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| Status |
Public on Jun 07, 2023 |
| Title |
Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion [scRNAseq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Accumulated genetic mutations or copy number alterations are frequently observed in esophageal squamous cell carcinoma (ESCC) patients. However, it is still elusive which gene is the driver to initiate ESCC. We identified key genetic determinants for ESCC development using CRISPR/Cas9-based multiple genes KO mouse esophageal organoid model. Trp53, Cdkn2a, and Notch1 triple KO (PCN) organoid showed the phenotypes of ESCC. These triple genes KO served for cell proliferation through building multiple root cell clusters and remodeling the immune landscape beneficial for tumorigenesis by Ccl2-Ccr2 mediated intercellular interactions. Ccl2-releasing PCN tumors were surrounded by exhausted T cells and M2 macrophages leading to immune evasion. The PCN-type tumor was observed in more than 30% of ESCC patients who express high levels of B2M, CCL2, and NF-kB. Our study unveiled genetic determinants for ESCC development crucial for cell-autonomous growth as well as non-cell autonomous interactions with immune cells.
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| Overall design |
organoids from WT, PC, PN, and PCN were collected 7 days after seeding and digested with 0.05% trypsin-EDTA at 37 ℃ for 30 min. After inactivating trypsin with 10% FBS DMEM, single-cell suspension was collected by passing through the 35 m cell strainer. Each group was tagged with 2 CMO tags from CellPlex kit (10x Genomics). The tagged cells of each group were pooled together with same number of cells after counting cells. cDNA library was prepared with the 10x Genomics 3’ v2 kit, cDNA library was sequenced on an Illumina NovaSeq (Novogene) and mapped to GRCm38/mm10 genome and demultiplexed using Cellranger.
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| Contributor(s) |
Ko K, Huang Y, Zhang S, Zou G, Kim BJ, Zhang J, Jun S, Park J |
| Citation(s) |
37257519 |
| |
| Submission date |
Sep 22, 2022 |
| Last update date |
Sep 07, 2023 |
| Contact name |
Jae-Il Park |
| E-mail(s) |
[email protected]
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| Organization name |
M.D. Anderson Cancer Center
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| Department |
Dept. of Experimental Radiation Oncology
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| Street address |
6565 MD Anderson BLVD
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| City |
Houston |
| State/province |
Texas |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE213929 |
Key Genetic Determinants Driving Esophageal Squamous Cell Carcinoma Initiation and Immune Evasion |
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| Relations |
| BioProject |
PRJNA883203 |
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