of healthy aging

Author

Girdhar, Kiran, primary, Bendl, Jaroslav, additional, Hoffman, Gabriel E, additional, Lee, Donghoon, additional, M, Prashant N, additional, Bennett, David A. A, additional, Haroutunian, Vahram, additional, Fullard, John F, additional, and Roussos, Panos, additional

Published
2023
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37. Comprehensive functional genomic resource and integrative model for the human brain

Author

PsychENCODE Consortium, Wang, Daifeng, Liu, Shuang, Warrell, Jonathan, Won, Hyejung, Shi, Xu, Navarro, Fabio C. P., Clarke, Declan, Gu, Mengting, Emani, Prashant, Yang, Yucheng T., Xu, Min, Gandal, Michael J., Lou, Shaoke, Zhang, Jing, Park, Jonathan J., Yan, Chengfei, Rhie, Suhn Kyong, Manakongtreecheep, Kasidet, Zhou, Holly, Nathan, Aparna, Peters, Mette, Mattei, Eugenio, Fitzgerald, Dominic, Brunetti, Tonya, Moore, Jill, Jiang, Yan, Girdhar, Kiran, Hoffman, Gabriel E., Kalayci, Selim, Gümüş, Zeynep H., Crawford, Gregory E., Roussos, Panos, Akbarian, Schahram, Jaffe, Andrew E., P.White, Kevin, Weng, Zhiping, Sestan, Nenad, Geschwind, Daniel H., Knowles, James A., and Gerstein, Mark B.

Published
2018

38. Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children

Author

Beckmann, Noam D., Comella, Phillip H., Cheng, Esther, Lepow, Lauren, Beckmann, Aviva G., Tyler, Scott R., Mouskas, Konstantinos, Simons, Nicole W., Hoffman, Gabriel E., Francoeur, Nancy J., Del Valle, Diane Marie, Kang, Gurpawan, Do, Anh, Moya, Emily, Wilkins, Lillian, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Yi, Nancy, Yu, Alex, Chung, Jonathan, Hartnett, Matthew, Eaton, Melody, Hatem, Sandra, Jamal, Hajra, Akyatan, Alara, Tabachnikova, Alexandra, Liharska, Lora E., Cotter, Liam, Fennessy, Brian, Vaid, Akhil, Barturen, Guillermo, Shah, Hardik, Wang, Ying-chih, Sridhar, Shwetha Hara, Soto, Juan, Bose, Swaroop, Madrid, Kent, Ellis, Ethan, Merzier, Elyze, Vlachos, Konstantinos, Fishman, Nataly, Tin, Manying, Smith, Melissa, Xie, Hui, Patel, Manishkumar, Nie, Kai, Argueta, Kimberly, Harris, Jocelyn, Karekar, Neha, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Tuballes, Kevin, Scott, Ieisha, Kumar, Arvind, Jaladanki, Suraj, Agashe, Charuta, Thompson, Ryan, Clark, Evan, Losic, Bojan, Peters, Lauren, Roussos, Panagiotis, Zhu, Jun, Wang, Wenhui, Kasarskis, Andrew, Glicksberg, Benjamin S., Nadkarni, Girish, Bogunovic, Dusan, Elaiho, Cordelia, Gangadharan, Sandeep, Ofori-Amanfo, George, Alesso-Carra, Kasey, Onel, Kenan, Wilson, Karen M., Argmann, Carmen, Bunyavanich, Supinda, Alarcón-Riquelme, Marta E., Marron, Thomas U., Rahman, Adeeb, Kim-Schulze, Seunghee, Gnjatic, Sacha, Gelb, Bruce D., Merad, Miriam, Sebra, Robert, Schadt, Eric E., and Charney, Alexander W.

Published
2021
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39. Single-nucleus transcriptome analysis of human brain immune response in patients with severe COVID-19

Author

Fullard, John F., Lee, Hao-Chih, Voloudakis, Georgios, Suo, Shengbao, Javidfar, Behnam, Shao, Zhiping, Peter, Cyril, Zhang, Wen, Jiang, Shan, Corvelo, André, Wargnier, Heather, Woodoff-Leith, Emma, Purohit, Dushyant P., Ahuja, Sadhna, Tsankova, Nadejda M., Jette, Nathalie, Hoffman, Gabriel E., Akbarian, Schahram, Fowkes, Mary, Crary, John F., Yuan, Guo-Cheng, and Roussos, Panos

Published
2021
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40. Neuronal impact of patient-specific aberrant NRXN1α splicing

Author

Flaherty, Erin, Zhu, Shijia, Barretto, Natalie, Cheng, Esther, Deans, P. J. Michael, Fernando, Michael B., Schrode, Nadine, Francoeur, Nancy, Antoine, Alesia, Alganem, Khaled, Halpern, Madeline, Deikus, Gintaras, Shah, Hardik, Fitzgerald, Megan, Ladran, Ian, Gochman, Peter, Rapoport, Judith, Tsankova, Nadejda M., McCullumsmith, Robert, Hoffman, Gabriel E., Sebra, Robert, Fang, Gang, and Brennand, Kristen J.

Published
2019
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41. Plasticity of Human Microglia and Brain Perivascular Macrophages in Aging and Alzheimer’s Disease

Author

Lee, Donghoon, primary, Porras, Christian, additional, Spencer, Collin, additional, Pjanic, Milos, additional, Weiler, Philipp, additional, Kosoy, Roman, additional, Bendl, Jaroslav, additional, Prashant, N M, additional, Wang, Xinyi, additional, Zheng, Shiwei, additional, Therrien, Karen, additional, Mathur, Deepika, additional, Kleopoulos, Steven P., additional, Shao, Zhiping, additional, Argyriou, Stathis, additional, Alvia, Marcela, additional, Casey, Clara, additional, Hong, Aram, additional, Beaumont, Kristin G., additional, Sebra, Robert, additional, Kellner, Christopher P., additional, Bennett, David A., additional, Yuan, Guo-Cheng, additional, Voloudakis, George, additional, Theis, Fabian J., additional, Haroutunian, Vahram, additional, Hoffman, Gabriel E., additional, Fullard, John F., additional, and Roussos, Panos, additional

Published
2023
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42. The neuronal chromatin landscape in adult schizophrenia brains is linked to early fetal development

Author

Girdhar, Kiran, primary, Bendl, Jaroslav, additional, Baumgartner, Andrew, additional, Therrien, Karen, additional, Venkatesh, Sanan, additional, Mathur, Deepika, additional, Dong, Pengfei, additional, Rahman, Samir, additional, Kleopoulos, Steven P., additional, Misir, Ruth, additional, Reach, Sarah M., additional, Auluck, Pavan K., additional, Marenco, Stefano, additional, Lewis, David A., additional, Haroutunian, Vahram, additional, Funk, Cory, additional, Voloudakis, Georgios, additional, Hoffman, Gabriel E., additional, Fullard, John F., additional, and Roussos, Panos, additional

Published
2023
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43. FUNCTIONAL CHARACTERIZATION OF GENETIC LIABILITY FOR AUTISM SPECTRUM DISORDER

Author

Voloudakis, Georgios, primary, Mathur, Deepika, additional, Venkatesh, Sanan, additional, Zeng, Biao, additional, Pjanic, Milos, additional, Coleman, Claire, additional, Hoffman, Gabriel, additional, Bendl, Jaroslav, additional, Lee, Donghoon, additional, Grove, Jakob, additional, Børglum, Anders, additional, and Roussos, Panos, additional

Published
2023
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45. Synergistic effects of common schizophrenia risk variants

Author

Schrode, Nadine, Ho, Seok-Man, Yamamuro, Kazuhiko, Dobbyn, Amanda, Huckins, Laura, Matos, Marliette R., Cheng, Esther, Deans, P. J. Michael, Flaherty, Erin, Barretto, Natalie, Topol, Aaron, Alganem, Khaled, Abadali, Sonya, Gregory, James, Hoelzli, Emily, Phatnani, Hemali, Singh, Vineeta, Girish, Deeptha, Aronow, Bruce, Mccullumsmith, Robert, Hoffman, Gabriel E., Stahl, Eli A., Morishita, Hirofumi, Sklar, Pamela, and Brennand, Kristen J.

Published
2019
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48. Efficient differential expression analysis of large-scale single cell transcriptomics data using dreamlet

Author

Hoffman, Gabriel, primary, Lee, Donghoon, additional, Bendl, Jaroslav, additional, Fnu, Prashant, additional, Hong, Aram, additional, Casey, Clara, additional, Alvia, Marcela, additional, Shao, Zhiping, additional, Argyriou, Stathis, additional, Therrien, Karen, additional, Venkatesh, Sanan, additional, Voloudakis, Georgios, additional, Haroutunian, Vahram, additional, Fullard, John, additional, and Roussos, Panos, additional

Published
2023
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