Reconstruction of kidney renal clear cell carcinoma evolution across pathological stages

Scientific Reports
Shichao PangYixue Li

Abstract

Although numerous studies on kidney renal clear cell carcinoma (KIRC) were carried out, the dynamic process of tumor formation was not clear yet. Inadequate attention was paid on the evolutionary paths among somatic mutations and their clinical implications. As the tumor initiation and evolution of KIRC were primarily associated with SNVs, we reconstructed an evolutionary process of KIRC using cross-sectional SNVs in different pathological stages. KIRC driver genes appeared early in the evolutionary tree, and the genes with moderate mutation frequency showed a pattern of stage-by-stage expansion. Although the individual gene mutations were not necessarily associated with survival outcome, the evolutionary paths such as VHL-PBRM1 and FMN2-PCLO could indicate stage-specific prognosis. Our results suggested that, besides mutation frequency, the evolutionary relationship among the mutated genes could facilitate to identify novel drivers and biomarkers for clinical utility.

References

Oct 1, 1976·Science·P C Nowell
Sep 5, 2002·Nature Reviews. Cancer·William G Kaelin
Dec 6, 2003·Proceedings of the National Academy of Sciences of the United States of America·Martin A NowakYoh Iwasa
May 28, 2004·Trends in Molecular Medicine·Maria F Czyzyk-Krzeska, Jaroslaw Meller
Jun 28, 2005·Nucleic Acids Research·Bing ZhangJay Snoddy
Nov 17, 2006·Nature Reviews. Cancer·Lauren M F MerloCarlo C Maley
Mar 9, 2007·Nature·Christopher GreenmanMichael R Stratton
Jan 29, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Kornelia Polyak
Dec 23, 2011·Journal of Biomedicine & Biotechnology·Katrin TöpferAchim Temme
Sep 29, 2012·BMC Medicine·Naveen S VasudevRosamonde E Banks
Dec 12, 2012·Urologic Oncology·W Marston Linehan, W Kimryn Rathmell
Apr 27, 2013·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·A Ari HakimiUNKNOWN ccRCC Cancer Genome Atlas (KIRC TCGA) Research Network investigators
May 25, 2013·Nucleic Acids Research·Jing WangBing Zhang
Jun 25, 2013·Nature·UNKNOWN Cancer Genome Atlas Research Network
Sep 28, 2013·Nature Genetics·UNKNOWN Cancer Genome Atlas Research NetworkJoshua M Stuart
Sep 28, 2013·Nature Genetics·Giovanni CirielloChris Sander
May 9, 2014·Bioinformatics·Navodit MisraMartin Vingron
Feb 11, 2015·Nature Genetics·Andrea SottorivaChristina Curtis
Feb 24, 2015·Human Mutation·Alex H RamosGad Getz
Mar 4, 2015·Trends in Genetics : TIG·Arend Sidow, Noah Spies
Jan 19, 2016·Nature Genetics·Marc J WilliamsAndrea Sottoriva
Jan 21, 2016·Nature·Bernhard C LechtenbergStefan J Riedl
Dec 14, 2016·Scientific Reports·Hannah GrunerPedro Miura
Feb 14, 2017·Nature Reviews. Genetics·Russell Schwartz, Alejandro A Schäffer
Jun 6, 2017·Nature Genetics·Ruping SunChristina Curtis

❮ Previous
Next ❯

Software Mentioned

R package “ survminer ”
UCSC cancer browser Xena
circRNA
R
Cytoscape
Bayesian Mutation Landscape ( BML )
GeneOverlap package
GEne SeT AnaLysis Toolkit
Oncotator

Related Concepts

Related Feeds

Adenocarcinoma, Clear Cell

Clear Cell Adenocarcinoma is a tumor that arises in the female genital tract and is characterized by cells that appear clear under the microscope. Discover the latest research here.