Estimating the population abundance of tissue-infiltrating immune and stromal cell populations using gene expression

By Etienne Becht, Nicolas A. Giraldo, L. Lacroix, Bénédicte Buttard, N. Elarouci, F. Petitprez, J. Selves, P. Laurent-Puig, C. Sautès-Fridman, W. Fridman and 1 more. Genome Biology, 2016

2,923 citations recorded by the source corpus.

We introduce the Microenvironment Cell Populations-counter (MCP-counter) method, which allows the robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data. We present in vitro mRNA mixture and ex vivo immunohistochemical data that quantitatively support the validity of our method’s estimates. Additionally, we demonstrate that MCP-counter overcomes several limitations or weaknesses of previously proposed computational approaches. MCP-counter is applied to draw a global picture of immune infiltrates across human healthy tissues and non-hematopoietic human tumors and recapitulates microenvironment-based patient stratifications associated with overall survival in lung adenocarcinoma and colorectal and breast cancer.

Subfields: Cancer Research, Molecular Biology, Oncology

View Paper: https://www.semanticscholar.org/paper/ec227d513cd486794ac85bd666a1123e5482b2df

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In Cancer Research

1. Valerie S. LeBleu
2. James P. Allison
3. Padmanee Sharma
4. William Y. Kim
5. Raghu Kalluri
6. E. Gibb
7. D. Hanahan

In Molecular Biology

1. Valerie S. LeBleu
2. D. Speiser
3. John N. Weinstein
4. V. Gopalakrishnan
5. David Gfeller
6. Zexian Zeng
7. Katherine A. Hoadley
8. Beth A. Helmink

In Oncology

1. Ton N. Schumacher
2. Padmanee Sharma
3. C. Sautès-Fridman
4. C. Blank
5. James P. Allison
6. John N. Weinstein
7. J. Bellmunt
8. D. Peeper

Citations in the corpus

• Tumor Microenvironment Characterization in Gastric Cancer Identifies Prognostic and Immunotherapeutically Relevant Gene Signatures (2019, methodology): “Proportions of stromal cells were estimated by applying the Microenvironment Cell Populations-counter method, which allows for robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data (17).”
• B cells and tertiary lymphoid structures promote immunotherapy response (2020, positive): “…most differentially expressed genes in R versus NR. Findings were corroborated using a computational method to estimate immune and stromal composition of tumor samples (MCP counter 18 ), and were corroborated in another melanoma cohort and in a cohort of renal cell carcinoma (RCC) patients on ICB.”
• IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures (2020, methodology): “MCP-counter conducts robust quantification of the absolute abundance of eight immune and two stromal cell populations in heterogeneous tissues from transcriptomic data (17).”
• Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data (2017, methodology): “We then collected publicly available IHC and single-cell RNA-Seq data of colorectal and melanoma tumors.”