Margaret G. Guo, David L. Reynolds, Cheen E. Ang, Yingfei Liu, Yang Zhao et al.
Noncoding variants of presumed regulatory function contribute to the heritability of neuropsychiatric disease. 2221 noncoding variants connected to risk for 10 neuropsychiatric disorders, including autism spectrum disorder, attention deficit hyperactivity disorder, bipolar disorder, borderline personality disorder, major depression, generalized anxiety disorder, panic disorder, post-traumatic stress disorder, obsessive-compulsive disorder, and schizophrenia, were studied in developing human neural cells. Integrating epigenomic and transcriptomic data with massively parallel reporter assays identified differentially-active single-nucleotide variants (daSNVs) in specific neural cell types. Expression-gene mapping, network analyses, and chromatin looping nominated candidate disease-relevant target genes modulated by these daSNVs. Follow up integration of daSNV gene editing with clinical cohort analyses suggested that magnesium transport dysfunction may increase neuropsychiatric disease risk and indicated that common genetic pathomechanisms may mediate specific symptoms that are shared across multiple neuropsychiatric diseases.
Margaret G. Guo, David L. Reynolds, Cheen E. Ang, Yingfei Liu, Yang Zhao, Laura K. H. Donohue, Zurab Siprashvili, Xue Yang, Yongjin Yoo, Smarajit Mondal, Audrey Hong, Jessica Kain, Lindsey Meservey, Tania Fabo, Ibtihal Elfaki, Laura N. Kellman, Nathan S. Abell, Yash Pershad, Vafa Bayat, Payam Etminani, Mark Holodniy, Daniel H. Geschwind, Stephen B. Montgomery, Laramie E. Duncan, Alexander E. Urban, Russ B. Altman, Marius Wernig, Paul A. Khavari. Integrative analyses highlight functional regulatory variants associated with neuropsychiatric diseases. 2023-10-19. https://doi.org/10.1038/s41588-023-01533-5
The candidate variant library was assayed two days after doxycycline-induced Ngn2 neuronal induction in human cells. Barcode RNA and plasmid DNA were measured for reference and alternate inserts.
The candidate variant library was tested in proliferating IMR-32 neuroblastoma cells using integrated lentiMPRA barcode RNA and plasmid DNA readouts.
The candidate variant library was assayed ten days after doxycycline-induced Ngn2 neuronal induction in human cells. Barcode RNA and plasmid DNA were measured for reference and alternate inserts.
A genome-wide candidate variant library was tested in primary human astrocytes using the integrated lentiviral MPRA. Reference and alternate 145-bp inserts were quantified through barcode RNA relative to plasmid DNA.
The candidate variant library was tested in D283 medulloblastoma cells using integrated lentiMPRA barcode RNA and plasmid DNA readouts.
The candidate variant library was assayed four days after doxycycline-induced Ngn2 neuronal induction in human cells. Barcode RNA and plasmid DNA were measured for reference and alternate inserts.
The candidate variant library was tested after chemical differentiation of IMR-32 neuroblastoma cells. Barcode RNA and plasmid DNA were quantified for the reference and alternate inserts.
The candidate variant library was tested after retinoic-acid differentiation of SH-SY5Y neuroblastoma cells. Barcode RNA and plasmid DNA were quantified for the reference and alternate inserts.
The candidate variant library was tested in proliferating SH-SY5Y neuroblastoma cells using integrated lentiMPRA barcode RNA and plasmid DNA readouts.
The candidate variant library was assayed in in-vitro differentiated posterior neural progenitor cells. The posterior neural program used SB431542, LDN193189 and CHIR99021 before barcode RNA/plasmid DNA quantification.
The candidate variant library was tested in HEK293T cells as a non-neural comparison condition using integrated lentiMPRA barcode RNA and plasmid DNA readouts.
A genome-wide candidate variant library was tested in H9/WA09 human embryonic stem cells using the integrated lentiviral MPRA. Reference and alternate 145-bp inserts were quantified through barcode RNA relative to plasmid DNA.
The candidate variant library was tested in D341 medulloblastoma cells using integrated lentiMPRA barcode RNA and plasmid DNA readouts.
The candidate variant library was assayed in in-vitro differentiated anterior neural progenitor cells. The anterior neural program used SB431542 and LDN193189 before barcode RNA/plasmid DNA quantification.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 7 files (ZIP)GSE221384_count_matrix_combined_wdna.csv.gzGSE221384_family.soft.gzSOURCE_MANIFEST.txtSupplementary_Data_3_MPRA_results_annotated.xlsxSupplementary_Data_5_MPRA_summary_and_raw_counts.xlsxSupplementary_Information.pdfSupplementary_Tables_1_15.xlsx