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| Status |
Public on May 22, 2021 |
| Title |
Single Cell Analyses of Renal Cell Cancers Reveal Insights into Tumor Microenvironment, Cell of Origin, and Therapy Response |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Diverse subtypes of renal cell carcinomas (RCC) display a wide spectrum of histomorphologies, proteogenomic alterations, immune cell infiltration patterns, and clinical behavior. Delineating the ontogeny of these malignancies with the identification of cells of origin for different RCC subtypes will provide mechanistic insights into their diverse pathobiology. With this aim, we performed single cell RNA sequencing (scRNA-seq) analysis of ~30,000 cells dissociated from benign human kidney and renal tumor specimens. The benign renal tissue cell atlas comprised 26 distinct cell clusters representing all known major and minor cell types, as well as two rare proximal tubule cell types (PT-B and PT-C) and one novel entity containing both intercalated and principal cell (IC-PC) phenotypes. In comparison, the tumor cell atlas was comprised of 13 different cell clusters encompassing neoplastic cells and components of the tumor microenvironment. Using a random forest model trained on the scRNA-seq data from benign tubular epithelial cell types, we predicted the putative cell of origin for more than 10 different RCC subtypes.
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| Overall design |
Single-cell suspensions from 8 renal tumor specimens and 6 benign human kidney specimens from clear cell cell carcinoma (ccRCC) and chromophobe renal cell carcinoma (chRCC) patients were obtained by enzymatic dissociation. The cell suspension was used to prepare single cell RNA-seq libraries using the 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).
*** This GEO submission contains only processed data (raw counts tables in HDF5 format), raw data (FASTQ files) will be submitted to dbGaP/SRA due to to patient privacy concerns.
The cell annotation file *csv files were added on Sep 23, 2022.
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| Contributor(s) |
Zhang Y, Narayanan SP, Dhanasekaran SM, Raskind G, Wang X, Vats P, Mannan R, Su F, Wang L, Cao X, Kumar-Sinha C, Giordono TJ, Morgan TM, Pitchaya S, Alva A, Mehra R, Cieslik M, Chinnaiyan AM |
| Citation(s) |
34099557 |
| Submission date |
Oct 06, 2020 |
| Last update date |
Sep 23, 2022 |
| Contact name |
Arul M. Chinnaiyan |
| Organization name |
University of Michigan
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| Street address |
1500 E. Medical Center Dr
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| City |
Ann Arbor |
| State/province |
MICHIGAN |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA667716 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE159115_RAW.tar |
115.0 Mb |
(http)(custom) |
TAR (of H5) |
| GSE159115_ccRCC_anno.csv.gz |
905.6 Kb |
(ftp)(http) |
CSV |
| GSE159115_chRCC_anno.csv.gz |
111.5 Kb |
(ftp)(http) |
CSV |
| GSE159115_normal_anno.csv.gz |
271.0 Kb |
(ftp)(http) |
CSV |
| Raw data not provided for this record |
| Processed data provided as supplementary file |
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