Dissecting cellular states of infiltrating microenvironment cells in melanoma by integrating single-cell and bulk transcriptome analysis.
Dissecting cellular states of infiltrating microenvironment cells in melanoma by integrating single-cell and bulk transcriptome analysis.
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DOI：
10.1186/s12865-023-00587-8
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发表时间：
2023-12-12
期刊：
影响因子：
3
通讯作者：
中科院分区：
文献类型：
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Cellular states of different immune cells can affect the activity of the whole immune microenvironment. Here, leveraging reference profiles of microenvironment cell states that were constructed based on single-cell RNA-seq data of melanoma, we dissected the composition of microenvironment cell states across 463 skin cutaneous melanoma (SKCM) bulk samples through CIBERSORT-based deconvolution of gene expression profiles and revealed high heterogeneity of their distribution. Correspondence analysis on the estimated cellular fractions of melanoma bulk samples was performed to identify immune phenotypes. Based on the publicly available clinical survival and therapy data, we analyzed the relationship between immune phenotypes and clinical outcomes of melanoma. By analysis of the relationships among those cell states, we further identified three distinct tumor microenvironment immune phenotypes: “immune hot/active”, “immune cold-suppressive” and “immune cold-exhausted”. They were characterized by markedly different patterns of cell states: most notably the CD8 T Cytotoxic state, CD8 T Mixed state, B non-regulatory state and cancer-associated fibroblasts (CAFs), depicting distinct types of antitumor immune response (or immune activity). These phenotypes had prognostic significance for progression-free survival and implications in response to immune therapy in an independent cohort of anti-PD1 treated melanoma patients. The proposed strategy of leveraging single-cell data to dissect the composition of microenvironment cell states in individual bulk tumors can also extend to other cancer types, and our results highlight the importance of microenvironment cell states for the understanding of tumor immunity. The online version contains supplementary material available at 10.1186/s12865-023-00587-8.
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影响因子：
46.9
作者：
Becht, Etienne;McInnes, Leland;Newell, Evan W.
通讯作者：
Newell, Evan W.
实现癌症基因组数据的共同愿景。
DOI：
10.1056/nejmp1607591
发表时间：
2016-09-22
期刊：
The New England journal of medicine
影响因子：
--
作者：
Grossman RL;Heath AP;Ferretti V;Varmus HE;Lowy DR;Kibbe WA;Staudt LM
通讯作者：
Staudt LM
影响因子：
64.8
作者：
Im SJ;Hashimoto M;Gerner MY;Lee J;Kissick HT;Burger MC;Shan Q;Hale JS;Lee J;Nasti TH;Sharpe AH;Freeman GJ;Germain RN;Nakaya HI;Xue HH;Ahmed R
通讯作者：
Ahmed R
乳腺癌中免疫浸润及其临床意义的模式：一项基于基因表达的回顾性研究。
影响因子：
15.8
作者：
Ali HR;Chlon L;Pharoah PD;Markowetz F;Caldas C
通讯作者：
Caldas C
DOI：
10.1093/annonc/mdy450
发表时间：
2018-12-01
期刊：
Annals of oncology : official journal of the European Society for Medical Oncology
影响因子：
--
作者：
Ciavarella S;Vegliante MC;Fabbri M;De Summa S;Melle F;Motta G;De Iuliis V;Opinto G;Enjuanes A;Rega S;Gulino A;Agostinelli C;Scattone A;Tommasi S;Mangia A;Mele F;Simone G;Zito AF;Ingravallo G;Vitolo U;Chiappella A;Tarella C;Gianni AM;Rambaldi A;Zinzani PL;Casadei B;Derenzini E;Loseto G;Pileri A;Tabanelli V;Fiori S;Rivas-Delgado A;López-Guillermo A;Venesio T;Sapino A;Campo E;Tripodo C;Guarini A;Pileri SA
通讯作者：
Pileri SA