O Uso do Sequenciamento Total do Exoma no Diagnóstico do Adenocarcinoma Ductal Pancreático

Autores

  • Jacques de Oliveira Bernardes Universidade Federal de Santa Catarina (UFSC). Departamento de Biologia Celular, Embriologia e Genética. Florianópolis (SC), Brasil. https://orcid.org/0000-0002-5162-5444
  • Guilherme Toledo-Silva Universidade Federal de Santa Catarina (UFSC). Departamento de Biologia Celular, Embriologia e Genética. Florianópolis (SC), Brasil. https://orcid.org/0000-0002-9953-2861

DOI:

https://doi.org/10.32635/2176-9745.RBC.2023v69n1.3006

Palavras-chave:

carcinoma ductal pancreático, sequenciamento completo do exoma, terapia de alvo molecular

Resumo

 

Introdução: O adenocarcinoma ductal pancreático (PDAC) é uma doença agressiva responsável no Brasil por 2% das neoplasias e 5% das mortes por câncer. A análise do exoma – parte do DNA que codifica as proteínas – permite identificar as variantes somáticas do tumor e as germinativas do paciente. Essa informação é necessária para implementar a terapia-alvo para o PDAC, pois fornece evidência para selecionar, ou excluir, tratamentos para a doença. Objetivo: Identificar as variantes de interesse clínico e farmacológico presentes no PDAC de quatro pacientes, por meio da técnica de sequenciamento total do exoma (WES). Método: Foram utilizados dados públicos de quatro amostras de pares tumor-normal de PDAC, localizados na cabeça do pâncreas de pacientes caucasianos, estádio T3N1M0, sequenciadas e publicizadas pelo Texas Cancer Research Biobank. Para identificar as variações somáticas e germinativas, utilizou-se o software GATK. As consequências clínicas e farmacológicas dessas variações foram anotadas por meio do software VEP e analisadas mediante o software estatístico R. Resultados: Dos quatro tumores, um possui variante estrutural com duplicação do gene AKT2; outro, variantes nos genes da via das ciclinas CDK14 e CDKN2C, o que altera o regime quimioterápico; na linhagem germinativa, um paciente tem variantes no gene XRCC1, que sugere aumento da resposta à platina. Conclusão: Embora a patologia classifique todos os tumores como PDAC, cada paciente – bem como o respectivo tumor – apresenta especificidades que afetam o diagnóstico e as possibilidades terapêuticas. O WES permite identificá-las a um custo baixo, o que amplia as possibilidades de tratamento do PDAC.

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Referências

Instituto Nacional de Câncer [Internet]. Rio de Janeiro: INCA; [data desconhecida]. Tipos de câncer: câncer de pâncreas; [atualizada 2021 ago 24; acesso 2022 jan 15]. Disponível em: https://www.inca.gov.br/tipos-de-cancer/cancer-de-pancreas

Siegel RL, Miller KD, Jemal A. Cancer statistics, 2020. CA Cancer J Clin. 2020;70(1):7-30. doi: https://doi.org/10.3322/caac.21590 DOI: https://doi.org/10.3322/caac.21590

Markham MJ, Wachter K, Agarwal N, et al. Clinical cancer advances 2020: annual report on progress against cancer from the American Society of Clinical Oncology. J Clin Oncol. 2020;38(10):1081. doi: https://doi.org/10.1200/JCO.19.03141. Erratum in: J Clin Oncol. 2020;38(26):3076. doi: https://doi.org/10.1200/JCO.20.02291 DOI: https://doi.org/10.1200/JCO.19.03141

Luchini C, Capelli P, Scarpa A. Pancreatic ductal adenocarcinoma and its variants. Surg Pathol Clin. 2016;9(4):547-60. doi: https://doi.org/10.1016/j.path.2016.05.003 DOI: https://doi.org/10.1016/j.path.2016.05.003

Porta M, Fabregat X, Malats N, et al. Exocrine pancreatic cancer: symptoms at presentation and their relation to tumour site and stage. Clin Transl Oncol. 2005;7(5):189-97. doi: https://doi.org/10.1007/BF02712816 DOI: https://doi.org/10.1007/BF02712816

National Comprehensive Cancer Network. Pancreatic adenocarcinoma [Internet]. Version 2.2021. Plymouth Meeting, PA: NCCN; 2021 Feb 25. [cited 2021 Oct 7]. Available from: https://www.nccn.org/guidelines/nccn-guidelines/guidelines-detail?category=1&id=1455

Amin MB, Edge S, Greene F, et al, editors. AJCC cancer staging manual. 8th ed. Springer International Publishing: American Joint Commission on Cancer; 2017.

Schmied BM, Z'graggen K, Redaelli CA, et al. Problems in staging of pancreatic and hepatobiliary tumours. Ann Oncol. 2000;11 Suppl 3:161-4. doi: https://doi.org/10.1093/annonc/11.suppl_3.161 DOI: https://doi.org/10.1093/annonc/11.suppl_3.161

Kamarajah SK, Burns WR, Frankel TL, et al. Validation of the American Joint Commission on Cancer (AJCC) 8th edition staging system for patients with pancreatic adenocarcinoma: a Surveillance, Epidemiology and End Results (SEER) Analysis. Ann Surg Oncol. 2017;24(7):2023-30. doi: https://doi.org/10.1245/s10434-017-5810-x DOI: https://doi.org/10.1245/s10434-017-5810-x

Cancer Genome Atlas Research Network, Weinstein JN, Collisson EA, et al. The Cancer Genome Atlas Pan-Cancer analysis project. Nat Genet. 2013;45(10):1113-20. doi: https://doi.org/10.1038/ng.2764 DOI: https://doi.org/10.1038/ng.2764

Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144(5):646-74. doi: https://doi.org/10.1016/j.cell.2011.02.013 DOI: https://doi.org/10.1016/j.cell.2011.02.013

McCombie WR, McPherson JD, Mardis ER. Next-generation sequencing technologies. Cold Spring Harb Perspect Med. 2019;9(11):a036798. doi: https://doi.org/10.1101/cshperspect.a036798 DOI: https://doi.org/10.1101/cshperspect.a036798

van Dijk EL, Auger H, Jaszczyszyn Y, et al. Ten years of next-generation sequencing technology. Trends Genet. 2014;30(9):418-26. doi: https://doi.org/10.1016/j.tig.2014.07.001 DOI: https://doi.org/10.1016/j.tig.2014.07.001

Ding L, Bailey MH, Porta-Pardo E, et al. Perspective on oncogenic processes at the end of the beginning of cancer genomics. Cell. 2018;173(2):305-20.e10. doi: https://doi.org/10.1016/j.cell.2018.03.033 DOI: https://doi.org/10.1016/j.cell.2018.03.033

Strom SP. Current practices and guidelines for clinical next-generation sequencing oncology testing. Cancer Biol Med. 2016;13(1):3-11. doi: https://doi.org/10.28092/j.issn.2095-3941.2016.0004 DOI: https://doi.org/10.20892/j.issn.2095-3941.2016.0004

Cancer Genome Atlas Research Network. Integrated genomic characterization of pancreatic ductal adenocarcinoma. Cancer Cell. 2017;32(2):185-203.e13. doi: https://doi.org/10.1016/j.ccell.2017.07.007 DOI: https://doi.org/10.1016/j.ccell.2017.07.007

Waddell N, Pajic M, Patch AM. et al. Whole genomes redefine the mutational landscape of pancreatic cancer. Nature. 2015;518(7540):495-501. doi: https://doi.org/10.1038/nature14169 DOI: https://doi.org/10.1038/nature14169

Dreyer SB, Upstill-Goddard R, Paulus-Hock V, et al. Targeting DNA damage response and replication stress in pancreatic cancer. Gastroenterology. 2021;160(1):362-77.e13. doi: https://doi.org/10.1053/j.gastro.2020.09.043 DOI: https://doi.org/10.1053/j.gastro.2020.09.043

Dreyer SB, Pinese M, Jamieson NB, et al. Precision oncology in surgery: patient selection for operable pancreatic cancer. Ann Surg. 2020;272(2):366-76. doi: https://doi.org/10.1097/SLA.0000000000003143 DOI: https://doi.org/10.1097/SLA.0000000000003143

Ychou M, Conroy T, Seitz JF, et al. An open phase I study assessing the feasibility of the triple combination: oxaliplatin plus irinotecan plus leucovorin/ 5-fluorouracil every 2 weeks in patients with advanced solid tumors. Ann Oncol. 2003;14(3):481-9. doi: https://doi.org/10.1093/annonc/mdg119 DOI: https://doi.org/10.1093/annonc/mdg119

Amstutz U, Henricks LM, Offer SM, et al. Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for dihydropyrimidine dehydrogenase genotype and fluoropyrimidine dosing: 2017 update. Clin Pharmacol Ther. 2018;103(2):210-6. doi: https://doi.org/10.1002/cpt.911 DOI: https://doi.org/10.1002/cpt.911

Swen JJ, Nijenhuis M, de Boer A, et al. Pharmacogenetics: from bench to byte--an update of guidelines. Clin Pharmacol Ther. 2011;89(5):662-73. doi: https://doi.org/10.1038/clpt.2011.34 DOI: https://doi.org/10.1038/clpt.2011.34

Whirl-Carrillo M, McDonagh EM, Hebert JM, et al. Pharmacogenomics knowledge for personalized medicine. Clin Pharmacol Ther. 2012;92(4):414-7. doi: https://doi.org/10.1038/clpt.2012.96 DOI: https://doi.org/10.1038/clpt.2012.96

PharmGKB [Internet]. Stanford (CA): Stanford University; c2001-2022. Clinical Annotation for UGT1A1*1, UGT1A1*28; FOLFIRI or irinotecan; Neutropenia (level 1A Toxicity); [cited 2022 Mar 13]. Available from: https://www.pharmgkb.org/clinicalAnnotation/1451204660

Becnel LB, Pereira S, Drummond JA, et al. An open access pilot freely sharing cancer genomic data from participants in Texas. Sci Data. 2016;3:160010. doi: https://doi.org/10.1038/sdata.2016.10 DOI: https://doi.org/10.1038/sdata.2016.10

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-60. doi: https://doi.org/10.1093/bioinformatics/btp324 DOI: https://doi.org/10.1093/bioinformatics/btp324

FastQC [Internet]. Version 0.11.9. Cambridge: Babraham Institute. [2010]. – [cited 2022 Jan 3]. Available from: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Benjamin D, Sato T, Cibulskis K, et al. Calling somatic SNVs and indels with Mutect2. BioRxiv [Preprint]. 2019. doi: https://doi.org/10.1101/861054 DOI: https://doi.org/10.1101/861054

Van der Auwera GA, Carneiro M, Hartl C, et al. From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline. Curr Protoc Bioinformatics. 2013;43(1110):11.10.1-11.10.33. doi: https://doi.org/10.1002/0471250953.bi1110s43 DOI: https://doi.org/10.1002/0471250953.bi1110s43

Kuilman T. CopywriteR: copy number information from targeted sequencing using off-target reads [Internet]. R package Version 2.26.0. [place unknown]: Bioconductor; c2003. doi: https://doi.org/10.18129/B9.bioc.CopywriteR

Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10(2):giab008. doi: https://doi.org/10.1093/gigascience/giab008 DOI: https://doi.org/10.1093/gigascience/giab008

McLaren W, Gil L, Hunt SE, et al. The ensembl variant effect predictor. Genome Biol. 2016;17(1):122. doi: https://doi.org/10.1186/s13059-016-0974-4 DOI: https://doi.org/10.1186/s13059-016-0974-4

Conselho Nacional de Saúde (BR). Resolução nº 466, de 12 de dezembro de 2012. Aprova as diretrizes e normas regulamentadoras de pesquisas envolvendo seres humanos [Internet]. Diário Oficial da União, Brasília, DF. 2013 jun 13 [acesso 2022 mar 20]; Seção 1:59. Disponível em: https://bvsms.saude.gov.br/bvs/saudelegis/cns/2013/res0466_12_12_2012.html

Conselho Nacional de Saúde (BR). Resolução nº 510, de 7 de abril de 2016. Dispõe sobre as normas aplicáveis a pesquisas em Ciências Humanas e Sociais cujos procedimentos metodológicos envolvam a utilização de dados diretamente obtidos com os participantes ou de informações identificáveis ou que possam acarretar riscos maiores do que os existentes na vida cotidiana, na forma definida nesta Resolução [Internet]. Diário Oficial da União, Brasília, DF. 2016 maio 24 [acesso 2022 mar 20]; Seção 1:44. Disponível em: http://bvsms.saude.gov.br/bvs/saudelegis/cns/2016/res0510_07_04_2016.html

Landrum MJ, Lee JM, Benson M, et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 2018;46(D1):D1062-7. doi: https://doi.org/10.1093/nar/gkx1153 DOI: https://doi.org/10.1093/nar/gkx1153

Clark K, Karsch-Mizrachi I, Lipman DJ, et al. GenBank. Nucleic Acids Res. 2016;44(D1):D67-72. doi: https://doi.org/10.1093/nar/gkv1276 DOI: https://doi.org/10.1093/nar/gkv1276

Mehra S, Deshpande N, Nagathihalli N. Targeting PI3K pathway in pancreatic ductal adenocarcinoma: rationale and progress. Cancers (Basel). 2021;13(17):4434. doi: https://doi.org/10.3390/cancers13174434 DOI: https://doi.org/10.3390/cancers13174434

Liu J, Kang R, Tang D. The KRAS-G12C inhibitor: activity and resistance. Cancer Gene Ther. 2021;29(7):875-878. doi: https://doi.org/10.1038/s41417-021-00383-9 DOI: https://doi.org/10.1038/s41417-021-00383-9

Wijnen R, Pecoraro C, Carbone D, et al. Cyclin Dependent Kinase-1 (CDK-1) Inhibition as a Novel Therapeutic Strategy against Pancreatic Ductal Adenocarcinoma (PDAC). Cancers (Basel). 2021;13(17):4389. doi: https://doi.org/10.3390/cancers13174389 DOI: https://doi.org/10.3390/cancers13174389

Publicado

2023-01-16

Como Citar

1.
Bernardes J de O, Toledo-Silva G. O Uso do Sequenciamento Total do Exoma no Diagnóstico do Adenocarcinoma Ductal Pancreático. Rev. Bras. Cancerol. [Internet]. 16º de janeiro de 2023 [citado 22º de novembro de 2024];69(1):e-053006. Disponível em: https://rbc.inca.gov.br/index.php/revista/article/view/3006

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