Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> Analysis
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...
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MDPI AG
2021-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/8/1254 |
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| author | Juliana Carron Rafael Della Coletta Gustavo Jacob Lourenço |
| author_facet | Juliana Carron Rafael Della Coletta Gustavo Jacob Lourenço |
| author_sort | Juliana Carron |
| collection | DOAJ |
| description | 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 <i>in silico</i> 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 <i>in silico</i> analysis identified 370 pseudogene transcripts associated with HNC, where <i>SPATA31D5P</i>, <i>HERC2P3</i>, <i>SPATA31C2</i>, <i>MAGEB6P1</i>, <i>SLC25A51P1</i>, <i>BAGE2</i>, <i>DNM1P47</i>, <i>SPATA31C1</i>, <i>ZNF733P</i> and <i>OR2W5</i> were found to be the most deregulated and presented several genetic alterations. <i>NBPF25P</i>, <i>HSP90AB2P</i>, <i>ZNF658B</i> and <i>DPY19L2P3</i> pseudogenes were predicted to interact with 12 genes known to participate in HNC, <i>DNM1P47</i> was predicted to interact with the <i>TP53</i> gene, and <i>HLA-H</i> pseudogene was predicted to interact with <i>HLA-A</i> and <i>HLA-B</i> 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 <i>SPATA31D5P</i>, <i>SPATA31C2</i>, <i>BAGE2</i>, <i>SPATA31C1</i>, <i>ZNF733P</i> and <i>OR2W5</i> 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. |
| first_indexed | 2024-03-10T08:47:49Z |
| format | Article |
| id | doaj.art-7921d408e0c042ae8d9895763cb905c2 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T08:47:49Z |
| publishDate | 2021-08-01 |
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| spelling | doaj.art-7921d408e0c042ae8d9895763cb905c22023-11-22T07:46:45ZengMDPI AGGenes2073-44252021-08-01128125410.3390/genes12081254Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> AnalysisJuliana Carron0Rafael Della Coletta1Gustavo Jacob Lourenço2Laboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, São Paulo, BrazilDepartment of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USALaboratory of Cancer Genetics, School of Medical Sciences, University of Campinas, Campinas 13083-888, São Paulo, BrazilOnce 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 <i>in silico</i> 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 <i>in silico</i> analysis identified 370 pseudogene transcripts associated with HNC, where <i>SPATA31D5P</i>, <i>HERC2P3</i>, <i>SPATA31C2</i>, <i>MAGEB6P1</i>, <i>SLC25A51P1</i>, <i>BAGE2</i>, <i>DNM1P47</i>, <i>SPATA31C1</i>, <i>ZNF733P</i> and <i>OR2W5</i> were found to be the most deregulated and presented several genetic alterations. <i>NBPF25P</i>, <i>HSP90AB2P</i>, <i>ZNF658B</i> and <i>DPY19L2P3</i> pseudogenes were predicted to interact with 12 genes known to participate in HNC, <i>DNM1P47</i> was predicted to interact with the <i>TP53</i> gene, and <i>HLA-H</i> pseudogene was predicted to interact with <i>HLA-A</i> and <i>HLA-B</i> 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 <i>SPATA31D5P</i>, <i>SPATA31C2</i>, <i>BAGE2</i>, <i>SPATA31C1</i>, <i>ZNF733P</i> and <i>OR2W5</i> 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.https://www.mdpi.com/2073-4425/12/8/1254head and neck cancerpseudogene transcriptsSNVco-expression networkgene ontology enrichment |
| spellingShingle | Juliana Carron Rafael Della Coletta Gustavo Jacob Lourenço Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> Analysis Genes head and neck cancer pseudogene transcripts SNV co-expression network gene ontology enrichment |
| title | Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> Analysis |
| title_full | Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> Analysis |
| title_fullStr | Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> Analysis |
| title_full_unstemmed | Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> Analysis |
| title_short | Pseudogene Transcripts in Head and Neck Cancer: Literature Review and <i>In Silico</i> Analysis |
| title_sort | pseudogene transcripts in head and neck cancer literature review and i in silico i analysis |
| topic | head and neck cancer pseudogene transcripts SNV co-expression network gene ontology enrichment |
| url | https://www.mdpi.com/2073-4425/12/8/1254 |
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