Abstract
Functional studies of long noncoding RNAs (lncRNAs) are often performed in the context of only a single cancer type. However, the tissue-specific expression patterns of lncRNAs raise the question of whether lncRNA associations identified in one cancer type are relevant to other cancer types. Here, we examine the relationships between the expression levels of 50 cancer-related lncRNAs and survival data from 24 types of cancer in The Cancer Genome Atlas (TCGA) with the goal of identifying prognosis related lncRNAs. Our results suggest that high expression levels of certain lncRNAs are consistently associated with worse/better survival in a number of cancers, while other lncRNAs have different prognostic roles in different types of cancer. Our analysis also identifies 20 novel unadjusted associations that have not been reported before. In addition, in low-grade glioma (LGG), prognostic-related lncRNAs are identified after conditioning on known clinical biomarker and common therapy, revealing that 2 lncRNAs, FOXP4-AS1, and NEAT1, are associated with temozolomide response—a standard-of-care in LGG. Pathway analysis suggests NF-kB/STAT3 signaling pathway enrichment in LGG patients with high NEAT1 expression and DNA repair/myc gene set enrichment in LGG patients with high expression of FOXP4-AS1. Our work demonstrates the context dependency of lncRNAs across cancer types and highlights a number of lncRNAs as potential novel cancer prognosis markers.
Original language | English (US) |
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Pages (from-to) | 98-110 |
Number of pages | 13 |
Journal | Translational Research |
Volume | 230 |
DOIs | |
State | Published - Apr 2021 |
Bibliographical note
Funding Information:Financial support: This work was supported by a NIH/NCI grant R01CA204856 . Y.H. receives 3M Fellowship. R.S.H. also receives support from a research grant from the Avon Foundation for Women; the NIH/NCI grant R01CA229618 ; and a University of Minnesota Faculty Research development grant.
Funding Information:
Financial support: This work was supported by a NIH/NCI grant R01CA204856. Y.H. receives 3M Fellowship. R.S.H. also receives support from a research grant from the Avon Foundation for Women; the NIH/NCI grant R01CA229618; and a University of Minnesota Faculty Research development grant. Declaration of competing interest: All authors have read the journal's policy on disclosure of potential conflicts of interest and declare no conflict of interest. All authors have read the journal's authorship agreement and the manuscript has been reviewed by and approved by all named authors. We thank Aritro Nath at the Department of Medical Oncology and Therapeutics Research at City of Hope for giving suggestions at the early stage of this project. We also thank the 3M Science and Technology Fellowship for their generous support.
Publisher Copyright:
© 2020 Elsevier Inc.
Keywords
- Long noncoding RNA
- TCGA
- cancer prognosis marker
- low-grade glioma
- pharmacogenomic