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Research Report

Identification of novel genes by targeted exome sequencing in Retinoblastoma

ORCID Icon, , , ORCID Icon, , & ORCID Icon show all
Pages 771-788 | Received 24 Feb 2022, Accepted 19 Jul 2022, Published online: 05 Aug 2022

References

  • Noone A, Howlader N, Krapcho M. SEER cancer statistics review, 1975-2015. Bethesda, MD: National Cancer Institute; 2018.
  • Knudson AG. Mutation and cancer: statistical study of retinoblastoma. Proc Nat Acad Sci. 1971;68(4):820–23. doi:10.1073/pnas.68.4.820.
  • Jain M, Rojanaporn D, Chawla B, Sundar G, Gopal L, Khetan V. Retinoblastoma in Asia. Eye. 2019;33(1):87–96. doi:10.1038/s41433-018-0244-7.
  • Dimaras H, Kimani K, Dimba EA, Gronsdahl P, White A, Chan HS, Gallie BL. Retinoblastoma. Lancet. 2012;379(9824):1436–46. doi:10.1016/S0140-6736(11)61137-9.
  • Pentimalli F, Indovina P, Giordano A. Retinoblastoma beyond RB1: recent advances in genetic biomarkers. Expert Rev Ophthalmol. 2010;5(6):717–21. doi:10.1586/eop.10.75.
  • Dimaras H, Khetan V, Halliday W, Orlic M, Prigoda NL, Piovesan B, Marrano P, Corson TW, Eagle RC, Squire JA. Loss of RB1 induces non-proliferative retinoma: increasing genomic instability correlates with progression to retinoblastoma. Hum Mol Genet. 2008;17(10):1363–72. doi:10.1093/hmg/ddn024.
  • Chen D, Gallie BL, Squire JA. Minimal regions of chromosomal imbalance in retinoblastoma detected by comparative genomic hybridization. Cancer Genet Cytogenet. 2001;129(1):57–63. doi:10.1016/s0165-4608(01)00427-7.
  • Thériault BL, Dimaras H, Gallie BL, Corson TW. The genomic landscape of retinoblastoma: a review. Clin Exp Ophthalmol. 2014;42(1):33–52. doi:10.1111/ceo.12132.
  • Sampieri K, Amenduni M, Papa FT, Katzaki E, Mencarelli MA, Marozza A, Epistolato MC, Toti P, Lazzi S, Bruttini M. Array comparative genomic hybridization in retinoma and retinoblastoma tissues. Cancer Sci. 2009;100(3):465–71. doi:10.1111/j.1349-7006.2008.01070.x.
  • Levin JZ, Berger MF, Adiconis X, Rogov P, Melnikov A, Fennell T, Nusbaum C, Garraway LA, Gnirke A. Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts. Genome Biol. 2009;10(10):1–8. doi:10.1186/gb-2009-10-10-r115.
  • Devarajan B, Prakash L, Kannan TR, Abraham AA, Kim U, Muthukkaruppan V, Vanniarajan A. Targeted next generation sequencing of RB1 gene for the molecular diagnosis of Retinoblastoma. BMC Cancer. 2015;15(1):320. doi:10.1186/s12885-015-1340-8.
  • Thirumalairaj K, Abraham A, Devarajan B, Gaikwad N, Kim U, Muthukkaruppan V, Vanniarajan A. A stepwise strategy for rapid and cost-effective RB1 screening in Indian retinoblastoma patients. J Hum Genet. 2015;60(9):547–52. doi:10.1038/jhg.2015.62.
  • Sambrook J, Russell DW. Isolation of high-molecular-weight DNA from mammalian cells using formamide. Cold Spring Harb Protoc. 2006;2006(1):pdb–prot3225.
  • Zhu K, Day T, Warshaviak D, Murrett C, Friesner R, Pearlman D. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction. Proteins Struct Funct Bioinf. 2014;82(8):1646–55. doi:10.1002/prot.24551.
  • Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang change Y. The I-TASSER Suite: protein structure and function prediction. Nat Methods. 2015;12(1):7–8. doi:10.1038/nmeth.3213.
  • Schwarz JM, Rödelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. Nat Methods. 2010;7(8):575–76. doi:10.1038/nmeth0810-575.
  • Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073. doi:10.1038/nprot.2009.86.
  • Sunyaev S, et al. Prediction of deleterious human alleles. Hum Mol Genet. 2001;10(6):591–97. doi:10.1093/hmg/10.6.591.
  • Giacinti C, Giordano A. RB and cell cycle progression. Oncogene. 2006;25(38):5220–27. doi:10.1038/sj.onc.1209615.
  • McEvoy J, Nagahawatte P, Finkelstein D, Richards-Yutz J, Valentine M, Ma J, Mullighan C, Song G, Chen X, Wilson M. RB1 gene inactivation by chromothripsis in human retinoblastoma. Oncotarget. 2014;5(2):438. doi:10.18632/oncotarget.1686.
  • Richter S, Vandezande K, Chen N, Zhang K, Sutherland J, Anderson J, Han L, Panton R, Branco P, Gallie B. Sensitive and efficient detection of RB1 gene mutations enhances care for families with retinoblastoma. Am J Hum Genet. 2003;72(2):253–69. doi:10.1086/345651.
  • Mandel CR, Bai Y, Tong L. Protein factors in pre-mRNA 3′-end processing. Cell Mol Life Sci. 2008;65(7–8):1099–122. doi:10.1007/s00018-007-7474-3.
  • Curinha A, Oliveira Braz S, Pereira-Castro I, Cruz A, Moreira A. Implications of polyadenylation in health and disease. Nucleus. 2014;5(6):508–19. doi:10.4161/nucl.36360.
  • Mayr C, Bartel DP. Widespread shortening of 3′ UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell. 2009;138(4):673–84. doi:10.1016/j.cell.2009.06.016.
  • Fabian MR, Sonenberg N, Filipowicz W. Regulation of mRNA translation and stability by microRnas. Ann Rev Biochem. 2010;79:351–79.
  • Chai Y-S, Yuan Z-Y, Lei F, Wang Y-G, Hu J, Du F, Lu X, Jiang J-F, Xing D-M, Du L-J. Inhibition of retinoblastoma mRNA degradation through Poly (A) involved in the neuroprotective effect of berberine against cerebral ischemia. PLoS One. 2014;9(3):e90850. doi:10.1371/journal.pone.0090850.
  • Leander C, Fu LC, Peña A, Howard SC, Rodriguez-Galindo C, Wilimas JA, Ribeiro RC, Haik B. Impact of an education program on late diagnosis of retinoblastoma in Honduras. Pediatr Blood Cancer. 2007;49(6):817–19. doi:10.1002/pbc.21052.
  • Friend SH, Bernards R, Rogelj S, Weinberg RA, Rapaport JM, Albert DM, Dryja TP. A human DNA segment with properties of the gene that predisposes to retinoblastoma and osteosarcoma. Nature. 1986;323(6089):643–46. doi:10.1038/323643a0.
  • Rushlow DE, Mol BM, Kennett JY, Yee S, Pajovic S, Thériault BL, Prigoda-Lee NL, Spencer C, Dimaras H, Corson TW. Characterisation of retinoblastomas without RB1 mutations: genomic, gene expression, and clinical studies. Lancet Oncol. 2013;14(4):327–34. doi:10.1016/S1470-2045(13)70045-7.
  • Stenfelt S, Blixt MKE, All‐ericsson C, Hallböök F, Boije H. Heterogeneity in retinoblastoma: a tale of molecules and models. Clin Transl Med. 2017;6(1):1–14. doi:10.1186/s40169-017-0173-2.
  • Arora R, Eden T, Kapoor G. Epidemiology of childhood cancer in India. Indian J Cancer. 2009;46(4):264. doi:10.4103/0019-509X.55546.
  • Gallie B Keynote lecture. World internet survey of classification of retinoblastoma. In XI International Congress of Ocular Oncology. Hyderabad, India; 2004.
  • Devarajan B, Prakash L, Kannan TR, Abraham AA, Kim U, Muthukkaruppan V, Vanniarajan A. Targeted next generation sequencing of RB1 gene for the molecular diagnosis of Retinoblastoma. BMC Cancer. 2015;15(1):1–10.
  • Tomar S, Sethi R, Sundar G, Quah TC, Quah BL, Lai PS. Mutation spectrum of RB1 mutations in retinoblastoma cases from Singapore with implications for genetic management and counselling. PLoS One. 2017;12(6):e0178776. doi:10.1371/journal.pone.0178776.
  • Domenico M, Cosimo L, Giovanni G. Retinoblastoma as an epigenetic disease: a proposal. J Cancer Ther. 2011.
  • Price EA, Price K, Kolkiewicz K, Hack S, Reddy MA, Hungerford JL, Kingston JE, Onadim Z. Spectrum of RB1 mutations identified in 403 retinoblastoma patients. J Med Genet. 2014;51(3):208–14. doi:10.1136/jmedgenet-2013-101821.
  • Jiang D, LaGory EL, Brož DK, Bieging KT, Brady CA, Link N, Abrams JM, Giaccia AJ, Attardi LD. Analysis of p53 transactivation domain mutants reveals Acad11 as a metabolic target important for p53 pro-survival function. Cell Rep. 2015;10(7):1096–109.
  • Yamada Y, Sakuma J, Takeuchi I, Yasukochi Y, Kato K, Oguri M, Fujimaki T, Horibe H, Muramatsu M, Sawabe M. Identification of C21orf59 and ATG2A as novel determinants of renal function-related traits in Japanese by exome-wide association studies. Oncotarget. 2017;8(28):45259. doi:10.18632/oncotarget.16696.
  • Hickman ES, Moroni MC, Helin K. The role of p53 and pRB in apoptosis and cancer. Curr Opin Gene Develop. 2002;12(1):60–66.
  • Chen L, Tweddle DA. P53, SKP2, and DKK3 as MYCN target genes and their potential therapeutic significance. Front Oncol. 2012;2:173. doi:10.3389/fonc.2012.00173.
  • Rosenbaum DM, Rasmussen SG, Kobilka BK. The structure and function of G-protein-coupled receptors. Nature. 2009;459(7245):356–63. doi:10.1038/nature08144.
  • Tuteja N. Signaling through G protein coupled receptors. Plant Signaling Behav. 2009;4(10):942–47. doi:10.4161/psb.4.10.9530.
  • Moore M, Gammon L, Dreger S, Koh J, Garbe JC, Stampfer MR, Philpott M, Jones L, Bishop CL. Ribosomal stress-induced senescence as a novel pro-senescence strategy for p16 positive basal-like breast cancer. bioRxiv. 2018:469445.
  • Labrecque MP, Takhar MK, Nason R, Santacruz S, Tam KJ, Massah S, Haegert A, Bell RH, Altamirano-Dimas M, Collins CC. The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. Oncotarget. 2016;7(17):24284. doi:10.18632/oncotarget.8301.
  • Singh A, Nunes JJ, Ateeq B. Role and therapeutic potential of G-protein coupled receptors in breast cancer progression and metastases. Eur J Pharmacol. 2015;763:178–83. doi:10.1016/j.ejphar.2015.05.011.
  • Jan LY, Jan YN. Voltage‐gated potassium channels and the diversity of electrical signalling. J Physiol. 2012;590(11):2591–99. doi:10.1113/jphysiol.2011.224212.
  • Shah NH, Aizenman E. Voltage-Gated potassium channels at the crossroads of neuronal function, ischemic tolerance, and neurodegeneration. Transl Stroke Res. 2014;5(1):38–58. doi:10.1007/s12975-013-0297-7.
  • Del Toro N, Lessard F, Tardif S, Bouchard J, Bourdeau V, Ferbeyre G, Brakier-Gingras L. The retinoblastoma tumor suppressor limits ribosomal readthrough during oncogene induced senescence. bioRxiv. 2019:788380.
  • Sarour SM, Zayed AM, Ibrahim MO, Albadry DE, Hassan MM, Yousif OE, Salih MA. New mutation found within OTOR gene involved in deafness in two Sudanese families from Al-Jazirah state-Sudan: using Next Generation Sequencing (NGS). Bio-Genet J. 2014;2(6):46–50.
  • Zhu H, Chen L, Zhou W, Huang Z, Hu J, Dai S, Wang X, Huang X, He C. Over-Expression of the ATP5J gene correlates with cell migration and 5-fluorouracil sensitivity in colorectal cancer. PLoS One. 2013;8(10):e76846. doi:10.1371/journal.pone.0076846.
  • Goding JW, Grobben B, Slegers H. Physiological and pathophysiological functions of the ecto-nucleotide pyrophosphatase/phosphodiesterase family. Biochim Biophys Acta. 2003;1638(1):1–19. doi:10.1016/s0925-4439(03)00058-9.
  • Han F, Liu W, Jiang X, Shi X, Yin L, Ao L, Cui Z, Li Y, Huang C, Cao J. SOX30, a novel epigenetic silenced tumor suppressor, promotes tumor cell apoptosis by transcriptional activating p53 in lung cancer. Oncogene. 2015;34(33):4391–402. doi:10.1038/onc.2014.370.
  • Feng C-W-A, Spiller C, Merriner DJ, O’Bryan MK, Bowles J, Koopman P. SOX30 is required for male fertility in mice. Sci Rep. 2017;7(1):1–12. doi:10.1038/s41598-017-17854-5.
  • Mansouri K, Mostafie A, Rezazadeh D, Shahlaei M, Modarressi MH. New function of TSGA10 gene in angiogenesis and tumor metastasis: a response to a challengeable paradox. Hum Mol Genet. 2016;25(2):233–44. doi:10.1093/hmg/ddv461.
  • Jen J, Wang Y-C. Zinc finger proteins in cancer progression. J Biomed Sci. 2016;23(1):53. doi:10.1186/s12929-016-0269-9.
  • Grudzien-Nogalska E, Jiao X, Song M-G, Hart RP, Kiledjian M. Nudt3 is an mRNA decapping enzyme that modulates cell migration. RNA. 2016;22(5):773–81. doi:10.1261/rna.055699.115.
  • Yendamuri S, Trapasso F, Calin GA. Arlts1–a novel tumor suppressor gene. Cancer Lett. 2008;264(1):11–20. doi:10.1016/j.canlet.2008.02.021.
  • Jiang Y, Zhao C-Y, Cheng L-C, Xu B, Lv H-Y. ARLTS1 polymorphism is associated with an increased risk of familial cancer: evidence from a meta-analysis. Hered Cancer Clin Pract. 2017;15(1):8. doi:10.1186/s13053-017-0068-7.
  • Fu S, Guo Y, Chen H, Xu Z-M, Qiu G-B, Zhong M, Sun K-L, Fu W-N. MYCT1-TV, a novel MYCT1 transcript, is regulated by c-Myc and may participate in laryngeal carcinogenesis. PLoS One. 2011;6(10):e25648. doi:10.1371/journal.pone.0025648.
  • Fu S, Fu Y, Chen F, Hu Y, Quan B, Zhang J. Overexpression of MYCT1 inhibits proliferation and induces apoptosis in human acute myeloid leukemia HL-60 and KG-1a cells in vitro and in vivo. Front Pharmacol. 2018;9:1045.
  • Woo C-W, Tan F, Cassano H, Lee J, Lee KC, Thiele CJ. Use of RNA interference to elucidate the effect of MYCN on cell cycle in neuroblastoma. Pediatr Blood Cancer. 2008;50(2):208–12. doi:10.1002/pbc.21195.
  • Barr FG, Duan F, Smith LM, Gustafson D, Pitts M, Hammond S, Gastier‐Foster JM. Genomic and clinical analyses of 2p24 and 12q13‐q14 amplification in alveolar rhabdomyosarcoma: a report from the Children’s Oncology Group. Genes Chromosomes Cancer. 2009;48(8):661–72.
  • Moreau LA, McGrady P, London WB, Shimada H, Cohn SL, Maris JM, Diller L, Look AT, George RE. Does MYCN Amplification Manifested as Homogeneously Staining Regions at Diagnosis Predict a Worse Outcome in Children with Neuroblastoma? a Children’s Oncology Group Study. Clin Cancer Res. 2006;12(19):5693–97. doi:10.1158/1078-0432.CCR-06-1500.
  • Kooi IE, Mol BM, Moll AC, van der Valk P, de Jong MC, de Graaf P, van Mil SE, Schouten-van Meeteren AYN, Meijers-Heijboer H, Kaspers GL. Loss of photoreceptorness and gain of genomic alterations in retinoblastoma reveal tumor progression. EBioMedicine. 2015;2(7):660–70. doi:10.1016/j.ebiom.2015.06.022.
  • Kumar SB, Chawla B, Bisht S, Yadav RK, Dada R, et al. Tobacco use increases oxidative DNA damage in sperm - possible etiology of childhood cancer. Asian Pac J Cancer Prev. 2015;16(16):6967–72. doi:10.7314/APJCP.2015.16.16.6967.
  • Bisht S, Chawla B, Dada R. 8-Hydroxy-2’-Deoxyguanosine in sperm DNA and increased risk of nonfamilial sporadic heritable retinoblastoma in the child. J Pediatr Genet. 2020;9(02):145–48. doi:10.1055/s-0039-1700974.
  • Mastrangelo D, Loré C, Grasso G. Retinoblastoma as an epigenetic disease: a proposal. J Cancer Ther. 2011;2(03):362. doi:10.4236/jct.2011.23049.
  • Bisht S, Chawla B, Dada R. Oxidative stress and polymorphism in MTHFR SNPs (677 and 1298) in paternal sperm DNA is associated with an increased risk of retinoblastoma in their children: a case–control study. J Pediatr Genet. 2018;7(03):103–13. doi:10.1055/s-0038-1667037.
  • Tunc O, Tremellen K. Oxidative DNA damage impairs global sperm DNA methylation in infertile men. J Assist Reprod Genet. 2009;26(9):537–44. doi:10.1007/s10815-009-9346-2.
  • Esteller M. Aberrant DNA methylation as a cancer-inducing mechanism. Ann Rev Pharmacol Toxicol. 2005;45(1):629–56. doi:10.1146/annurev.pharmtox.45.120403.095832.
  • Kooi I. Somatic genomic alterations in retinoblastoma beyond RB1 are rare and limited to copy number changes. Sci Rep. 2016;6(1):25264. doi:10.1038/srep25264.

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