Research Paper Volume 12, Issue 1 pp 767—783

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

Juncheng Wang 1, *, , Xun Chen 2, *, , Yuxi Tian 3, , Gangcai Zhu 4, , Yuexiang Qin 5, , Xuan Chen 6, , Leiming Pi 7, , Ming Wei 1, , Guancheng Liu 8, , Zhexuan Li 1, , Changhan Chen 1, , Yunxia Lv 9, , Gengming Cai 10, ,

  • 1 Department of Otolaryngology, Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha 410008, People’s Republic of China
  • 2 Department of Oral and Maxillofacial Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People’s Republic of China
  • 3 Department of Oncology, Xiangya Hospital, Central South University, Changsha, 410008 People’s Republic of China
  • 4 Department of Otolaryngology, Head and Neck Surgery, The Second Xiangya Hospital, Central South University, Changsha 410011, People’s Republic of China
  • 5 Department of Health Management, The Third Xiangya Hospital, Central South University, Changsha 410011, People’s Republic of China
  • 6 Department of Stomatology, Changzheng Hospital, Second Military Medcial University, Shanghai 200003, People’s Republic of China
  • 7 Department of Otolaryngology, Head and Neck Surgery, HeYuan People's Hospital, Jinan University, He Yuan 517000, People’s Republic of China
  • 8 Department of Otolaryngology, Head and Neck Surgery, Affiliated Hospital of Guilin University, Guilin 541000, People’s Republic of China
  • 9 Department of Thyroid Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, People’s Republic of China
  • 10 Department of Otolaryngology, Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, Quanzhou 362000, People’s Republic of China
* Equal contribution

received: September 16, 2019 ; accepted: December 24, 2019 ; published: January 12, 2020 ;

https://doi.org/10.18632/aging.102655
How to Cite

Copyright © 2020 Wang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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.

Abbreviations

HNSCC: head and neck squamous cell carcinoma; TCGA: the cancer genome atlas; GEO: group on earth observations; SNPs: single nucleotide polymorphisms; CNV: copy number variation; SCC-A: squamous cell carcinoma antigen; HPV: human papilloma virus; MFA: the mutation annotation information; OS: overall survival; GO: gene ontology; KEGG: kyoto encyclopedia of genes and genomes; KM: Kaplan-Meier; HR: higher risk; PPI: protein-protein interaction.