Integrated analysis of single-cell RNA-seq and bulk RNA-seq unravels tumour heterogeneity plus M2-like tumour-associated macrophage infiltration and aggressiveness in TNBC.

Cancer Immunology, Immunotherapy : CII
Xuanwen BaoWeijia Fang

Abstract

Triple-negative breast cancer (TNBC) is characterized by a more aggressive clinical course with extensive inter- and intra-tumour heterogeneity. Combination of single-cell and bulk tissue transcriptome profiling allows the characterization of tumour heterogeneity and identifies the association of the immune landscape with clinical outcomes. We identified inter- and intra-tumour heterogeneity at a single-cell resolution. Tumour cells shared a high correlation amongst stemness, angiogenesis, and EMT in TNBC. A subset of cells with concurrent high EMT, stemness and angiogenesis was identified at the single-cell level. Amongst tumour-infiltrating immune cells, M2-like tumour-associated macrophages (TAMs) made up the majority of macrophages and displayed immunosuppressive characteristics. CIBERSORT was applied to estimate the abundance of M2-like TAM in bulk tissue transcriptome file from The Cancer Genome Atlas (TCGA). M2-like TAMs were associated with unfavourable prognosis in TNBC patients. A TAM-related gene signature serves as a promising marker for predicting prognosis and response to immunotherapy. Two commonly used machine learning methods, random forest and SVM, were applied to find the genes that were mostly associated wit...Continue Reading

References

Aug 2, 2005·Cell Metabolism·Adriana DonovanNancy C Andrews
Feb 6, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Cornelia LiedtkeLajos Pusztai
Dec 31, 2008·BMC Bioinformatics·Peter Langfelder, Steve Horvath
Jun 25, 2009·Annals of Oncology : Official Journal of the European Society for Medical Oncology·B K LinderholmR Lewensohn
Apr 30, 2010·Bioinformatics·Matthew D Wilkerson, D Neil Hayes
Nov 12, 2010·The New England Journal of Medicine·William D FoulkesJorge S Reis-Filho
Mar 8, 2011·Cell·Douglas Hanahan, Robert A Weinberg
Nov 26, 2011·Surgery Today·Ken ShirabeYoshihiko Maehara
Aug 28, 2012·Nature Genetics·David CoelhoMatthias R Baumgartner
Jan 18, 2013·BMC Bioinformatics·Sonja HänzelmannJustin Guinney
Aug 27, 2013·Epigenetics : Official Journal of the DNA Methylation Society·Stephanie-May RuchatLuigi Bouchard
Jul 19, 2014·Immunity·Roy Noy, Jeffrey W Pollard
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
May 16, 2015·Cancer Research·Michele W L TengMark J Smyth
Oct 16, 2015·Molecular Medicine Reports·Chung-Hsin TsaiYi-Ming Shyr
Jan 21, 2017·Journal of Cellular Biochemistry·Muhammad TariqBo Yang
Feb 25, 2017·Nature Communications·Atul BhardwajFrank Wuest
Apr 13, 2018·Frontiers in Oncology·Judith A SeidelKenji Kabashima
Sep 6, 2018·Nature Communications·Mihriban KaraayvazLeif W Ellisen
Nov 22, 2019·Journal of Translational Medicine·Xuanwen BaoMichael Rosemann

❮ Previous
Next ❯

Citations

Mar 11, 2021·Computational and Mathematical Methods in Medicine·Chunni FanNing Liu
May 1, 2021·International Journal of Molecular Sciences·Marco Del GiudiceMatteo Cereda
Jun 21, 2021·Seminars in Cancer Biology·Zhan HuaJianjun Zhou
Jun 16, 2021·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Jing YangYu Shyr

❮ Previous
Next ❯

Related Concepts

Related Feeds

Cancer -Omics

A variety of different high-throughput technologies can be used to identify the complete catalog of changes that characterize the molecular profile of cohorts of tumor samples. Discover the latest insights gained from cancer 'omics' in this feed.

Breast Cancer Triple-N

Breast cancer cells have receptors for estrogen, progesterone, HER2 receptors (also called ERBB2). Triple-negative breast cancers do not have any of these receptors. Here are the latest discoveries pertaining to triple-negative breast cancers.