Comprehensive gene cluster analysis of head and neck squamous cell carcinoma TCGA RNA‐seq data defines B cell immunity‐related genes as a robust survival predictor

Abstract

Background The authors aimed to define novel gene expression signatures that are associated with patients' survival with head and neck squamous cell carcinoma (HNSCC). Methods TCGA RNA‐seq data were used for gene expression clusters extraction from 499 tumor samples by the “EPIG” method. Tumor samples were then partitioned into lower and higher than median level groups for survival relevant analysis by Kaplan–Meier estimator. Results We found that two gene clusters (_1, _2) are favorably, while two (_3, _4) are unfavorably, associated with patients' survival with HNSCC. Notably, most genes on the top lists of cluster_2 are associated with B cells. A gene expression signature with combined genes from cluster_2 and _4 was further determined to be associated with HNSCC survival rate. Conclusion Our work strongly supported a favorable role of B cells in patients' survival with HNSCC and identified a novel coexpressed gene signature as prognostic biomarker for patients' survival with HNSCC estimation.

Prognosis and Dissection of the Immune Microenvironment in Head and Neck Squamous Cell Carcinoma Based on Fatty Acid Metabolism-Related Signatures

“…JCHAIN is also a new B-cell prognostic biomarker that can predict OS in HNSCC [32,33]. Many studies have shown a relationship between B-cell immunity and a good prognosis for patients with HNSCC [32][33][34]. We found that JCHAIN was a highly expressed protective gene in the low-risk group.…”

“…JCHAIN (also known as IGJ) encodes the immunoglobulin J chain, the unit that connects IgA and IgM monomers, and it has decreased expression in HNSCC and is related to a better prognosis [31]. JCHAIN is also a new B-cell prognostic biomarker that can predict OS in HNSCC [32,33]. Many studies have shown a relationship between B-cell immunity and a good prognosis for patients with HNSCC [32][33][34].…”

Live or Heat-Killed Lactobacillus rhamnosus Aerosolization Decreases Adenomatous Lung Cancer Development in a Mouse Carcinogen-Induced Tumor Model

“…An association between J chain expression and an increased OS has been observed in other tumor types, supporting our observation. Xin Feng et al identified a gene signature that includes the J chain gene able to discriminate head and neck squamous cell carcinoma patients with better overall survival probability [ 68 ]. Moreover, recent studies revealed that a high J chain expression is associated with better prognosis in sarcoma [ 69 ] and breast cancer patients [ 70 , 71 ].…”

Y‐Chromosome‐Linked Genes Are Associated With Sex‐Related Head‐Neck Squamous Cell Carcinoma Survival

“…The Y-linked genes favorable to overall survival were extracted by a previously reported method, "extracting gene expression patterns and identifying co-expressed genes" (EPIG). 15,26 EPIG is an unsupervised cluster extraction method that goes through a pair-wised correlation evaluation among all the genes to extract all the possible clusters with a given correlation threshold. The genes in each of the extracted patterns are highly similar in their expression profiles, which may be caused by coexpression to underlying biological cause.…”

“…14 We have recently identified several clusters of coexpressed genes that are associated with HNSCC overall survival by 1 Departments of Otolaryngology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA analyzing TCGA dataset. 15 Briefly, 4 clusters of coexpressed genes were identified, with 2 of them favorable and 2 of them unfavorable to HNSCC overall survival. In addition, their association with survival is independent of other clinical condition, for instance, HPV status or tumor sites.…”