| Accession | PRJCA031633 | ||||||||||
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| Title | Single-cell transcriptome profiling elucidates the cellular determinants of immunotherapy response in gastric cancer peritoneal metastasis | ||||||||||
| Relevance | Medical | ||||||||||
| Umbrella project |
IDP: The Immunity Deciphering Project |
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| Data types | Single cell sequencing | ||||||||||
| Organisms | Homo sapiens | ||||||||||
| Description | We performed a phase-II trial involving patients with GCPM treated with ICB (sintilimab) combined with chemotherapy. The cohorts were derived from a phase II study with patients with GCPM treated with injectable paclitaxel (albumin-binding) via intraperitoneal perfusion combined with intravenous sindilimab, S-1 and Oxaliplatin (GC-IP001 study; https://www.chictr.org.cn/showproj.html?proj=191640). scRNA-seq was performed on 21 surgical resection and biopsy GCPM samples, 7 primary GC samples, 5 peritumoral gastric normal (GN) samples, one peritoneal normal (PE) sample, and 4 peripheral blood mononuclear cell (PBMC) samples. The samples were derived from 19 GC patients, with 14 cases treated with ICB therapy, of which 5 patients exhibited partial response (PR) after treatment, 4 patients exhibited stable disease (SD), and 5 patients exhibited progressive disease (PD). 4 patients treated by ICB had paired samples of GN, GC, GCPM and PBMC, and 1 patient treated by ICB had paired samples of GC and GCPM. The samples were sequenced using the Droplet 10x platforms to fetch scRNA-seq data. The obtained scRNA-seq data were combined with a previously published scRNA-seq GC atlas with additional three cases of GCPM (GSE183904). The cells were subjected to quality control on the basis of many parameters. Cells with fewer than 500 identified genes and those with greater than 20% mitochondrial content were eliminated. To further exclude probable doublets, cells containing more than 8000 identified genes were discarded. Possible doublets predicted by the DoubletFinder software were eliminated to avoid confounding the analysis. After rigorous quality control and filtering, we obtained 410,612 qualified single-cell transcriptomes across five tissue types including 24 GCPM and 31 GC samples. | ||||||||||
| Sample scope | Single cell | ||||||||||
| Release date | 2024-11-13 | ||||||||||
| Publication |
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| Submitter | Huiyan Luo (luohy@sysucc.org.cn) | ||||||||||
| Organization | Sun Yat-sen University Cancer Center | ||||||||||
| Submission date | 2024-10-25 |
| Resource name | Description |
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