The Landscape of Long Non-Coding RNA Dysregulation and Clinical Relevance in Muscle Invasive Bladder Urothelial Carcinoma
by
Haotian Shen 1,†, Lindsay M. Wong 1,†, Wei Tse Li 1,†, Megan Chu 1, Rachel A. High 2,3, Eric Y. Chang 2,3, Jessica Wang-Rodriguez 4,5 and Weg M. Ongkeko 1,*
Haotian Shen 1,†, Lindsay M. Wong 1,†, Wei Tse Li 1,†, Megan Chu 1, Rachel A. High 2,3, Eric Y. Chang 2,3, Jessica Wang-Rodriguez 4,5 and Weg M. Ongkeko 1,*
1
Department of Otolaryngology-Head and Neck Surgery, University of California San Diego, La Jolla, CA 92093, USA
2
Department of Radiology, University of California San Diego, La Jolla, CA 92093, USA
3
Radiology Service, VA San Diego Healthcare System San Diego, La Jolla, CA 92161, USA
4
Department of Pathology, University of California San Diego, La Jolla, CA 92093, USA
5
Pathology Service, VA San Diego Healthcare System, San Diego, CA 92161, USA
*
Author to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Cancers 2019, 11(12), 1919; https://doi.org/10.3390/cancers11121919
Received: 28 October 2019 / Revised: 18 November 2019 / Accepted: 22 November 2019 / Published: 2 December 2019
(This article belongs to the Special Issue Non-Coding RNAs as Emerging Regulators of Signalling Pathways and Novel Therapeutic Targets in Human Cancers)
Bladder cancer is one of the most common cancers in the United States, but few advancements in treatment options have occurred in the past few decades. This study aims to identify the most clinically relevant long non-coding RNAs (lncRNAs) to serve as potential biomarkers and treatment targets for muscle invasive bladder cancer (MIBC). Using RNA-sequencing data from 406 patients in The Cancer Genome Atlas (TCGA) database, we identified differentially expressed lncRNAs in MIBC vs. normal tissues. We then associated lncRNA expression with patient survival, clinical variables, oncogenic signatures, cancer- and immune-associated pathways, and genomic alterations. We identified a panel of 20 key lncRNAs that were most implicated in MIBC prognosis after differential expression analysis and prognostic correlations. Almost all lncRNAs we identified are correlated significantly with oncogenic processes. In conclusion, we discovered previously undescribed lncRNAs strongly implicated in the MIBC disease course that may be leveraged for diagnostic and treatment purposes in the future. Functional analysis of these lncRNAs may also reveal distinct mechanisms of bladder cancer carcinogenesis.
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Keywords:
lncRNAs; lncRNA-protein interaction; bladder carcinoma; TCGA
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MDPI and ACS Style
Shen, H.; Wong, L.M.; Li, W.T.; Chu, M.; High, R.A.; Chang, E.Y.; Wang-Rodriguez, J.; Ongkeko, W.M. The Landscape of Long Non-Coding RNA Dysregulation and Clinical Relevance in Muscle Invasive Bladder Urothelial Carcinoma. Cancers 2019, 11, 1919.
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