Metastatik kolorektal kanserde dolaşan tümör DNA'sına dayalı yeni nesil dizileme tekniği ile tespit edilen genetik değişikliklerin prognoz ve sağ kalım üzerine etkisi

Year 2025, Volume: 18 Issue: 1, 6 - 6

Ahmet Ünlü Atike Gökçen Demiray Aydın Demiray Arzu Yaren Hakan Akça

https://doi.org/10.31362/patd.1482575

Abstract

Amaç: Şu ana kadar yapılan çalışmalar; dolaşan tümör DNA'sı (ctDNA) tabanlı next-generation sequencing (NGS) panellerinin, metastatik kolorektal kanserli (mCRC) hastalarda tedavi stratejilerinde yarar sağladığını göstermiştir. Biz de bu çalışmamızda; mCRC'li hastalarda ctDNA tabanlı NGS analizleriyle çeşitli gen değişikliklerinin sıklıklarını saptamayı, bu sonuçları standart polimeraz zincir reaksiyonu (PCR) analizlerindeki sonuçlarla karşılaştırarak uyum oranlarını değerlendirmeyi ve saptanan değişikliklerin genel sağ kalım ve progresyonsuz sağ kalıma etkisini araştırmayı planladık.
Gereç ve yöntem: Çalışma; mCRC tanısı ile takip edilen, kemoterapi ve/veya biyolojik ajan alan 48 hastaya ait bilgilerin retrospektif olarak taranması ve analiz edilmesi ile hazırlandı. Veriler SPSS 25.0 [IBM SPSS Statistics 25 software (Armonk, NY: IBM Corp.)] paket programı kullanılarak analiz edildi.
Bulgular: Çalışmada; ctDNA tabanlı NGS analizlerinin, kantitatif PCR tabanlı altın standart yönteme kıyasla KRAS mutasyonu için %64,7 duyarlılık, %55,6 özgüllük ve %59,1 uyum oranına; NRAS mutasyonu için %100 duyarlılık, %86,7 özgüllük ve %87,1 uyum oranına; BRAF mutasyonu için %50 duyarlılık, %96,4 özgüllük ve %90,6 uyum oranına sahip olduğu gösterildi. Ayrıca, likit biyopsi ile doku biyopsisi örneklerinin alınma zamanları arasındaki süreye göre uyum oranları da değerlendirildi. Sonuçta; uyum oranları bu süre 6 aydan kısa olanlarda KRAS, NRAS, BRAF mutasyonları için sırasıyla %60,9, %100, %100 olurken; süre 6 aydan uzun olanlarda sırasıyla %57,1, %78,9, %85 olarak saptandı. Bunun yanında, yapılan kapsamlı analizler sonucunda; mCRC'de birçok moleküler değişikliğin sıklığı ve bu değişikliklerin klinikopatolojik özellikler ve sağ kalım süreleriyle ilişkisi ortaya koyuldu.
Sonuç: Çalışmamız; mCRC'li hastalarda, ctDNA tabanlı NGS analizlerinin klinik yararını göstermektedir.

Keywords

ctDNA, gen dizileme, kolorektal kanser, likit biyopsi, yeni nesil dizileme

The effect of genetic alterations detected by the circulating tumor DNA-based next-generation sequencing technique on prognosis and survival in metastatic colorectal cancer

Abstract

Purpose: Studies conducted to date showed that circulating tumor DNA (ctDNA)-based next generation sequencing (NGS) panels are beneficial in the treatment strategies of patients with metastatic colorectal cancer (mCRC). In this study; we planned to determine the frequencies of various genetic alterations in patients with mCRC by ctDNA-based NGS analyses, evaluate the concordance rates by comparing these results with the results in standard polymerase chain reaction (PCR) analyses, and investigate the effect of the detected alterations on overall survival and progression-free survival.
Materials and methods: The study was conducted by retrospective screening and analysis of the data on 48 patients, who were followed up with a diagnosis of mCRC and who received chemotherapy and/or biological agents. The data were analyzed using SPSS 25.0 [IBM SPSS Statistics 25 software (Armonk, NY: IBM Corp.)] package program.
Results: In this study, ctDNA-based NGS analyses, compared to the quantitative PCR-based gold standard method, were found to have a sensitivity rate of 64.7%, specificity rate of 55.6% and concordance rate of 59.1% for KRAS mutation; a sensitivity rate of 100%, specificity rate of 86.7% and concordance rate of 87.1% for NRAS mutation; a sensitivity rate of 50%, specificity rate of 96.4% and concordance rate of 90.6% for BRAF mutation. In addition, concordance rates were evaluated based on to the time elapsed between the time of taking the liquid biopsy and tissue biopsy samples. As a result, concordance rates for KRAS, NRAS, and BRAF mutations were found to be 60.9%, 100%, and 100% respectively, in cases where this elapsed time was less than 6 months; and were found to be 57.1%, 78.9%, and 85% respectively, in cases where this elapsed time was more than 6 months. Furthermore, the comprehensive analyzes revealed that the frequency of many molecular changes in mCRC as well as the relationship of these changes with clinicopathological features and survival times.
Conclusion: Our study demonstrates the clinical benefit of ctDNA-based NGS analyzes in patients with mCRC.

Keywords

Colorectal cancer, ctDNA, gene sequencing, liquid biopsy, next generation sequencing

References

• 1. World Health Organization. Fact sheets. Colorectal cancer, 2023. Available at: https://www.who.int/news-room/fact-sheets/detail/colorectal-cancer? Accessed May 14, 2024
• 2. Wolpin BM, Mayer RJ. Systemic treatment of colorectal cancer. Gastroenterology 2008;134:1296-1310. https://doi.org/10.1053/j.gastro.2008.02.098
• 3. American Cancer Society. Colorectal Cancer Facts & Figures 2023-2025. Atlanta: American Cancer Society; 2023. Available at: https://www.cancer.org/research/cancer-facts-statistics/colorectal-cancer-facts-figures.html. Accessed May 14, 2024
• 4. Cutsem EV, Nordlinger B, Adam R, et al. Towards a pan-European consensus on the treatment of patients with colorectal liver metastases. Eur J Cancer 2006;42:2212-2221. https://doi.org/10.1016/j.ejca.2006.04.012
• 5. Colomer R, Mondejar R, Romero Laorden N, Alfranca A, Sanchez Madrid F, Quintela Fandino M. When should we order a next generation sequencing test in a patient with cancer? E Clinical Medicine 2020;25:100487. https://doi.org/10.1016/j.eclinm.2020.100487
• 6. Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science 2013;339:1546-1558. https://doi.org/10.1126/science.1235122
• 7. Haber DA, Velculescu VE. Blood-based analyses of cancer: circulating tumor cells and circulating tumor DNA. Cancer Discov 2014;4:650-661. https://doi.org/10.1158/2159-8290.CD-13-1014
• 8. U.S. Food and Drug Administration. FDA approves first liquid biopsy next-generation sequencing companion diagnostic test. 2020. Available at: https://www.fda.gov/news-events/press-announcements/fda-approves-first-liquid-biopsy-next-generation-sequencing-companion-diagnostic-test. Accessed May 14, 2024
• 9. U.S. Food and drug administration. FDA approves liquid biopsy NGS companion diagnostic test for multiple cancers and biomarkers. 2020. Available at: https://www.fda.gov/drugs/fda-approves-liquid-biopsy-ngs-companion-diagnostic-test-multiple-cancers-and-biomarkers. Accessed May 14, 2024
• 10. Innocenti F, Rashid N, Wancen M, et al. 5240- Next-generation sequencing (NGS) in metastatic colorectal cancer (mCRC): novel mutated genes and their effect on response to therapy (Alliance). Ann Oncol 2019;30:198-199. https://doi.org/10.1093/annonc/mdz246.002
• 11. Dinu D, Dobre M, Panaitescu E, et al. Prognostic significance of KRAS gene mutations in colorectal cancer - preliminary study. J Med Life 2014;7:581-587.
• 12. Yoon HH, Tougeron D, Shi Q, et al. KRAS codon 12 and 13 mutations in relation to disease-free survival in BRAF-wild-type stage III colon cancers from an adjuvant chemotherapy trial (N0147 alliance). Clin Cancer Res 2014;20:3033-3043. https://doi.org/10.1158/1078-0432.CCR-13-3140
• 13. Jauhri M, Bhatnagar A, Gupta S, et al. Prevalence and coexistence of KRAS, BRAF, PIK3CA, NRAS, TP53, and APC mutations in Indian colorectal cancer patients : next-generation sequencing – based cohort study. Tumour Biol 2017;39:1-11. https://doi.org/10.1177/1010428317692265
• 14. Schirripa M, Cremolini C, Loupakis F, et al. Role of NRAS mutations as prognostic and predictive markers in metastatic colorectal cancer. Int J Cancer 2015;136:83-90. https://doi.org/10.1002/ijc.28955 15. Davies H, Bignell GR, Cox C, et al. Mutations of the BRAF gene in human cancer. Nature 2002;417:949-954. https://doi.org/10.1038/nature00766
• 16. Van Cutsem E, Köhne CH, Lang I, et al. Cetuximab plus irinotecan, fluorouracil, and leucovorin as first-line treatment for metastatic colorectal cancer: updated analysis of overall survival according to tumor KRAS and BRAF mutation status. J Clin Oncol 2011;29:2011-2019. https://doi.org/10.1200/JCO.2010.33.5091
• 17. Li W, Qiu T, Guo L, Ying J, Zhou A. NGS-based oncogenic mutations analysis in advanced colorectal cancer patients improves targeted therapy prediction. Pathol Res Pract 2019;215:483-489. https://doi.org/10.1016/j.prp.2018.12.037
• 18. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 2012;487:330-337. https://doi.org/10.1038/nature11252
• 19. Thierry AR, Mouliere F, Messaoudi SE, et al. Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA. Nat Med 2014;20:430-435. https://doi.org/10.1038/nm.3511
• 20. Yao J, Zang W, Ge Y, et al. RAS/BRAF Circulating tumor DNA mutations as a predictor of response to first-line chemotherapy in metastatic colorectal cancer patients. Can J Gastroenterol Hepatol 2018;2018:4248971. https://doi.org/10.1155/2018/4248971
• 21. Osumi H, Shinozaki E, Takeda Y, et al. Clinical relevance of circulating tumor DNA assessed through deep sequencing in patients with metastatic colorectal cancer. Cancer Med 2019;8:408-417. https://doi.org/10.1002/cam4.1913
• 22. Kang JK, Heo S, Kim HP, et al. Liquid biopsy-based tumor profiling for metastatic colorectal cancer patients with ultra-deep targeted sequencing. PLoS One 2020;15:1-14. https://doi.org/10.1371/journal.pone.0232754
• 23. Schwaederle M, Husain H, Fanta PT, et al. Use of liquid biopsies in clinical oncology: pilot experience in 168 patients. Clin Cancer Res 2016;22:5497-5505. https://doi.org/10.1158/1078-0432