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| Status |
Public on Mar 24, 2022 |
| Title |
Single cell RNA sequencing and TCR repertoire analysis of Adult T-cell Leukemia/Lymphoma (ATLL) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We examined ATLL using archived fresh frozen tissue after the biopsy by single-cell RNA sequencing (scRNA-seq) with T-cell receptor (TCR) clonal analysis. Highly clonal tumor cells showed multiple activating pathways, suggesting dynamic evolution of the malignancy. Dissecting diverse cell types comprising the TME led to the identification of a novel subset of cancer-associated fibroblast which showed enriched epidermal growth factor receptor (EGFR)-related transcripts.
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| Overall design |
Human skin samples were obtained using remnants of biopsy tissue taken for diagnostic purposes.Specimens were placed in phosphate-buffered saline (PBS) on ice. Biopsy samples were cryopreserved in optimal cutting temperature (OCT) compound and stored at -80ºC. Single cell dissociates were loaded into the Chromium system (10x Genomics, USA) targeting 25,000 cells. The Chromium Single Cell 5’ Kit (10x Genomics, USA) was used to generate scRNA-seq and TCR libraries, according to the manufacturer’s instructions. scRNA-seq and TCR-seq data were aligned to the human reference genome (GRCh38) and processed using the CellRanger 4.0.0 pipeline (10x Genomics). In this study, we observed that the clonally expanded malignant tumor cells in ATLL are CD4 T-cells through scRNA-seq combined with TCR clonal analysis.
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| Contributor(s) |
Kim HJ |
| Citation(s) |
35464471 |
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| Submission date |
Jan 28, 2022 |
| Last update date |
Jun 24, 2022 |
| Contact name |
EUN-HYE JOO |
| Organization name |
Samsung Medical Center
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| Department |
Samsung Genome Institute
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| Street address |
81, Irwon-ro, Gangnam-gu
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| City |
Seoul |
| ZIP/Postal code |
KS013 |
| Country |
South Korea |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA801697 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE195674_RAW.tar |
83.8 Mb |
(http)(custom) |
TAR (of CSV, MTX, TSV) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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