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Research Paper

PRKCE non-coding variants influence on transcription as well as translation of its gene

, , , , , & show all
Pages 1115-1129 | Received 15 Aug 2022, Accepted 17 Oct 2022, Published online: 26 Oct 2022

References

  • Valle L, Vilar E, Tavtigian SV, et al. Genetic predisposition to colorectal cancer: syndromes, genes, classification of genetic variants and implications for precision medicine. J Pathol. 2019;247:574–588.
  • Mooney SD, Krishnan VG, Evani US. Bioinformatic tools for identifying disease gene and SNP candidates. Genetic Variation. Methods in Molecular Biology. Genetic Variation. 2010;628:307–319.
  • Shabbir M, Badshah Y, Khan K, et al. Association of CTLA-4 and IL-4 polymorphisms in viral induced liver cancer. BMC Cancer. 2022;22(1):1–9.
  • Carubbi C, Masselli E, Pozzi G, et al. Combination of Platelet expression of PKCepsilon and cardiac troponin-I for early diagnosis of chest pain patients in the emergency department. Sci Rep. 2019;9:1–8.
  • Khan TK, Sen A, Hongpaisan J, et al. PKCε deficits in Alzheimer’s disease brains and skin fibroblasts. J Alzheimers Dis. 2015;43:491–509.
  • Gassaway BM, Petersen MC, Surovtseva YV, et al. PKCε contributes to lipid-induced insulin resistance through cross talk with p70S6K and through previously unknown regulators of insulin signaling. Proc Nat Acad Sci. 2018;115:E8996–E9005.
  • Martini S, Soliman T, Gobbi G, et al. PKCϵ controls mitotic progression by regulating centrosome migration and mitotic spindle assembly. Molecular Cancer Research. 2018;16(1):3–15.
  • Parker PJ, Lockwood N, Davis K, et al. A cancer-associated, genome protective programme engaging PKCε. Adv Biol Regul. 2020;78:100759.
  • Nicholson RL. The role of protein kinase C epsilon in the pathogenesis and treatment resistance of Acute Myeloid Leukaemia. Cardiff, Wales, UK: Cardiff University; 2021.
  • Li L, Zhang L, Binkley PF, et al. Regulatory variants modulate protein kinase C α (PRKCA) gene expression in human heart. Pharm Res. 2017;34:1648–1657.
  • Lavender NA, Rogers EN, Yeyeodu S, et al. Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer. BMC Med Genomics. 2012;5:1–15.
  • Li Q, Gu C, Zhu Y, et al. Two novel PRKCI polymorphisms and prostate cancer risk in an Eastern Chinese Han population. Mol Carcinog. 2015;54:632–641.
  • Lu H, Zhu L, Lian L, et al. Genetic variations in the PRKCG gene and osteosarcoma risk in a Chinese population: a case-control study. Tumor Biol. 2015;36:5241–5247.
  • Kubo M, Hata J, Ninomiya T, et al. A nonsynonymous SNP in PRKCH (protein kinase C η) increases the risk of cerebral infarction. Nat Genet. 2007;39:212–217.
  • Riera P, Virgili AC, Salazar J, et al. Genetic variants in the VEGF pathway as prognostic factors in stages II and III colon cancer. Pharmacogenomics J. 2018;18:556–564.
  • Pu X, Wang L, Chang JY, et al. Inflammation‐related genetic variants predict toxicity following definitive radiotherapy for lung cancer. Clin Pharmacol Ther. 2014;96:609–615.
  • Khan K, Shah H, Rehman A, et al. Influence of PRKCE non-synonymous variants on protein dynamics and functionality. Hum Mol Genet. 2022;31(13):2236–2261.
  • Bhagwat M. Searching NCBI’s dbSNP database. Curr Protoc Bioinform. 2010;32:1.19. 1–1. 8.
  • McLaren W, Gil L, Hunt SE, et al. The ensembl variant effect predictor. Genome Biol. 2016;17:1–14.
  • Institute WTS. Catalogue of somatic mutations in cancer (COSMIC). Hinxton, United Kingdom: Institute WTS; 2017.
  • Server EV. NHLBI GO exome sequencing project (ESP). Seattle WA: Exome Variant Server; 2017.
  • Karczewski KJ, Francioli LC, Tiao G, et al. Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. BioRxiv. 2019;1:531210.
  • Boyle AP, Hong EL, Hariharan M, et al. Annotation of functional variation in personal genomes using RegulomeDB. Genome Res. 2012;22:1790–1797.
  • Koch L. Exploring human genomic diversity with gnomAD. Nat Rev Genet. 2020;21:448.
  • Sayers EW, Beck J, Bolton EE, et al. Database resources of the national center for biotechnology information. Nucleic Acids Res. 2021;49:D10.
  • Taliun D, Harris DN, Kessler MD, et al. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed program. Nature. 2021;590:290–299.
  • Kanai M, Tanaka T, Okada Y. Empirical estimation of genome-wide significance thresholds based on the 1000 Genomes project data set. J Hum Genet. 2016;61(10):861–866.
  • Rentzsch P, Witten D, Cooper GM, et al. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 2019;47(D1):D886–D94.
  • Grabe N. AliBaba2: context specific identification of transcription factor binding sites. silico biology. 2002;2:S1–S15.
  • Liu X, Yu X, Zack DJ, et al. TiGER: a database for tissue-specific gene expression and regulation. BMC Bioinf. 2008;9:1–7.
  • Yu X, Lin J, Zack DJ, et al. Identification of tissue-specific cis-regulatory modules based on interactions between transcription factors. BMC Bioinf. 2007;8:1–13.
  • Yu X, Lin J, Zack DJ, et al. Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues. Nucleic Acids Res. 2006;34:4925–4936.
  • Aoki-Kinoshita KF, Kanehisa M. Gene annotation and pathway mapping in KEGG. Comparative genomics. Heidelberg, Germany: Springer; 2007. p. 71–91.
  • Zhang Y-H, Zeng T, Chen L, et al. Determining protein–protein functional associations by functional rules based on gene ontology and KEGG pathway. Biochim Biophys Acta. 2021;1869:140621.
  • Oualline S, Oualline G. Drawing with Inkscape. Practical free alternatives to commercial software. Heidelberg, Germany: Springer; 2018. p. 187–219.
  • Mathews DH. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA. 2004;10:1178–1190.
  • Mathews DH, Moss WN, Turner DH. Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol. 2010;2:a003665.
  • Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res. 2003;31:3429–3431.
  • Mavrevski RA, Traykov, MV, Trenchev, IV, Trencheva, MI. Approaches to modeling of biological experimental data with GraphPad Prism software. WSEAS Trans. Syst. Control. 2018;13:242–7.
  • Andrés-León E, González Peña D, Gómez-López G, et al. miRGate: a curated database of human, mouse and rat miRNA–mRNA targets. Database. 2015;2015. DOI:10.1093/database/bav035
  • Andrés-León E, Gómez-López G, Pisano DG. Prediction of miRNA–mRNA interactions using miRGate. MicroRNA detection and target identification. Heidelberg, Germany: Springer; 2017. p. 225–237.
  • Rehmsmeier M, Steffen P, Höchsmann M, et al. Fast and effective prediction of microRNA/target duplexes. Rna. 2004;10(10):1507–1517.
  • van Waveren C, Moraes CT. Transcriptional co-expression and co-regulation of genes coding for components of the oxidative phosphorylation system. BMC Genomics. 2008;9(1):1–15.
  • Eferl R, Wagner EF. AP-1: a double-edged sword in tumorigenesis. Nat Rev Cancer. 2003;3:859–868.
  • Funnell AP, Norton LJ, Mak KS, et al. The CACCC-binding protein KLF3/BKLF represses a subset of KLF1/EKLF target genes and is required for proper erythroid maturation in vivo. Mol Cell Biol. 2012;32:3281–3292.
  • Thiel G, Rössler OG. Resveratrol stimulates c-Fos gene transcription via activation of ERK1/2 involving multiple genetic elements. Gene. 2018;658:70–75.
  • Lukey MJ, Greene KS, Erickson JW, et al. The oncogenic transcription factor c-Jun regulates glutaminase expression and sensitizes cells to glutaminase-targeted therapy. Nat Commun. 2016;7:1–14.
  • Madden SK, de Araujo AD, Gerhardt M, et al. Taking the Myc out of cancer: toward therapeutic strategies to directly inhibit c-Myc. Mol Cancer. 2021;20:1–18.
  • Fang Z, Lin A, Chen J, et al. CREB1 directly activates the transcription of ribonucleotide reductase small subunit M2 and promotes the aggressiveness of human colorectal cancer. Oncotarget. 2016;7:78055.
  • Kent LN, Leone G. The broken cycle: E2F dysfunction in cancer. Nat Rev Cancer. 2019;19:326–338.
  • Wu F, Qin Y, Jiang Q, et al. MyoD1 suppresses cell migration and invasion by inhibiting FUT4 transcription in human gastric cancer cells. Cancer Gene Ther. 2020;27:773–784.
  • Feng J, Zhang X, Zhu H, et al. High expression of FoxP1 is associated with improved survival in patients with non–small cell lung cancer. Am J Clin Pathol. 2012;138:230–235.
  • O’Connor L, Gilmour J, Bonifer C. Focus: epigenetics: the role of the ubiquitously expressed transcription factor Sp1 in tissue-specific transcriptional regulation and in disease. Yale J Biol Med. 2016;89:513.
  • Huang Y, Chen R, Zhou J. E2F1 and NF-κB: key mediators of inflammation-associated cancers and potential therapeutic targets. Curr Cancer Drug Targets. 2016;16:765–772.
  • Giuliani C, Bucci I, Napolitano G. The role of the transcription factor nuclear factor-kappa B in thyroid autoimmunity and cancer. Front Endocrinol (Lausanne). 2018;9:471.
  • Wang I-M, Contursi C, Masumi A, et al. An IFN-γ-inducible transcription factor, IFN consensus sequence binding protein (ICSBP), stimulates IL-12 p40 expression in macrophages. J Immunol. 2000;165:271–279.
  • Ribeiro JR, Lovasco LA, Vanderhyden BC, et al. Targeting TBP-associated factors in ovarian cancer. Front Oncol. 2014;4:45.
  • Borja N, Bivona S, Peart LS, et al. Genome sequencing reveals novel noncoding variants in PLA2G6 and LMNB1 causing progressive neurologic disease. Mol Genet Genomic Med. 2022;10:e1892.
  • Pagni S, Mills JD, Frankish A, et al. Non-coding regulatory elements: potential roles in disease and the case of epilepsy. Neuropathol Appl Neurobiol. 2022;48(3):e12775.
  • Doane AS, Elemento O. Alterations in transcriptional networks in cancer: the role of noncoding somatic driver mutations. Curr Opin Genet Dev. 2022;75:101919.
  • Vaz-Drago R, Custódio N, Carmo-Fonseca M. Deep intronic mutations and human disease. Hum Genet. 2017;136:1093–1111.
  • Steri M, Idda ML, Whalen MB, et al. Genetic variants in mRNA untranslated regions. Wiley Interdiscip Rev RNA. 2018;9:e1474.
  • Soukarieh O, Meguerditchian C, Proust C, et al. Common and rare 5′ UTR variants altering upstream open reading frames in cardiovascular genomics. Front Cardiovasc Med. 2022;9: DOI:10.3389/fcvm.2022.841032.
  • Nicholson R, Menezes AC, Azevedo A, et al. Protein kinase C epsilon overexpression is associated with poor patient outcomes in AML and promotes daunorubicin resistance through p-glycoprotein-mediated drug efflux. Front Oncol. 2022;12:2434.
  • Peng Y, Wang L, Zhao X, et al. Puerarin attenuates lipopolysaccharide-induced myocardial injury via the 14-3-3γ/PKCε pathway activating adaptive autophagy. Int Immunopharmacol. 2022;108:108905.
  • Garg R, Cooke M, Wang S, et al. Requirement for PKC epsilon in KRAS-driven lung tumorigenesis. bioRxiv. 2020;1:1–19.
  • Garg R, Cooke M, Benavides F, et al. PKCε is required for KRAS-driven lung tumorigenesis. Cancer Res. 2020;80:5166–5173.
  • Garg R, Blando J, Perez CJ, et al. Activation of nuclear factor κB (NF-κB) in prostate cancer is mediated by protein kinase C ϵ (PKCϵ). J Biol Chem. 2012;287:37570–37582.
  • Zahra K, Shabbir M, Badshah Y, et al. Determining KLF14 tertiary structure and diagnostic significance in brain cancer progression. Sci Rep. 2022;12:1–18.
  • Zhang G-F, J-C W, Wang H-Y, et al. Overexpression of microRNA-205-5p exerts suppressive effects on stem cell drug resistance in gallbladder cancer by down-regulating PRKCE. Biosci Rep. 2020;40:BSR20194509.
  • Khan K, Safi S, Abbas A, et al. Unravelling structure, localization, and genetic crosstalk of KLF3 in human breast cancer. Biomed Res Int. 2020;2020:1–15.
  • Barrett LW, Fletcher S, Wilton SD. Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell Mol Life Sci. 2012;69:3613–3634.
  • Mohebian K, Hesse D, Arends D, et al., A 5'UTR mutation contributes to down-regulation of Bbs7. The Berlin Fat Mouse.2022
  • Wang X, Li A, Raza SHA, et al. Transcription Factors ZEB1 and CREB promote the transcription of bovine ABHD 5 Gene. DNA Cell Biol. 2021;40:219–230.
  • Spitz F, Furlong EE. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13:613–626.
  • Amrani N, Ganesan R, Kervestin S, et al. A faux 3′-UTR promotes aberrant termination and triggers nonsense-mediated mRNA decay. Nature. 2004;432:112–118.
  • Nguyen HT, Najih M, Martin LJ. The AP-1 family of transcription factors are important regulators of gene expression within Leydig cells. Endocrine. 2021;74(3):498–507.
  • Yang -C-C, Hsiao L-D, Shih Y-F, et al. Induction of heme oxygenase-1 by 15d-Prostaglandin J2 mediated via a ROS-dependent Sp1 and AP-1 cascade suppresses lipopolysaccharide-triggered interleukin-6 expression in mouse brain microvascular endothelial cells. Antioxidants. 2022;11:719.
  • Yao CD, Haensel D, Gaddam S, et al. AP-1 and TGFß cooperativity drives non-canonical Hedgehog signaling in resistant basal cell carcinoma. Nat Commun. 2020;11:1–17.
  • Kumar V, Weng Y-C, Wu Y-C, et al. PKCε phosphorylation regulates the mitochondrial translocation of ATF2 in ischemia-induced neurodegeneration. BMC Neurosci. 2018;19:1–8.
  • Bai L, Kee HJ, Han X, et al. Protocatechuic acid attenuates isoproterenol-induced cardiac hypertrophy via downregulation of ROCK1–Sp1–PKCγ axis. Sci Rep. 2021;11:1–16.
  • Leppek K, Das R, Barna M. Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them. Nat Rev Mol Cell Biol. 2018;19:158–174.
  • Haizel SA, Bhardwaj U, Gonzalez RL, et al. 5′-UTR recruitment of the translation initiation factor eIF4GI or DAP5 drives cap-independent translation of a subset of human mRNAs. J Biol Chem. 2020;295(33):11693–11706.
  • Mayr C. What are 3′ UTRs doing? Cold spring Harbor perspectives in biology. Cold Spring Harbor Perspectives in Biology. 2019;11(10):a034728.
  • Gray NK, Hentze MW. Iron regulatory protein prevents binding of the 43S translation pre‐initiation complex to ferritin and eALAS mRNAs. EMBO J. 1994;13:3882–3891.
  • Muckenthaler MU, Rivella S, Hentze MW, et al. A red carpet for iron metabolism. Cell. 2017;168:344–361.
  • Lytle JR, Yario TA, Steitz JA. Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc Natl Acad Sci. 2007;104:9667–9672.
  • Ørom UA, Nielsen FC, Lund AH. MicroRNA-10a binds the 5′ UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell. 2008;30:460–471.
  • Pu M, Chen J, Tao Z, et al. Regulatory network of miRNA on its target: coordination between transcriptional and post-transcriptional regulation of gene expression. Cell Mol Life Sci. 2019;76:441–451.