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

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. ORCID: https://orcid.org/0000-0002-4357-574X, 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., Hwang, Ahyeon, Iatrou, Artemis, Inoue, Fumitaka, Jajoo, Aarti, Jensen, Matthew, Jiang, Lihua, Jin, Peng, Jin, Ting, Jops, Connor, Jourdon, Alexandre, Kawaguchi, Riki, Kellis, Manolis, Kleopoulos, Steven P., Kozlenkov, Alex, Kriegstein, Arnold, Kundaje, Anshul, Kundu, Soumya, Lee, Cheyu, Lee, Donghoon, Li, Junhao, Li, Mingfeng, Lin, Xiao, Liu, Shuang, Liu, Jason, Liu, Jianyin, Liu, Shuang, Lou, Shaoke, Loupe, Jacob M., Lu, Dan, Ma, Shaojie, Ma, Liang, Mariani, Jessica, Martinowich, Keri, Maynard, Kristen R., Mazariegos, Samantha, Meng, Ran, Myers, Richard M., Micallef, Courtney, Mikhailova, Tatiana, Ming, Guo-li, Mohammadi, Shahin, Monte, Emma, Montgomery, Kelsey S., Moore, Jill E., Moran, Jennifer R., Mukamel, Eran A., Nairn, Angus C., Nemeroff, Charles B., Ni, Pengyu, Norton, Scott, Nowakowski, Tomasz, Omberg, Larsson, Page, Stephanie C., Park, Saejeong, Patowary, Ashok, Pattni, Reenal, Pertea, Geo, Phalke, Nishigandha, Pinto, Dalila, Pjanic, Milos, Pochareddy, Sirisha, Pollen, Alex, Purmann, Carolin, Qin, Zhaohui S., Qu, Ping-Ping, Quintero, Diana, Raj, Towfique, Rajagopalan, Ananya S., Reach, Sarah, Reimonn, Thomas, Ressler, Kerry J., Ross, Deanna, Roussos, Panos, Rozowsky, Joel, Ruth, Misir, Ruzicka, W. Brad, Sanders, Stephan J., Schneider, Juliane M., Scuderi, Soraya, Sebra, Robert, Seyfried, Nicholas, Shao, Zhiping, Shedd, Nicole, Shieh, Annie W., Shin, Joo Heon, Skarica, Mario, Snijders, Clara, Song, Hongjun, State, Matthew W., Steyert, Marilyn, Subburaju, Sivan, Sudhof, Thomas, Snyder, Michael, Tao, Ran, Therrien, Karen, Tsai, Li-Huei, Urban, Alexander E., Vaccarino, Flora M., van Bakel, Harm, Voloudakis, Georgios, Wamsley, Brie, Wang, Tao, Wang, Sidney H., Wang, Daifeng, Wang, Yifan, Warrell, Jonathan, Wei, Yu, Weimer, Annika K., Whalen, Sean, White, Kevin P., Willsey, A. Jeremy, Won, Hyejung, Wong, Wing, Wu, Hao, Wu, Feinan, Wuchty, Stefan, Wylie, Dennis, Xu, Siwei, Yap, Chloe X., Zeng, Biao, Zhang, Chunling, Zhang, Bin, Zhang, Jing, Zhang, Yanqiong, Zhou, Xiao, Ziffra, Ryan, Zeier, Zane R. and Zintel, Trisha M. 2024. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science 384 (6698) , eadh0829. 10.1126/science.adh0829

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Abstract

INTRODUCTION Genome-wide association studies (GWASs) have identified thousands of loci associated with neurodevelopmental and psychiatric disorders, yet our lack of understanding of the target genes and biological mechanisms underlying these associations remains a major challenge. GWAS signals for many neuropsychiatric disorders, including autism spectrum disorder, schizophrenia, and bipolar disorder, are particularly enriched for gene-regulatory elements active during human brain development. However, the lack of a unified population-scale, ancestrally diverse gene-regulatory atlas of human brain development has been a major obstacle for the functional assessment of top loci and post-GWAS integrative analyses. RATIONALE To address this critical gap in knowledge, we have uniformly processed and systematically characterized gene, isoform, and splicing quantitative trait loci (cumulatively referred to as xQTLs) in the developing human brain across 672 unique samples from 4 to 39 postconception weeks spanning European, African-American, and Latino/admixed American ancestries). With this expanded atlas, we sought to specifically localize the timing and molecular features mediating the greatest proportion of neuropsychiatric GWAS heritability, to prioritize candidate risk genes and mechanisms for top loci, and to compare with analogous results using larger adult brain functional genomic reference panels. RESULTS In total, we identified 15,752 genes harboring a gene, isoform and/or splicing cis-xQTL, including 49 genes associated with four large, recurrent inversions. Highly concordant effect sizes were observed across populations, and our diverse reference panel improved resolution to fine-map underlying candidate causal regulatory variants. Substantially more genes were found to harbor QTLs in the first versus second trimester of brain development, with a notable drop in gene expression and splicing heritability observed from 10 to 18 weeks coinciding with a period of rapidly increasing cellular heterogeneity in the developing brain. Isoform-level regulation, particularly in the second trimester, mediated a greater proportion of heritability across multiple psychiatric GWASs compared with gene expression regulation. Through colocalization and transcriptome-wide association studies, we prioritized biological mechanisms for ~60% of GWAS loci across five neuropsychiatric disorders, with >2-fold more colocalizations observed compared with larger adult brain functional genomic reference panels. We observed convergence between common and rare-variant associations, including a cryptic splicing event in the high-confidence schizophrenia risk gene SP4. Finally, we constructed a comprehensive set of developmentally regulated gene and isoform coexpression networks harboring unique cell-type specificity and genetic enrichments. Leveraging this cell-type specificity, we identified >8000 module interaction QTLs, many of which exhibited additional GWAS colocalizations. Overall, neuropsychiatric GWASs and rare variant signals localized more strongly within maturing excitatory- and interneuron-associated modules compared with those enriched for neural progenitor cell types. Results can be visualized at devbrainhub.gandallab.org. CONCLUSION We have generated a large-scale, cross-population resource of gene, isoform, and splicing regulation in the developing human brain, providing comprehensive developmental and cell-type-informed mechanistic insights into the genetic underpinnings of complex neurodevelopmental and psychiatric disorders.

Item Type:	Article
Date Type:	Publication
Status:	Published
Schools:	Medicine
Publisher:	American Association for the Advancement of Science
ISSN:	0036-8075
Date of First Compliant Deposit:	31 May 2024
Date of Acceptance:	7 March 2024
Last Modified:	04 Jun 2024 03:34
URI:	https://orca.cardiff.ac.uk/id/eprint/169350

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