Six-gene signature for predicting survival in patients with head and neck squamous cell carcinoma

Abstract

The prognosis of head and neck squamous cell carcinoma (HNSCC) patients remains poor. High-throughput sequencing data have laid a solid foundation for identifying genes related to cancer prognosis, but a gene marker is needed to predict clinical outcomes in HNSCC. In our study, we downloaded RNA Seq, single nucleotide polymorphism, copy number variation, and clinical follow-up data from TCGA. The samples were randomly divided into training and test. In the training set, we screened genes and used random forests for feature selection. Gene-related prognostic models were established and validated in a test set and GEO verification set. Six genes (PEX11A, NLRP2, SERPINE1, UPK, CTTN, D2HGDH) were ultimately obtained through random forest feature selection. Cox regression analysis confirmed the 6-gene signature is an independent prognostic factor in HNSCC patients. This signature effectively stratified samples in the training, test, and external verification sets (P < 0.01). The 5-year survival AUC in the training and verification sets was greater than 0.74. Thus, we have constructed a 6-gene signature as a new prognostic marker for predicting survival of HNSCC patients.

An individualized immune signature of pretreatment biopsies predicts pathological complete response to neoadjuvant chemoradiotherapy and outcomes in patients with esophageal squamous cell carcinoma

“…SERPINE1, an endothelial plasminogen activator inhibitor, also known as PAI-1, was reported widely expressed in various cancers and closely related to patients' outcomes. 29,30 Interestingly, Ostheimer et al pointed out that low PAI-1 levels were associated with a significantly reduced OS and PFS in patients with lung cancer undergoing radiotherapy. 31 This stands in accordance with our results.…”

(2R,3S)-Dihydroxybutanoic Acid Synthesis as a Novel Metabolic Function of Mutant Isocitrate Dehydrogenase 1 and 2 in Acute Myeloid Leukemia

“…There are known mutations in the D2HGDH gene leading to an inert enzyme. High expression of D2HGDH has also been found in head and neck squamous cell carcinoma (HNSCC), where it was reported to be a protective factor conferring low risk [ 54 ]. To date, the expression of D2HGDH in AML has not been reported, but as with HNSCC, it is possible that a high expression D2HGDH phenotype exists, which, if associated with IDH1/2, might explain the meager 7-fold difference in median plasma 2R-HG between mutated and WT IDH.…”

Prediction of Overall Survival for Early-stage Non-small Cell Lung Cancer via a Novel 7-gene Prognostic Signature and Allele Frequency Deviation (AFD)

“…Recently, molecular biomarkers and gene signatures occupied a great deal of interest from researchers and are used in clinical practice for many aspects of cancer including tumorigenesis, progression and prognosis [52]. Gene signatures [53] as well as TMB and bTMB [54,55] survival of TCGA-LUAD and GSE11969 datasets respectively. On the contrary, the AUC of our 7-gene signature was higher with using 7 genes, this makes it appropriately suitable for clinical application.…”