Pseudogene Transcripts in Head/Neck Cancer: Comparison
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Please note this is a comparison between Version 2 by Bruce Ren and Version 1 by Gustavo Jacob Lourenço.

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. Our study can guide new research to HNC understanding and development of new target therapies.

  • head and neck cancer
  • pseudogene transcripts
  • SNV
  • co-expression network
  • gene ontology enrichment
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References

  1. Bray, F.; Me, J.F.; Soerjomataram, I.; Siegel, R.L.; Torre, L.A.; Jemal, A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA A Cancer J. Clin. 2018, 68, 394–424.
  2. Belcher, R.; Hayes, K.; Fedewa, S.; Chen, A.Y. Current treatment of head and neck squamous cell cancer. J. Surg. Oncol. 2014, 110, 551–574.
  3. Mendenhall, W.; Werning, J.; Pfister, D. Treatment of head and neck cancers. In Cancer: Principles & Practice of Oncology, 9th ed.; DeVita, V.T., Lawrence, T.S., Rosenberg, S.A., Eds.; Lippincott Williams & Wilkins: Philadelphia, PA, USA, 2011; pp. 729–780.
  4. Dayyani, F.; Etzel, C.J.; Liu, M.; Ho, C.-H.; Lippman, S.M.; Tsao, A.S. Meta-analysis of the impact of human papillomavirus (HPV) on cancer risk and overall survival in head and neck squamous cell carcinomas (HNSCC). Head Neck Oncol. 2010, 2, 15.
  5. O’Sullivan, B.; Huang, S.H.; Su, J.; Garden, A.; Sturgis, E.M.; Dahlstrom, K.; Lee, N.; Riaz, N.; Pei, X.; Koyfman, S.A.; et al. Development and validation of a staging system for HPV-related oropharyngeal cancer by the International Collaboration on Oropharyngeal cancer Network for Staging (ICON-S): A multicentre cohort study. Lancet Oncol. 2016, 17, 440–451.
  6. Siu, L.L.; Waldron, J.N.; Chen, B.E.; Winquist, E.; Wright, J.R.; Nabid, A.; Parulekar, W.R. Effect of Standard Radiotherapy With Cisplatin vs Accelerated Radiotherapy With Panitumumab in Locoregionally Advanced Squamous Cell Head and Neck Carcinoma: A Randomized Clinical Trial. JAMA Oncol. 2017, 3, 220–226.
  7. Bussmann, L.; Busch, C.-J.; Lörincz, B.B.; Rieckmann, T.; Block, A.R.; Knecht, R. Perspectives in chemosensitivity and chemoresistance assays and their implementation in head and neck cancer. Eur. Arch. Otorhinolaryngol. 2016, 273, 4073–4080.
  8. Lacko, M.; Braakhuis, B.J.; Sturgis, E.M.; Boedeker, C.C.; Suárez, C.; Rinaldo, A.; Ferlito, A.; Takes, R.P. Genetic Susceptibility to Head and Neck Squamous Cell Carcinoma. Int. J. Radiat. Oncol. 2014, 89, 38–48.
  9. Bakhtiar, S.M.; Ali, A.; Barh, D. Epigenetics in Head and Neck Cancer. Methods Mol. Biol. 2014, 1238, 751–769.
  10. Jacq, C.; Miller, J.R.; Brownlee, G.G. A pseudogene structure in 5S DNA of Xenopus laevis. Cell 1977, 12, 109–120.
  11. Tutar, Y. Pseudogenes. Comp. Funct. Genomics 2012, 2012, 424526.
  12. Singh, R.K.; Singh, D.; Yadava, A.; Srivastava, A.K. Molecular fossils “pseudogenes” as functional signature in biological system. Genes Genom. 2020, 42, 619–630.
  13. Balakirev, E.S.; Ayala, F.J. Pseudogenes: Are they “junk” or functional DNA? Annu. Rev. Genet. 2003, 37, 123–151.
  14. Vinckenbosch, N.; Dupanloup, I.; Kaessmann, H. Evolutionary fate of retroposed gene copies in the human genome. Proc. Natl. Acad. Sci. USA 2006, 103, 3220–3225.
  15. Pan, Y.; Sun, C.; Huang, M.; Liu, Y.; Qi, F.; Liu, L.; Wen, J.; Liu, J.; Xie, K.; Ma, H.; et al. A genetic variant in pseudogene E2F3P1 contributes to prognosis of hepatocellular carcinoma. J. Biomed. Res. 2014, 28, 194–200.
  16. Lynn, H.; Sun, X.; Ayshiev, D.; Siegler, J.H.; Rizzo, A.N.; Karnes, J.H.; Gonzalez-Garay, M.; Wang, T.; Casanova, N.; Camp, S.M.; et al. Single nucleotide polymorphisms in the MYLKP1 pseudogene are associated with increased colon cancer risk in African Americans. PLoS ONE 2018, 13, e0200916.
  17. Ma, G.; Liu, H.; Du, M.; Zhang, G.; Lin, Y.; Ge, Y.; Wang, M.; Jin, G.; Zhao, Q.; Chu, H.; et al. A genetic variation in the CpG island of pseudogene GBAP1 promoter is associated with gastric cancer susceptibility. Cancer 2019, 125, 2465–2473.
  18. Poliseno, L. Pseudogenes: Newly Discovered Players in Human Cancer. Sci. Signal. 2012, 5, re5.
  19. Hu, X.; Yang, L.; Mo, Y.-Y. Role of Pseudogenes in Tumorigenesis. Cancers 2018, 10, 256.
  20. Xiao-Jie, L.; Ai-Mei, G.; Li-Juan, J.; Jiang, X. Pseudogene in cancer: Real functions and promising signature. J. Med. Genet. 2014, 52, 17–24.
  21. Poliseno, L.; Salmena, L.; Zhang, J.; Carver, B.; Haveman, W.J.; Pandolfi, P.P. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nat. Cell Biol. 2010, 465, 1033–1038.
  22. Russo, F.; Fiscon, G.; Conte, F.; Rizzo, M.; Paci, P.; Pellegrini, M. Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer. Methods Mol. Biol. 2018, 1819, 75–92.
  23. Conte, F.; Fiscon, G.; Sibilio, P.; Licursi, V.; Paci, P. An Overview of the Computational Models Dealing with the Regulatory ceRNA Mechanism and ceRNA Deregulation in Cancer. Breast Cancer 2021, 2324, 149–164.
  24. Xing, L.; Zhang, X.; Guo, M.; Zhang, X.; Liu, F. Application of Machine Learning in Developing a Novelty Five-Pseudogene Signature to Predict Prognosis of Head and Neck Squamous Cell Carcinoma: A New Aspect of “Junk Genes” in Biomedical Practice. DNA Cell Biol. 2020, 39, 709–723.
  25. Liu, J.; Xing, Y.; Xu, L.; Chen, W.; Cao, W.; Zhang, C. Decreased expression of pseudogene PTENP1 promotes malignant behaviours and is associated with the poor survival of patients with HNSCC. Sci. Rep. 2017, 7, 41179.
  26. Yang, Y.-F.; Feng, L.; Shi, Q.; Ma, H.-Z.; He, S.-Z.; Hou, L.-Z.; Wang, R.; Fang, J.-G. Silencing novel long non-coding RNA FKBP9P1 represses malignant progression and inhibits PI3K/AKT signaling of head and neck squamous cell carcinoma in vitro. Chin. Med. J. 2020, 133, 2037–2043.
  27. Grzechowiak, I.; Graś, J.; Szymańska, D.; Biernacka, M.; Guglas, K.; Poter, P.; Kolenda, T. The oncogenic roles of PTTG1 and PTTG2 Genes and Pseudogene PTTG3P in Head and Neck Squamous Cell Carcinomas. Diagnostics 2020, 10, 606.
  28. Salyakina, D.; Tsinoremas, N.F. Non-coding RNAs profiling in head and neck cancers. Npj. Genom. Med. 2016, 1, 15004.
  29. Zhang, S.; Tian, L.; Ma, P.; Sun, Q.; Zhang, K.; Wang, G.; Liu, H.; Xu, B. Potential role of differentially expressed lncRNAs in the pathogenesis of oral squamous cell carcinoma. Arch. Oral Biol. 2015, 60, 1581–1587.
  30. Zhang, C.-Z. Long non-coding RNA FTH1P3 facilitates oral squamous cell carcinoma progression by acting as a molecular sponge of miR-224-5p to modulate fizzled 5 expression. Gene 2017, 607, 47–55.
  31. Liu, M.; Gao, X.; Liu, C.-L. Increased expression of lncRNA FTH1P3 promotes oral squamous cell carcinoma cells migration and invasion by enhancing PI3K/Akt/GSK3b/ Wnt/β-catenin signaling. Eur. Rev. Med. Pharmacol. Sci. 2018, 22, 8306–8314.
  32. Gao, L.; Ren, W.; Zhang, L.; Li, S.; Kong, X.; Zhang, H.; Dong, J.; Cai, G.; Jin, C.; Zheng, D.; et al. PTENp1, a natural sponge of miR-21, mediates PTEN expression to inhibit the proliferation of oral squamous cell carcinoma. Mol. Carcinog. 2016, 56, 1322–1334.
  33. Palumbo, A., Jr.; De Martino, M.; Esposito, F.; Fraggetta, F.; Neto, P.N.; Fernandes, P.V.; Santos, I.C.; Dias, F.L.; Nasciutti, L.E.; Da Costa, N.M.; et al. HMGA2, but not HMGA1, is overexpressed in human larynx carcinomas. Histopathology 2017, 72, 1102–1114.
  34. Feenstra, M.; Bakema, J.; Verdaasdonk, M.; Rozemuller, E.; Tweel, J.V.D.; Slootweg, P.; de Weger, R.; Tilanus, M. Detection of a putativeHLA-A*31012 processed (intronless) pseudogene in a laryngeal squamous cell carcinoma. Genes Chromosom. Cancer 2000, 27, 26–34.
  35. Yuan, H.; Jiang, H.; Wang, Y.; Dong, Y. Increased expression of lncRNA FTH1P3 predicts a poor prognosis and promotes aggressive phenotypes of laryngeal squamous cell carcinoma. Biosci. Rep. 2019, 39.
  36. Zhang, G.; Fan, E.; Yue, G.; Zhong, Q.; Shuai, Y.; Wu, M.; Feng, G.; Chen, Q.; Gou, X. Five genes as a novel signature for predicting the prognosis of patients with laryngeal cancer. J. Cell. Biochem. 2019, 121, 3804–3813.
  37. Eisen, M.; Spellman, P.T.; Brown, P.O.; Botstein, D. Cluster analysis and display of genome-wide expression patterns. Proc. Natl. Acad. Sci. USA 1998, 95, 14863–14868.
  38. Langfelder, P.; Horvath, S. WGCNA: An R package for weighted correlation network analysis. BMC Bioinform. 2008, 9, 1–13.
  39. Zhang, B.; Horvath, S. A General Framework for Weighted Gene Co-Expression Network Analysis. Stat. Appl. Genet. Mol. Biol. 2005, 4, 1–43.
  40. Klopfenstein, D.V.; Zhang, L.; Pedersen, B.S.; Ramírez, F.; Vesztrocy, A.W.; Naldi, A.; Mungall, C.J.; Yunes, J.M.; Botvinnik, O.; Weigel, M.; et al. GOATOOLS: A Python library for Gene Ontology analyses. Sci. Rep. 2018, 8, 1–17.
  41. Supek, F.; Bošnjak, M.; Škunca, N.; Smuc, T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 2011, 6, e21800.
  42. Nagy, Á.; Munkácsy, G.; Győrffy, B. Pancancer survival analysis of cancer hallmark genes. Sci. Rep. 2021, 11, 1–10.
  43. Johnson, D.E.; Burtness, B.; Leemans, C.R.; Lui, V.W.Y.; Bauman, J.E.; Grandis, J.R. Head and neck squamous cell carcinoma. Nat. Rev. Dis. Primers 2020, 6, 92.
  44. Chen, J.; Cai, H.; Xie, Y.; Jiang, H. Targeting long non-coding RNA HERC2P3 inhibits cell growth and migration in human gastric cancer cells. Int. J. Clin. Exp. Pathol. 2017, 10, 7632–7639.
  45. Brun, M.-E.; Ruault, M.; Ventura, M.; Roizès, G.; De Sario, A. Juxtacentromeric region of human chromosome 21: A boundary between centromeric heterochromatin and euchromatic chromosome arms. Gene 2003, 312, 41–50.
  46. Zhang, Z.; Wu, H.; Zhou, H.; Gu, Y.; Bai, Y.; Yu, S.; An, R.; Qi, J. Identification of potential key genes and high-frequency mutant genes in prostate cancer by using RNA-Seq data. Oncol. Lett. 2018, 15, 4550–4556.
  47. Schulten, H.-J.; Bangash, M.; Karim, S.; Dallol, A.; Hussein, D.; Merdad, A.; Althoubaity, F.; Al-Maghrabi, J.; Jamal, A.; Al-Ghamdi, F.; et al. Comprehensive molecular biomarker identification in breast cancer brain metastases. J. Transl. Med. 2017, 15, 1–20.
  48. Qi, L.; Yao, Y.; Zhang, T.; Feng, F.; Zhou, C.; Xu, X.; Sun, C. A four-mRNA model to improve the prediction of breast cancer prognosis. Gene 2019, 721, 144100.
  49. Park, C.; Kim, J.-I.; Hong, S.N.; Jung, H.M.; Kim, T.J.; Lee, S.; Kim, S.J.; Kim, H.C.; Kim, D.-H.; Cho, B.; et al. A copy number variation in PKD1L2 is associated with colorectal cancer predisposition in korean population. Int. J. Cancer 2016, 140, 86–94.
  50. Jiao, X.; Liu, W.; Mahdessian, H.; Bryant, P.; Ringdahl, J.; Timofeeva, M.; Farrington, S.M.; Dunlop, M.; Lindblom, A. Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population. PLoS ONE 2018, 13, e0193547.
  51. Chen, B.; Wang, C.; Zhang, J.; Zhou, Y.; Hu, W.; Guo, T. New insights into long noncoding RNAs and pseudogenes in prognosis of renal cell carcinoma. Cancer Cell Int. 2018, 18, 1–12.
  52. Roychowdhury, A.; Samadder, S.; Das, P.; Mazumder, D.I.; Chatterjee, A.; Addya, S.; Mondal, R.; Roy, A.; Roychoudhury, S.; Panda, C.K. Deregulation of H19 is associated with cervical carcinoma. Genomics 2019, 112, 961–970.
  53. Qin, N.; Wang, C.; Zhu, M.; Lu, Q.; Ma, Z.; Huang, M.; Dai, J.; Ma, H.; Jin, G.; Hu, Z.; et al. Fine-mapping the MHC region in Asian populations identified novel variants modifying susceptibility to lung cancer. Lung Cancer 2017, 112, 169–175.
  54. Ying, J.F.; Zhang, Y.N.; Song, S.S.; Hu, Z.M.; He, X.L.; Pan, H.Y.; Zhang, C.W.; Wang, H.J.; Li, W.F.; Mou, X.Z. Decreased expression of GBA3 correlates with a poor prognosis in hepatocellular carcinoma patients. Neoplasma 2020, 67.
  55. Chen, J.; Li, Y.; Li, Z.; Cao, L. LncRNA MST1P2/miR-133b axis affects the chemoresistance of bladder cancer to cisplatin-based therapy via Sirt1/p53 signaling. J. Biochem. Mol. Toxicol. 2020, 34, e22452.
  56. Xu, R.; Zhang, X.; Xu, Y.; Wang, J.; Li, Z.; Cui, X. Long noncoding RNA MST1P2 promotes cervical cancer progression by sponging with microRNA miR-133b. Bioengineered 2021, 12, 1851–1860.
  57. Li, Y.; Zhu, Y.; Dai, G.; Wu, D.; Gao, Z.; Zhang, L.; Fan, Y. Screening and validating the core biomarkers in patients with pancreatic ductal adenocarcinoma. Math. Biosci. Eng. 2020, 17, 910–927.
  58. Shaw, S.-W.; Chen, C.-P.; Cheng, P.-J.; Wang, T.-H.; Hou, J.-W.; Lin, C.-T.; Chang, S.-D.; Hwa, H.-L.; Lin, J.-L.; Chao, A.-S.; et al. Gene dosage change of TPTE and BAGE2 and breakpoint analysis in Robertsonian Down syndrome. J. Hum. Genet. 2007, 53, 136–143.
  59. Bekpen, C.; Xie, C.; Nebel, A.; Tautz, D. Involvement of SPATA31 copy number variable genes in human lifespan. Aging 2018, 10, 674–688.
  60. Zamunér, F.T.; Karia, B.T.; de Oliveira, C.Z.; Santos, C.R.; Carvalho, A.L.; Vettore, A.L. A Comprehensive Expression Analysis of Cancer Testis Antigens in Head and Neck Squamous Cell Carcinoma Revels MAGEA3/6 as a Marker for Recurrence. Mol. Cancer Ther. 2015, 14, 828–834.
  61. Luongo, T.S.; Eller, J.M.; Lu, M.-J.; Niere, M.; Raith, F.; Perry, C.; Bornstein, M.R.; Oliphint, P.; Wang, L.; McReynolds, M.R.; et al. SLC25A51 is a mammalian mitochondrial NAD. Nat. Cell Biol. 2020, 588, 174–179.
  62. Yamada, R.; Takahashi, A.; Torigoe, T.; Morita, R.; Tamura, Y.; Tsukahara, T.; Kanaseki, T.; Kubo, T.; Watarai, K.; Kondo, T.; et al. Preferential expression of cancer/testis genes in cancer stem-like cells: Proposal of a novel sub-category, cancer/testis/stem gene. Tissue Antigens 2013, 81, 428–434.
  63. Imoto, Y.; Itoh, K.; Fujiki, Y. Molecular Basis of Mitochondrial and Peroxisomal Division Machineries. Int. J. Mol. Sci. 2020, 21, 5452.
  64. Cassandri, M.; Smirnov, A.; Novelli, F.; Pitolli, C.; Agostini, M.; Malewicz, M.; Melino, G.; Raschellà, G. Zinc-finger proteins in health and disease. Cell Death Discov. 2017, 3, 17071.
  65. Flegel, C.; Manteniotis, S.; Osthold, S.; Hatt, H.; Gisselmann, G. Expression Profile of Ectopic Olfactory Receptors Determined by Deep Sequencing. PLoS ONE 2013, 8, e55368.
  66. Wu, H.; Zhai, L.T.; Guo, X.X.; Rety, S.; Xi, X.G. The N-terminal of NBPF15 causes multiple types of aggregates and mediates phase transition. Biochem. J. 2020, 477, 445–458.
  67. Gulla, A.; Kazlauskas, E.; Liang, H.; Strupas, K.; Petrauskas, V.; Matulis, D.; Eshleman, J.R. Heat Shock Protein 90 Inhibitor Effects on Pancreatic Cancer Cell Cultures. Pancreas 2021, 50, 625–632.
  68. Tan, W.; Zolotukhin, A.S.; Tretyakova, I.; Bear, J.; Lindtner, S.; Smulevitch, S.V.; Felber, B.K. Identification and characterization of the mouse nuclear export factor (Nxf) family members. Nucleic Acids Res. 2005, 33, 3855–3865.
  69. Francis, M.; Cheng, H.; Ma, P.; Grider, A. Genomic Characterization of the Zinc Transcriptional Regulatory Element Reveals Potential Functional Roles of ZNF658. Biol. Trace Element Res. 2019, 192, 83–90.
  70. Tanabe, S.; Quader, S.; Ono, R.; Cabral, H.; Aoyagi, K.; Hirose, A.; Yokozaki, H.; Sasaki, H. Molecular Network Profiling in Intestinal—and Diffuse—Type Gastric Cancer. Cancers 2020, 12, 3833.
  71. Zheng, W.; Hu, H.; Zhang, S.; Xu, X.; Gao, Y.; Gong, F.; Lu, G.; Lin, G. The comprehensive variant and phenotypic spectrum of TUBB8 in female infertility. J. Assist. Reprod. Genet. 2021, 1–12.
  72. Nachef, M.; Ali, A.K.; Almutairi, S.M.; Lee, S.-H. Targeting SLC1A5 and SLC3A2/SLC7A5 as a Potential Strategy to Strengthen Anti-Tumor Immunity in the Tumor Microenvironment. Front. Immunol. 2021, 12, 624324.
  73. Hu, R.-J.; Lee, M.P.; Connors, T.D.; Johnson, L.A.; Burn, T.C.; Sub, K.; Landes, G.M.; Feinberg, A. A 2.5-Mb Transcript Map of a Tumor-Suppressing Subchromosomal Transferable Fragment from 11p15.5, and Isolation and Sequence Analysis of Three Novel Genes. Genomics 1997, 46, 9–17.
  74. Gubas, A.; Karantanou, C.; Popovic, D.; Tascher, G.; Hoffmann, M.E.; Platzek, A.; Dawe, N.; Dikic, I.; Krause, D.S.; McEwan, D.G. The endolysosomal adaptor PLEKHM1 is a direct target for both mTOR and MAPK pathways. FEBS Lett. 2021, 595, 864–880.
  75. Rocks, N.; Paulissen, G.; El Hour, M.; Quesada, F.; Crahay, C.; Gueders, M.; Foidart, J.; Noel, A.; Cataldo, D. Emerging roles of ADAM and ADAMTS metalloproteinases in cancer. Biochimie 2008, 90, 369–379.
  76. Riaz, N.; Morris, L.G.; Lee, W.; Chan, T.A. Unraveling the molecular genetics of head and neck cancer through genome-wide approaches. Genes Dis. 2014, 1, 75–86.
  77. Network CGA. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 2015, 517, 576–582.
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