Identification of prognostic genes in uveal melanoma microenvironment

PloS One
Huan Luo, Chao Ma

Abstract

Uveal melanoma (UM) is the most common primary intraocular malignancy in adults. Many previous studies have demonstrated that the infiltrating of immune and stromal cells in the tumor microenvironment contributes significantly to prognosis. Dataset TCGA-UVM, download from TCGA portal, was taken as the training cohort, and GSE22138, obtained from GEO database, was set as the validation cohort. ESTIMATE algorithm was applied to find intersection differentially expressed genes (DEGs) among tumor microenvironment. Kaplan-Meier analysis and univariate Cox regression model were performed on intersection DEGs to initial screen for potential prognostic genes. Then these genes entered into the validation cohort for validation using the same methods as that in the training cohort. Moreover, we conducted correlation analyses between the genes obtained in the validation cohort and the status of chromosome 3, chromosome 8q, and tumor metastasis to get prognosis genes. At last, the immune infiltration analysis was performed between the prognostic genes and 6 main kinds of tumor-infiltrating immune cells (TICs) for understanding the role of the genes in the tumor microenvironment. 959 intersection DEGs were found in the UM microenvironment. K...Continue Reading

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Citations

Apr 4, 2021·International Journal of Molecular Sciences·Sandra García-MuleroJosep M Piulats
Jun 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Richelly CardosoCláudio Nahum Alves
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Aug 27, 2021·Analytical Cellular Pathology (Amsterdam)·Zhongjun Tang, Kebo Cai
Nov 9, 2021·Frontiers in Oncology·Thi Hai Yen NguyenDuc-Hau Le

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Datasets Mentioned

BETA
GSE22138
GSE72094

Methods Mentioned

BETA
chromosomal aberrations

Software Mentioned

UM
limma
DecisionDx
Metascape
pheatmap
ESTIMATE
TIMER
R
limma R package
canvasXpress

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