Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of cutaneous melanoma

Sheng Yang, Tong Liu, Hongmei Nan, Yan Wang, Hao Chen, Xiaomei Zhang, Yan Zhang, Bo Shen, Pudong Qian, Siyi Xu, Jing Sui, Geyu Liang

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Cutaneous malignant melanoma (hereafter called melanoma) is one of the most aggressive cancers with increasing incidence and mortality rates worldwide. In this study, we performed a systematic investigation of the tumor microenvironmental and genetic factors associated with melanoma to identify prognostic biomarkers for melanoma. We calculated the immune and stromal scores of melanoma patients from the Cancer Genome Atlas (TCGA) using the ESTIMATE algorithm and found that they were closely associated with patients’ prognosis. Then the differentially expressed genes were obtained based on the immune and stromal scores, and prognostic immune-related genes further identified. Functional analysis and the protein–protein interaction network further revealed that these genes enriched in many immune-related biological processes. In addition, the abundance of six infiltrating immune cells was analyzed using prognostic immune-related genes by TIMER algorithm. The unsupervised clustering analysis using immune-cell proportions revealed eight clusters with distinct survival patterns, suggesting that dendritic cells were most abundant in the microenvironment and CD8+ T cells and neutrophils were significantly related to patients’ prognosis. Finally, we validated these genes in three independent cohorts from the Gene Expression Omnibus database. In conclusion, this study comprehensively analyzed the tumor microenvironment and identified prognostic immune-related biomarkers for melanoma.

Original languageEnglish (US)
Pages (from-to)1025-1035
Number of pages11
JournalJournal of cellular physiology
Volume235
Issue number2
DOIs
StatePublished - Feb 1 2020

Fingerprint

Tumor Microenvironment
Tumors
Melanoma
Genes
Skin
Biomarkers
Biological Phenomena
Neoplasms
Atlases
Functional analysis
T-cells
Dendritic Cells
Cluster Analysis
Gene expression
Neutrophils
Genome
Databases
T-Lymphocytes
Gene Expression
Survival

Keywords

  • cutaneous melanoma
  • GEO
  • prognosis
  • TCGA
  • tumor microenvironment

ASJC Scopus subject areas

  • Physiology
  • Clinical Biochemistry
  • Cell Biology

Cite this

Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of cutaneous melanoma. / Yang, Sheng; Liu, Tong; Nan, Hongmei; Wang, Yan; Chen, Hao; Zhang, Xiaomei; Zhang, Yan; Shen, Bo; Qian, Pudong; Xu, Siyi; Sui, Jing; Liang, Geyu.

In: Journal of cellular physiology, Vol. 235, No. 2, 01.02.2020, p. 1025-1035.

Research output: Contribution to journalArticle

Yang, S, Liu, T, Nan, H, Wang, Y, Chen, H, Zhang, X, Zhang, Y, Shen, B, Qian, P, Xu, S, Sui, J & Liang, G 2020, 'Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of cutaneous melanoma', Journal of cellular physiology, vol. 235, no. 2, pp. 1025-1035. https://doi.org/10.1002/jcp.29018
Yang, Sheng ; Liu, Tong ; Nan, Hongmei ; Wang, Yan ; Chen, Hao ; Zhang, Xiaomei ; Zhang, Yan ; Shen, Bo ; Qian, Pudong ; Xu, Siyi ; Sui, Jing ; Liang, Geyu. / Comprehensive analysis of prognostic immune-related genes in the tumor microenvironment of cutaneous melanoma. In: Journal of cellular physiology. 2020 ; Vol. 235, No. 2. pp. 1025-1035.
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