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Series GSE210681 Query DataSets for GSE210681
Status Public on Nov 01, 2022
Title High-content CRISPR screens link coronary artery disease genes to endothelial cell programs [scRNAseq]
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Genome-wide association studies (GWAS) have discovered thousands of risk loci for common, complex diseases, each of which could point to genes and gene programs that influence disease. For some diseases, it has been observed that GWAS signals converge on a smaller number of biological programs, and that this convergence can help to identify causal genes. However, identifying such convergence remains challenging: each GWAS locus can have 2-20 candidate genes, the cellular programs a gene participates in are difficult to define in an unbiased fashion, and it remains unclear which genes and programs would be likely to influence disease risk. Here, we explored a new approach to address this challenge, by creating an unbiased catalog of gene programs and their regulators in endothelial cells to link variants to functions for coronary artery disease (CAD). To do so, we applied CRISPRi-Perturb-seq to knock down all expressed genes within 500 Kb of all CAD GWAS loci (2,285 genes in total) and measure their effects on the transcriptome using single-cell RNA-seq. We used consensus non-negative matrix factorization to define 60 gene expression programs—including core cellular programs, such as ribosome biogenesis, and endothelial cell-specific programs, such as flow response and angiogenesis—and link these programs to upstream regulators including transcription factors, chromatin regulators, metabolic enzymes, and signaling cascades. By combining this gene-to-program catalog with variant-to-gene maps, we find that candidate CAD genes converge onto 6 interrelated gene programs, together involving known and novel genes in 39 of 229 CAD GWAS loci. Analysis of these programs revealed that the cerebral cavernous malformations (CCM) complex—whose potential connection to CAD has not been previously explored—acts upstream to regulate other CAD genes involved in cytoskeletal organization, extracellular matrix remodeling, and cell migration. The strongest regulator of these programs is TLNRD1, a highly conserved but poorly studied gene that we show acts in the CCM pathway and regulates actin organization and endothelial cell barrier function. Together, our study nominates new genes that likely influence risk for CAD, identifies convergence of CAD risk loci into certain gene programs in endothelial cells, and demonstrates a generalizable strategy to catalog gene programs to connect disease variants to functions.
Overall design Human immortalized endothelial cells engineered to contain doxycycline inducible CRISPR interference machinery (CRISPRi TeloHAEC), were transduced with a library of 36,880 guide RNAs targeting gene promoters, in a CROP-seq vector. After 5 days of doxycycline treatment, cells were run on 20 lanes of a 10X Chromium Controller and scRNA-seq libraries generated. polyA+ cDNA surrounding the guide sequences was amplified to make "dialout" libraries, used to link guide RNA sequences to scRNAseq cell barcodes.
Contributor(s) Schnitzler GR, Kang H, Lee-Kim V, Ma XR, Zeng T, Vellarikkal SK, Zhou R, Guo K, Sias-Garcia O, Bloemendal A, Munson G, Guckelberger P, Nguyen TH, Bergman DT, Atri D, Cheng N, Cleary B, Lander ES, Finucane HK, Gupta RM, Engreitz JM
Citation(s) 38326615
Submission date Aug 07, 2022
Last update date Mar 04, 2024
Contact name Jesse Engreitz
Organization name Broad Institute
Street address 415 Main Street
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (40)
GSM6435403 scRNAseq_2kG_11AMDox_1
GSM6435404 scRNAseq_2kG_11AMDox_2
GSM6435405 scRNAseq_2kG_11AMDox_3
This SubSeries is part of SuperSeries:
GSE210523 High-content CRISPR screens link coronary artery disease genes to endothelial cell programs
BioProject PRJNA867016
SRA SRP475373

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE210681_2kG.library.gene_spectra_score.k_60.dt_0_2.txt.gz 9.9 Mb (ftp)(http) TXT
GSE210681_2kG.library.spectra.k_60.dt_0_2.consensus.txt.gz 5.3 Mb (ftp)(http) TXT
GSE210681_2kG.library.usages.k_60.dt_0_2.consensus.txt.gz 80.6 Mb (ftp)(http) TXT
GSE210681_2kG.library_MAST_DEtopics.txt.gz 7.5 Mb (ftp)(http) TXT
GSE210681_ALL_Pvalues_dup4_s4n3.99x.txt.gz 414.5 Mb (ftp)(http) TXT
GSE210681_ALL_log2fcs_dup4_s4n3.99x.txt.gz 475.4 Mb (ftp)(http) TXT
GSE210681_Dialout_guides_per_CBC.txt.gz 12.3 Mb (ftp)(http) TXT
GSE210681_RAW.tar 6.4 Gb (http)(custom) TAR (of MTX, TSV)
GSE210681_Table.S2.X.AllMASTStatisticalTestResults.txt.gz 5.4 Mb (ftp)(http) TXT
GSE210681_aggregated.2kG.library.mtx.gene_x_cell.RDS.gz 1.4 Gb (ftp)(http) RDS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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