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| Status |
Public on Sep 20, 2018 |
| Title |
High-throughput single cell transcriptome analysis and CRISPR screen identify key β cell-specific disease genes |
| Organisms |
Homo sapiens; Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Pancreatic endocrine cells orchestrate the precise control of blood glucose levels, but the contribution of each cell type to diabetes or obesity remains elusive. Here we used a massively parallel single-cell RNA-seq technology (Drop-Seq) to analyze the transcriptome of 26,677 pancreatic islets cells from both healthy and type II diabetic (T2D) donors. We have analyzed cell type-specific gene signatures, and detected several rare α or β cell subpopulations with high sensitivity. We also developed RePACT, a sensitive single cell analysis algorithm to identify genes associated with rare disease causing cells, or to capture the subtle disease-relevant cellular variation. We successfully identified both common and specific signature genes of obesity and T2D with only a small number of islet samples. We also performed an unbiased genome-wide CRISPR screen and mapped these Drop-Seq signature genes to the core insulin regulatory network in β cells. Notably, our integrative analysis discovered a β cell-specific function of the cohesin loading complex in regulating insulin gene transcription, and a previously unrecognized role of the NuA4/Tip60 histone acetyltransferase complex in regulating insulin release. These data demonstrated that single-cell trancriptomics is necessary to dissect the heterogeneity, disease state, and functionality of islet β cells and other cell types.
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| Overall design |
Single cell sequencing (Drop-seq) for Human Pancreatic islet from 9 individuals respectively. Including 6 Healthy donor and 3 Type II diabetes patient donor. 4 Chipseq for further validation.
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| Contributor(s) |
Weng C, Jin F, Lu L |
| Citation(s) |
30865899 |
| Submission date |
Jul 11, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Chen Weng |
| E-mail(s) |
cweng@wi.mit.edu
|
| Organization name |
Broad Institute and Whitehead Institute
|
| Department |
Genetics
|
| Lab |
Vijay Sankaran lab and Jonathan Weissman lab
|
| Street address |
415 Main St, Cambridge
|
| City |
Boston |
| State/province |
OH |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA393886 |
| SRA |
SRP111557 |
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