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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jan 15, 2022 |
| Title |
Perturb-map coupled with spatial transcriptomics identifies mutation associated gene signatures in a mouse model of lung adenocarcinoma |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
The cellular architecture of a tumor has a major impact on cancer outcome, and thus there is interest in identifying genes controlling the tumor microenvironment (TME). While CRISPR screens are helping uncover genes regulating many cell-intrinsic processes, existing approaches are suboptimal for identifying gene functions operating extracellularly or within a tissue context. To address this, we developed an approach for spatial functional genomics called Perturb-map, which utilizes protein barcodes (Pro-Code) to enable spatial detection of barcoded cells within tissue. We applied Perturb-map to knockout dozens of genes in parallel in a mouse model of lung cancer and simultaneously assessed how each knockout influenced tumor growth, histopathology, and immune composition. Additionally, we paired Perturb-map and spatial transcriptomics for unbiased molecular analysis of Pro-Code/CRISPR lesions. Our studies found in Tgfbr2 knockout lesions, the TME was converted to a fibro-mucinous state and T-cells excluded, concomitant with upregulated TGFb and TGFb-mediated stroma activation, suggesting Tgfbr2 loss on lung cancer cells increased TGFb bioavailability and enhanced its suppressive effects on the TME. These studies establish Perturb-map for functional genomics within a tissue at single cell-resolution with spatial architecture preserved.
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| Overall design |
Male C57BL/6J mice were injected intravenously with KP (Kras G12D, p53 deleted) cells transduced with a Pro-Code/CRISPR library targeting 35 different genes associated with tumor-immune interaction. 10X Visium spatial transcriptomics profiling was performed on 4 separate sections of mouse lung from 3 different mice. Annotations for specific genes targeted in visium spots capturing tumor cells were generated by parallel hyperion imaging on a serial section to identify the linked protein barcode.
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| Contributor(s) |
Rose SA, Dhainaut M, Brown BD |
| Citation(s) |
35290801 |
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| Submission date |
Jan 11, 2022 |
| Last update date |
Apr 29, 2022 |
| Contact name |
Dana Pe'er |
| E-mail(s) |
peerd@mskcc.org
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| Organization name |
Memorial Sloan Kettering Cancer Center
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| Department |
Computational and Systems Biology
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| Street address |
417 E 68th St
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA796304 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE193460_RAW.tar |
143.3 Mb |
(http)(custom) |
TAR (of CSV, H5, JPG, JSON, PNG) |
| GSE193460_additional_files_metadata_20220428.xlsx |
10.0 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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