Cis - and Trans -Acting Expression Quantitative Trait Loci of Long Non-Coding RNA in 2,549 Cancers With Potential Clinical and Therapeutic Implications

Frontiers in Oncology
Wenzhi LiQiyuan Li

Abstract

Many cancer risk loci act as expression quantitative trait loci (eQTLs) of transcripts including non-coding RNA. Long non-coding RNAs (lncRNAs) are implicated in various human cancers. However, the pathological and clinical impacts of the genetic determinants of lncRNAs in cancers remain largely unknown. In this study, we performed eQTL mapping of lncRNA expression (elncRNA) in 11 TCGA cancer types and characterized the biological processes of elncRNAs in the setting of genomic location, cancer treatment responses, and immune microenvironment. As a result, 10.86% of the cis-eQTLs and 1.67% of the trans-eQTLs of lncRNA were related to known genome-wide association studies (GWAS) cancer risk loci. The elncRNAs are significantly enriched for those which are previously annotated as predictive of drug sensitivities in cancer cell lines. We further revealed the downstream transcriptomic effectors of eQTL-elncRNA pairs. Our data specifically suggested that the genes affected by eQTL-elncRNA associations are enriched in the immune system processes and eQTL-elncRNA associations influence the constitution of tumor infiltrating lymphocytes. In ovarian cancer, the "rs34631313-AC092580.4" pair was associated with increased fraction of CD8+ ...Continue Reading

References

Feb 5, 2003·Nature Genetics·Vivian G CheungRichard S Spielman
Apr 23, 2003·The Journal of Immunology : Official Journal of the American Association of Immunologists·Xiaoyu HuLionel B Ivashkiv
Oct 4, 2003·Journal of Leukocyte Biology·Kate SchroderDavid A Hume
Oct 19, 2006·Nature Reviews. Genetics·Matthew V Rockman, Leonid Kruglyak
Nov 8, 2006·The Journal of Biological Chemistry·Andy WullaertRudi Beyaert
Feb 27, 2007·Cell·Peter A Jones, Stephen B Baylin
Oct 3, 2007·PLoS Genetics·Jeffrey T Leek, John D Storey
Jul 3, 2009·Proceedings of the National Academy of Sciences of the United States of America·Ahmad M KhalilJohn L Rinn
Nov 17, 2009·Proceedings of the National Academy of Sciences of the United States of America·Dusan BogunovicNina Bhardwaj
Mar 12, 2010·Nature·Stephen B MontgomeryEmmanouil T Dermitzakis
May 27, 2011·Nature Genetics·Matthew L FreedmanIan G Mills
Aug 2, 2011·Cell·Leonardo SalmenaPier Paolo Pandolfi
Sep 20, 2011·Molecular Cell·Kevin C Wang, Howard Y Chang
Nov 19, 2011·Cancer Discovery·John R Prensner, Arul M Chinnaiyan
Apr 12, 2012·Bioinformatics·Andrey A Shabalin
May 16, 2012·Proceedings of the National Academy of Sciences of the United States of America·Jaroslaw JendrzejewskiAlbert de la Chapelle
Mar 7, 2013·Genetics·Johnny T Y KungJeannie T Lee
Mar 29, 2013·Nature Genetics·Kyriaki MichailidouDouglas F Easton
May 29, 2013·Genome Biology·Wilfried Haerty, Chris P Ponting
Sep 10, 2014·Biochemical Pharmacology·Dympna J Connolly, Andrew G Bowie
Jan 20, 2015·Nature Genetics·Matthew K IyerArul M Chinnaiyan
Mar 31, 2015·Nature Methods·Aaron M NewmanAsh A Alizadeh
Apr 8, 2015·Cell Death and Differentiation·M E PeterP Ceppi
Oct 4, 2015·Nature·UNKNOWN 1000 Genomes Project ConsortiumGonçalo R Abecasis
Dec 5, 2015·Nature Communications·Dvir AranAtul J Butte
Dec 3, 2016·Nucleic Acids Research·Jacqueline MacArthurHelen Parkinson
Mar 14, 2017·American Journal of Human Genetics·Boel BrynedalChris Cotsapas
Mar 14, 2017·American Journal of Human Genetics·Chen YaoDaniel Levy
Aug 23, 2017·Nature Immunology·Y Grace ChenHoward Y Chang
Dec 1, 2017·Nature Communications·Kyoko WatanabeDanielle Posthuma
Oct 3, 2018·Journal of Cellular Biochemistry·Masoud NajafiKeywan Mortezaee
Nov 23, 2018·Proceedings of the National Academy of Sciences of the United States of America·Yoong Wearn LimMatthew L Albert
Apr 13, 2019·Lancet Neurology·Martin DichgansJonathan Rosand

❮ Previous
Next ❯

Software Mentioned

Weinberg R package
FUMA
R package PEER
ANNOVAR
R package MatrixEQTL
Plink
Bedtools
R package ( meta )
RegulomeDB
Hardy

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2021 Meta ULC. All rights reserved