Abstract
Once considered nonfunctional, pseudogene transcripts are now known to provide valuable information for cancer susceptibility, including head and neck cancer (HNC), a serious health problem worldwide, with about 50% unimproved overall survival over the last decades. The present review focuses on the role of pseudogene transcripts involved in HNC risk and prognosis. We combined current literature and in silico analyses from The Cancer Genome Atlas (TCGA) database to identify the most deregulated pseudogene transcripts in HNC and their genetic variations. We then built a co-expression network and performed gene ontology enrichment analysis to better understand the pseudogenes’ interactions and pathways in HNC. In the literature, few pseudogenes have been studied in HNC. Our in silico analysis identified 370 pseudogene transcripts associated with HNC, where SPATA31D5P, HERC2P3, SPATA31C2, MAGEB6P1, SLC25A51P1, BAGE2, DNM1P47, SPATA31C1, ZNF733P and OR2W5 were found to be the most deregulated and presented several genetic alterations. NBPF25P, HSP90AB2P, ZNF658B and DPY19L2P3 pseudogenes were predicted to interact with 12 genes known to participate in HNC, DNM1P47 was predicted to interact with the TP53 gene, and HLA-H pseudogene was predicted to interact with HLA-A and HLA-B genes. The identified pseudogenes were associated with cancer biology pathways involving cell communication, response to stress, cell death, regulation of the immune system, regulation of gene expression, and Wnt signaling. Finally, we assessed the prognostic values of the pseudogenes with the Kaplan–Meier Plotter database, and found that expression of SPATA31D5P, SPATA31C2, BAGE2, SPATA31C1, ZNF733P and OR2W5 pseudogenes were associated with patients’ survival. Due to pseudogene transcripts’ potential for cancer diagnosis, progression, and as therapeutic targets, our study can guide new research to HNC understanding and development of new target therapies.
Highlights
Head and neck cancer (HNC) is the eighth most common cancer worldwide, with more than 835,000 new cases and 431,000 deaths due to the disease per year [1]
We identified 370 pseudogene transcripts associated with HNC, where SPATA31D5P (SPATA31 subfamily D member 5 pseudogene), HERC2P3, SPATA31C2 (SPATA31 subfamily C member 2), MAGEB6P1, SLC25A51P1, BAGE2 (B melanoma antigen family member 2), DNM1P47 (DNM1 pseudogene 47), SPATA31C1 (SPATA31 subfamily C member 1), ZNF733P, and OR2W5 were found to be the most deregulated in HNC
We identified 993 somatic genetic alterations in the 370 pseudogene transcripts identified in HNC, and single-nucleotide variation (SNV) was the most common type (96.8%), followed by deletions (1.9%) and insertions (1.3%)
Summary
Head and neck cancer (HNC) is the eighth most common cancer worldwide, with more than 835,000 new cases and 431,000 deaths due to the disease per year [1]. The classical risk factors for developing HNC are smoking habits and alcohol consumption [3]. The human papillomavirus (HPV), in particular HPV16, is detected in approximately 25% of HNC cases, especially in tumors located at the oropharynx, and serves as a favorable prognostic factor for these patients [4]. Most HNC patients are diagnosed with measurable locally advanced disease, and only about half of these patients achieve complete or partial responses after treatment [5]. Cisplatin (CDDP), combined or not with radiotherapy (RT), has been used in HNC patients’ treatment [6], but therapy resistance has been reported [7]
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