Development of cancer prognostic signature based on pan-cancer proteomics

Abstract

Utilizing genomic data to predict cancer prognosis was insufficient. Proteomics can improve our understanding of the etiology and progression of cancer and improve the assessment of cancer prognosis. And the Clinical Proteomic Tumor Analysis Consortium (CPTAC) has generated extensive proteomics data of the vast majority of tumors. Based on CPTAC, we can perform a proteomic pan-carcinoma analysis. We collected the proteomics data and clinical features of cancer patients from CPTAC. Then, we screened 69 differentially expressed proteins (DEPs) with R software in five cancers: hepatocellular carcinoma (HCC), children’s brain tumor tissue consortium (CBTTC), clear cell renal cell carcinoma (CCRC), lung adenocarcinoma (LUAD) and uterine corpus endometrial carcinoma (UCEC). GO and KEGG analysis were performed to clarify the function of these proteins. We also identified their interactions. The DEPs-based prognostic model for predicting over survival was identified by least absolute shrinkage and selection operator (LASSO)-Cox regression model in training cohort. Then, we used the time-dependent receiver operating characteristics analysis to evaluate the ability of the prognostic model to predict overall survival and validated it in validation cohort. The results showed that the DEPs-based prognostic model could accurately and effectively predict the survival rate of most cancers.

A Microarray Study on the Expression of ANKRD49 in Lung Squamous Cell Carcinoma and Its Clinicopathologic Significance

“…With the help of CRTAC database, SPOCK2, HSD17B4, ACAA1, and PXMP4 were identified as the novel biomarkers for NSCLC diagnosis and prognosis 24,25. Next, we will furtherly analyze the expression pattern and function of ANKRD49 in LUSC by integrating into the CPTAC proteomics database, Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO) database 26,27. Moreover, lung adenocarcinoma, another subtype of NSCLC will be incorporated to analyze the expression pattern and function of ANKRD49 by using joint analysis of the microarray-based and CPTAC-based data to explore the value of ANKRD49 as a biomarker for NSCLC.…”

p-Coumaric acid regulates macrophage polarization in myocardial ischemia/reperfusion by promoting the expression of indoleamine 2, 3-dioxygenase

“…As previous study, RIPA lysis buffer was used to extract total protein from mouse BMDMs and heart tissues [ 25 ]. Protein concentration was detected using a BCA kit.…”