Unique protein expression signatures of survival time in kidney renal clear cell carcinoma through a pan-cancer screening

BMC Genomics

Research

Peilin Jia¹  Guangchun Han¹  Zhongming Zhao²  Xiaofeng Song³  Eric Jonasch⁴  Gordon B. Mills⁵  Zhiyong Ding⁵  Wei Zhao⁵  Jose A. Karam⁶  Patrick Kwok-Shing Ng⁷ 

[1] Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, 77030, Houston, TX, USA;Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St., Suite 820, 77030, Houston, TX, USA;Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, 77030, Houston, TX, USA;Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, 211106, Nanjing, Jiangsu, China;Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA;Department of Systems Biology, University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA;Department of Urology, Division of Surgery, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA;Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 77030, Houston, TX, USA;

关键词: Pan-cancer screening;    Kidney renal clear cell carcinoma (KIRC);    Reverse phase protein Array (RPPA);    Protein expression;    Prognostic biomarker;   

DOI  :  10.1186/s12864-017-4026-6

来源: Springer

【 摘 要 】

BackgroundIn 2016, it is estimated that there will be 62,700 new cases of kidney cancer in the United States, and 14,240 patients will die from the disease. Because the incidence of kidney renal clear cell carcinoma (KIRC), the most common type of kidney cancer, is expected to continue to increase in the US, there is an urgent need to find effective diagnostic biomarkers for KIRC that could help earlier detection of and customized treatment strategies for the disease. Accordingly, in this study we systematically investigated KIRC’s prognostic biomarkers for survival using the reverse phase protein array (RPPA) data and the high throughput sequencing data from The Cancer Genome Atlas (TCGA).ResultsWith comprehensive data available in TCGA, we systematically screened protein expression based survival biomarkers in 10 major cancer types, among which KIRC presented many protein prognostic biomarkers of survival time. This is in agreement with a previous report that expression level changes (mRNAs, microRNA and protein) may have a better performance for prognosis of KIRC. In this study, we also identified 52 prognostic genes for KIRC, many of which are involved in cell-cycle and cancer signaling, as well as 15 tumor-stage-specific prognostic biomarkers. Notably, we found fewer prognostic biomarkers for early-stage than for late-stage KIRC. Four biomarkers (the RPPA protein IDs: FASN, ACC1, Cyclin_B1 and Rad51) were found to be prognostic for survival based on both protein and mRNA expression data.ConclusionsThrough pan-cancer screening, we found that many protein biomarkers were prognostic for patients’ survival in KIRC. Stage-specific survival biomarkers in KIRC were also identified. Our study indicated that these protein biomarkers might have potential clinical value in terms of predicting survival in KIRC patients and developing individualized treatment strategies. Importantly, we found many biomarkers in KIRC at both the mRNA expression level and the protein expression level. These biomarkers shared a significant overlap, indicating that they were technically replicable.

【 授权许可】

CC BY   
© The Author(s). 2017