The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers
Abstract
:1. Introduction
1.1. Next-Generation Sequencing
1.2. Oral Squamous Cell Carcinoma
2. Gene Alterations
3. Targeted Gene Therapy
4. Immune Checkpoint Inhibitors
5. Differential Expressions of miRNAs
6. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Genes/Driver Mutations | Research Method | Type of Variant | Location of Mutation | Regulatory Function | References |
---|---|---|---|---|---|
TP53 NM_000546.5 (p.Arg248Trp) (p.Arg213Gln) (p.Pro72Arg) (p.Pro152Leu) (p.Val274Gly) (p.Val274Phe) (p.Glu204Ter*) (p.Gln165Ter*) | Ion Torrent [48,53,54,56,58,61,62,63] Ion AmpliSeq [55] Ion Proton [60] Illumina [57,59,62] | Missense [48,53,54,55,56,57,58,59,60,61,63] Nonsense [48,53,54,56,57,58,59,60,63] Deletion [54,55,56,57,58,60] Insertion [55,56,57,60] Splice-site mutation [53,54,56,59,60,63] | DNA-binding domain [53,54,56] | p53 induces apoptosis (tumor suppressor) | [48,53,54,55,56,57,58,59,60,61,62,63] |
CDKN2A NM_000077 (p.Pro81His) (p.Arg80Ter*) (p.Trp110Ter*) | Ion Torrent [53,54,56,58,61,63] Ion Proton [60] Illumina [59] | Missense [54,56,59,60] Nonsense [54,56,58,60,63] Deletion [54,58,60,63] Insertion [54,56,60,63] Splice-site mutation [54,56,60,63] | Ankyrin repeats [56] | p16 and p14 function as tumor suppressors | [53,54,56,58,59,60,61,63] |
NOTCH1 NM_017617.5 (p.Gly310Arg) (p.Asp352Gly) (p.Arg365Cys) (p.Thr1014Met) (p.Cys1383Tyr) (p.Gln1957Pro) | Ion Torrent[48,54,56] Ion Proton[60] Illumina[49,59] | Missense [48,54,56,59,60] Nonsense [48,60] Insertions [54,56] Deletions [56] Splice-site [54,56] | EGF-like repeats [48,49,54,56] | Cell growth and division | [48,49,54,56,58,59,60] |
HRAS NM_005343 (p.Gly12Ser) (p.Gly13Ser) (p.Gly13Arg) (p.Gly13Val) | Ion Torrent [53,58,61,63] Ion AmpliSeq [55] Ion Proton [60] Illumina [59] | Missense [55,58,60,63] | Cell growth and division | [53,55,58,59,60,61,63] | |
PIK3CA NM_006213.2 NM_006218.1 (p.Glu545Lys) (p.His1048Ser) (p.His1047Arg) (p.Glu542Ala) (p.Glu542Lys) (p.His1047Arg) | Ion Torrent [53,54,58,63] Ion AmpliSeq [55] Ion Proton [60] Illumina [57,59] | Missense [55,56,57,58,59,60,63] Nonsense [63] Splice-site [60] | Cell growth and division | [53,54,55,57,58,59,60,63] | |
CASP8 NM_001080125 (p.Ile354Asn) (p.Arg472Ter) (p.Cys404Tyr) | Ion Torrent [56,62] | Nonsense [56] Deletion [56] | Caspase homologues domain [56] | Regulates cell apoptosis | [56,62] |
FBXW7 NM_033632.3 (p.Ser462Phe) | Illumina [57] Ion Torrent [54,61] Ion Proton [60] | Missense [54,57,60] | Tumor suppressor | [57,60,61] | |
RB1 NM_000321.3 (p.Ile680Thr) | Ion Torrent [58,61] Ion Proton [60] | Missense [60] Nonsense [60] | Tumor suppressor | [58,60,61] | |
PTEN NM_000314.4 (p.Arg161Lys) (p.His185Tyr) (p.Val249Met) | Ion AmpliSeq [55] Ion Proton [60] | Missense [55] Nonsense [60] Deletion [55] | Cell growth and division | [55,60,63] | |
EGFR NM_005228 (p.Ile107Val) | Ion Torrent [54,56,58,59,63] Ion AmpliSeq [55] Illumina [57] | Missense [56] Insertion [59] Deletion [58] | Furin-like repeats [56] | Regulates cell proliferation | [53,54,55,56,57,58,59,63] |
p53 Targeted | EGFR Targeted | VEGF Targeted | mTOR Inhibitors | PD-1 Targeted | Others |
---|---|---|---|---|---|
PRIMA-1 | Cetuximab | Bevacizumab | Rapamycin | Pembrolizumab | COX-2 inhibitor |
PRIMA-1MET (APR-246) | Nimotuzumab | Aflibercept | Temsirolimus | Nivolumab | - |
MIRA-1 | Gefitinib | Sorafenib | Everolimus | Durvalumab | - |
STIMA-1 | Erlotinib | Vandetanib | Sirolimus | Atezolizumab | - |
COTI-2 | - | - | - | - | - |
Oncogenic (Up-Regulated) miRNA | Suppressive (Down-Regulated) miRNA |
---|---|
miR-21: [138,139,140,141] | miR-92b: [139] |
miR-22: [140] | miR-199: [143] |
miR-26a: [139] | miR-214: [143] |
miR-34c: [141] | miR-375: [139] |
miR-34c: [141] | miR-486: [139] |
miR-34b: [141] | miR-504: [141] |
miR-117: [141] | miR-499: [141] |
miR-118: [141] | miR-486: [141] |
miR-130b: [141,142] | |
miR-135: [141] | |
miR-142: [141] | |
miR-143: [140] | |
miR-148a: [139] | |
miR-150: [142] | |
miR-221: [142] | |
miR-222: [142] | |
miR-423: [142] | |
miR-542: [141] | |
miR-1269a: [143] |
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Kim, S.; Lee, J.W.; Park, Y.-S. The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers. Life 2020, 10, 228. https://doi.org/10.3390/life10100228
Kim S, Lee JW, Park Y-S. The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers. Life. 2020; 10(10):228. https://doi.org/10.3390/life10100228
Chicago/Turabian StyleKim, Soyeon, Joo Won Lee, and Young-Seok Park. 2020. "The Application of Next-Generation Sequencing to Define Factors Related to Oral Cancer and Discover Novel Biomarkers" Life 10, no. 10: 228. https://doi.org/10.3390/life10100228