Transcriptome and epigenome landscape of human cortical development modeled in organoids
Authors: Amiri Anahita , Coppola Gianfilippo , Scuderi Soraya , Wu Feinan , Roychowdhury Tanmoy , Liu Fuchen , Pochareddy Sirisha , Shin Yurae , Safi Alexias , Song Lingyun , Zhu Ying , Sousa André M. M. ,   The PsychENCODE Consortium, 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 C. P. , Park Royce B. , Peters Mette A. , Pinto Dalila , Pochareddy Sirisha , Polioudakis Damon , Pratt Henry , Price Amanda J. , Purcaro Michael , Ray Mohana , Reddy Timothy E. , Rhie Suhn K. , Roussos Panos , Sanders Stephan J. , Santpere Gabriel , Schreiner Shannon , Sheppard Brooke , Shi Xu , Shieh Annie W. , Shin Joo Heon , Skarica Mario , Song Lingyun , Sousa Andre M.M. , Spitsyna Valeria N. , State Matthew W. , Sullivan Patrick F. , Swarup Vivek , Szatkiewicz Jin , Szekely Anna , Tao Ran , van Bakel Harm , Wang Yongjun , Wang Daifeng , Warrell Jonathan , Webster Maree J. , Weissman Sherman , Weng Zhiping , Werling Donna M. , White Kevin P. , Willsey Jeremy A. , Wiseman Jennifer R. , Witt Heather , Won Hyejung , Wray Gregory A. , Xia Yan , Xu Min , Yang Yucheng T. , Yang Mo , Zandi Peter , Zhang Jing , Zharovsky Elizabeth 
Published: December 2018

INTRODUCTION
The human cerebral cortex has undergone an extraordinary increase in size and complexity during mammalian evolution. Cortical cell lineages are specified in the embryo, and genetic and epidemiological evidence implicates early cortical development in the etiology of neuropsychiatric disorders such as autism spectrum disorder (ASD), intellectual disabilities, and schizophrenia. Most of the disease-implicated genomic variants are located outside of genes, and the interpretation of noncoding mutations is lagging behind owing to limited annotation of functional elements in the noncoding genome.

RATIONALE
We set out to discover gene-regulatory elements and chart their dynamic activity during prenatal human cortical development, focusing on enhancers, which carry most of the weight upon regulation of gene expression. We longitudinally modeled human brain development using human induced pluripotent stem cell (hiPSC)–derived cortical organoids and compared organoids to isogenic fetal brain tissue.

RESULTS
Fetal fibroblast–derived hiPSC lines were used to generate cortically patterned organoids and to compare oganoids’ epigenome and transcriptome to that of isogenic fetal brains and external datasets. Organoids model cortical development between 5 and 16 postconception weeks, thus enabling us to study transitions from cortical stem cells to progenitors to early neurons. The greatest changes occur at the transition from stem cells to progenitors. The regulatory landscape encompasses a total set of 96,375 enhancers linked to target genes, with 49,640 enhancers being active in organoids but not in mid-fetal brain, suggesting major roles in cortical neuron specification. Enhancers that gained activity in the human lineage are active in the earliest stages of organoid development, when they target genes that regulate the growth of radial glial cells.
Parallel weighted gene coexpression network analysis (WGCNA) of transcriptome and enhancer activities defined a number of modules of coexpressed genes and coactive enhancers, following just six and four global temporal patterns that we refer to as supermodules, likely reflecting fundamental programs in embryonic and fetal brain. Correlations between gene expression and enhancer activity allowed stratifying enhancers into two categories: activating regulators (A-regs) and repressive regulators (R-regs). Several enhancer modules converged with gene modules, suggesting that coexpressed genes are regulated by enhancers with correlated patterns of activity. Furthermore, enhancers active in organoids and fetal brains were enriched for ASD de novo variants that disrupt binding sites of homeodomain, Hes1, NR4A2, Sox3, and NFIX transcription factors.

CONCLUSION
We validated hiPSC-derived cortical organoids as a suitable model system for studying gene regulation in human embryonic brain development, evolution, and disease. Our results suggest that organoids may reveal how noncoding mutations contribute to ASD etiology.

Summary of the study, analyses, and main results.
Data were generated for iPSC-derived human telencephalic organoids and isogenic fetal cortex. Organoids modeled embryonic and early fetal cortex and show a larger repertoire of enhancers. Enhancers could be divided into activators and repressors of gene expression. We derived networks of modules and supermodules with correlated gene and enhancer activities, some of which were implicated in autism spectrum disorders (ASD).