Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival--Evidence from TCGA Pan-Cancer Data

Scientific Reports
Xiu HuangHongyu Zhao

Abstract

Although normal tissue samples adjacent to tumors are sometimes collected from patients in cancer studies, they are often used as normal controls to identify genes differentially expressed between tumor and normal samples. However, it is in general more difficult to obtain and clearly define paired normal samples, and whether these samples should be treated as "normal" due to their close proximity to tumors. In this article, by analyzing the accrued data in The Cancer Genome Atlas (TCGA), we show the surprising results that the paired normal samples are in general more informative on patient survival than tumors. Different lines of evidence suggest that this is likely due to tumor micro-environment instead of tumor cell contamination or field cancerization effect. Pathway analyses suggest that tumor micro-environment may play an important role in cancer patient survival either by boosting the adjacent metabolism or the in situ immunization. Our results suggest the potential benefit of collecting and profiling matched normal tissues to gain more insights on disease etiology and patient progression.

References

Dec 1, 1996·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Z S ZengJ G Guillem
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Oct 4, 2005·Proceedings of the National Academy of Sciences of the United States of America·Aravind SubramanianJill P Mesirov
Feb 11, 2009·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Joel S ParkerPhilip S Bernard
Mar 25, 2009·Nature Reviews. Cancer·Don X NguyenJoan Massagué
Aug 18, 2009·Breast Cancer Research and Treatment·Christopher M HeaphyMarco Bisoffi
Nov 6, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Melissa A TroesterSallie Smith Schneider
Apr 16, 2010·Nature·UNKNOWN International Cancer Genome ConsortiumHuanming Yang
Sep 13, 2011·Genome Research·Giovanni CirielloNikolaus Schultz
Mar 21, 2012·Breast Cancer Research : BCR·Erick Román-PérezMelissa A Troester
Oct 30, 2012·Breast Cancer Research and Treatment·Anguraj SadanandamChristopher C Benz
May 30, 2013·PLoS Computational Biology·Mark D M LeisersonBenjamin J Raphael
May 29, 2014·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Wen-Qing LiPhilip R Taylor
Jun 14, 2014·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Paul LochheadShuji Ogino
Jul 26, 2014·World Journal of Surgical Oncology·Ha-Young LeeSang Joon Shin

❮ Previous
Next ❯

Citations

Apr 6, 2018·Statistical Methods in Medical Research·Qianya QiLili Tian
Jan 14, 2018·Scientific Reports·Kelly A MercierBenjamin Alman
Aug 25, 2019·Biometrics·Jun Young Park, Eric F Lock
May 12, 2017·Gastric Cancer : Official Journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association·Meng XieJia-Fu Ji
Aug 3, 2016·Tumour Biology : the Journal of the International Society for Oncodevelopmental Biology and Medicine·Donatella ConconiMarialuisa Lavitrano
Apr 25, 2019·Scientific Data·Maria SuntsovaAnton Buzdin
Dec 29, 2018·Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association for Cancer Research, Cosponsored by the American Society of Preventive Oncology·Kevin H KenslerYujing J Heng
May 1, 2021·Cancers·Mathushan SubasriDean H Betts
Jun 19, 2021·PLoS Computational Biology·H Robert Frost
Jul 18, 2021·Molecular and Cellular Endocrinology·Ana Paula Santin BertoniTania Weber Furlanetto

❮ Previous
Next ❯

Methods Mentioned

BETA
exome sequencing
PCA

Software Mentioned

R
Gene Set Enrichment Analysis ( GSEA )
Random Forests
GSEA

Related Concepts

Related Feeds

Cancer Metabolism

In order for cancer cells to maintain rapid, uncontrolled cell proliferation, they must acquire a source of energy. Cancer cells acquire metabolic energy from their surrounding environment and utilize the host cell nutrients to do so. Here is the latest research on cancer metabolism.