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| Status |
Public on Jun 28, 2018 |
| Title |
Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment - 5' RNA sequencing and TCR sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mechanisms of cancer progression and immunotherapy response. We created an immune map of breast cancer using single-cell RNA-seq data from 45,000 immune cells from eight breast carcinomas, as well as matched normal breast tissue, blood, and lymph node. We developed a preprocessing pipeline, SEQC, and a Bayesian clustering and normalization method, Biscuit, to address computational challenges inherent to single-cell data. Despite significant similarity between normal and tumor tissue-resident immune cells, we observed continuous phenotypic expansions specific to the tumor microenvironment. Analysis of paired single-cell RNA and T cell receptor (TCR) sequencing data from 27,000 additional T cells revealed the combinatorial impact of TCR utilization on phenotypic diversity. Our results support a model of continuous activation in T cells and do not comport with the macrophage polarization model in cancer, with important implications for characterizing tumor-infiltrating immune cells.
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| Overall design |
Single-cell RNA sequencing was performed on three patients using the 10x genomics TCR profiling kits. For each patient, populations of T-cells were assayed for both TCR sequence and trancriptome-wide RNA-sequence. Two donors have a replicate experiment.
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| Contributor(s) |
Azizi E, Carr AJ, Plitas G, Cornish AE, Konopacki C, Prabhakaran S, Nainys J, Wu K, Kiseliovas V, Setty M, Choi K, Fromme RM, Dao P, McKenney PT, Wasti RC, Kadaveru K |
| Citation(s) |
29961579 |
| Submission date |
May 21, 2018 |
| Last update date |
Mar 27, 2019 |
| Contact name |
Ambrose J Carr |
| Organization name |
Memorial Sloan Kettering Cancer Center
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| Department |
Computational and Systems Biology Program, SKI
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| Lab |
Dana Pe'er
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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 (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (10)
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| This SubSeries is part of SuperSeries: |
| GSE114727 |
Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment |
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| Relations |
| BioProject |
PRJNA472381 |
| SRA |
SRP148594 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE114724_RAW.tar |
155.7 Mb |
(http)(custom) |
TAR (of CSV, MTX, TSV) |
| GSE114724_rna_imputed.tsv.gz |
57.2 Mb |
(ftp)(http) |
TSV |
| GSE114724_rna_raw.tsv.gz |
55.2 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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