Systematic Profiling of Alternative Splicing for Sarcoma Patients Reveals Novel Prognostic Biomarkers Associated with Tumor Microenvironment and Immune Cells.

Medical Science Monitor : International Medical Journal of Experimental and Clinical Research
Chuan HuShaoqi Tian

Abstract

BACKGROUND Alternative splicing (AS) events is a novel biomarker of tumor prognosis, but the role of AS events in sarcoma patients remains unclear. MATERIAL AND METHODS RNA-seq and clinicopathologic data of the sarcoma cohort were extracted from the TCGA database and data on AS events were downloaded from the TCGASpliceSeq database. Univariate Cox analysis, LASSO regression analysis, and multivariate Cox analysis were performed to determine the overall survival (OS)- and disease-free survival (DFS)-related AS events. Two nomograms were developed based on the independent variables, and subgroup analysis was performed. The area under the curve (AUC), calibration curve, and decision curve analysis (DCA) were used to evaluate the nomograms. Then, we used the CIBERSORT and ESTIMATE package to determine the immune cell proportion and tumor microenvironment (TME) score, respectively. The associations between AS events-based clusters and TME and immune cells were studied. RESULTS We identified 1945 and 1831 AS events as OS- and DFS-related AS events, respectively. Two nomograms based on the AS events and clinical data were established and the AUCs of nomograms ranged from 0.807 to 0.894. The calibration curve and DCA showed excellent p...Continue Reading

Citations

Jan 12, 2021·Computational and Structural Biotechnology Journal·Wei Jiang, Liang Chen

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Methods Mentioned

BETA
RNA-seq
X-tile

Software Mentioned

Consensus Cluster Plus
Cytoscape
tile
R
Metascape
LASSO
CIBERSORT

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Alternative splicing

Alternative splicing a regulated gene expression process that allows a single genetic sequence to code for multiple proteins. Here is that latest research.

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