Consensus Analysis of Whole Transcriptome Profiles from Two Breast Cancer Patient Cohorts Reveals Long Non-Coding RNAs Associated with Intrinsic Subtype and the Tumour Microenvironment.
Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of cellular processes and diseases such as cancer; however, their functions remain poorly characterised. Several studies have demonstrated that lncRNAs are typically disease and tumour subtype specific, particularly in breast cancer where lncRNA expression alone is sufficient to discriminate samples based on hormone status and molecular intrinsic subtype. However, little attempt has been made to assess the reproducibility of lncRNA signatures across more than one dataset. In this work, we derive consensus lncRNA signatures indicative of breast cancer subtype based on two clinical RNA-Seq datasets: the Utah Breast Cancer Study and The Cancer Genome Atlas, through integration of differential expression and hypothesis-free clustering analyses. The most consistent signature is associated with breast cancers of the basal-like subtype, leading us to generate a putative set of six lncRNA basal-like breast cancer markers, at least two of which may have a role in cis-regulation of known poor prognosis markers. Through in silico functional characterization of individual signatures and integration of expression data from pre-clinical cancer models, we discover that discordance between signatures derived from different clinical cohorts can arise from the strong influence of non-cancerous cells in tumour samples. As a consequence, we identify nine lncRNAs putatively associated with breast cancer associated fibroblasts, or the immune response. Overall, our study establishes the confounding effects of tumour purity on lncRNA signature derivation, and generates several novel hypotheses on the role of lncRNAs in basal-like breast cancers and the tumour microenvironment.
Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, South Yorkshire, United Kingdom.
James R
0000-0002-7771-914X
JR
Bradford
Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, South Yorkshire, United Kingdom.
Angela
A
Cox
Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States.
Philip
P
Bernard
Department of Internal Medicine, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, United States.
Nicola J
NJ
Camp
D014408:Biomarkers, Tumor / Q000235:genetics; D001940:Breast / Q000473:pathology; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D016000:Cluster Analysis; D015331:Cohort Studies; D019295:Computational Biology; D018450:Disease Progression; D005260:Female; D015972:Gene Expression Regulation, Neoplastic; D015894:Genome, Human; D006801:Humans; D011379:Prognosis; D062085:RNA, Long Noncoding / Q000235:genetics*; D015203:Reproducibility of Results; D059467:Transcriptome; D059016:Tumor Microenvironment
D014408:Biomarkers, Tumor; D062085:RNA, Long Noncoding
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