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Investigation of the Relationship Between DNA Mismatch Repair Genes and Microsatellite Instability in Solid Tumors

Yıl 2024, Cilt: 34 Sayı: 5, 689 - 695, 31.10.2024
https://doi.org/10.54005/geneltip.1510108

Öz

Aim: In this study, we aimed to detect the MSI status and somatic mutations in MMR genes (MSH2, MSH6, MLH1, PMS2) of a total of 55 solid tumors diagnosed with colorectal, endometrium and ovarian cancer by NGS method and to reveal the relationship between them.
Material and Method: DNA isolation was performed by taking 10-micron sections from paraffin-embedded tissue samples of 55 patients diagnosed with kolorektal, endometrium ve ovarian solid tümörlerinin and Kapa NGS DNA extraction kit was used for sequence analysis. The purity and concentration of the DNA obtained was measured by Qubit fluoremeter, and NadPrep DNA Universal Library Preparation Kit was used for high quality library preparation. Bioinformatics analyses were performed on the Genomize Seq platform. The MSI value was analysed by Roche Navify Mutation Caller software and percentage MSI values were determined using the MSIsensor2 pipeline for secondary analysis of NGS.
Results: All ovarian tumors were in the MSI-Stable category. The average MSI value was 2.01. One sample had an MSI of zero. In addition, no mutations in the MSH2 and MLH1 genes were detected in any of the ovarian tumors. 3 of 4 endometrial tumors were in the MSI-Stable category, and 1 tumor was in the MSI-low (MSI value: 13.2) category. No variants were detected in the MSH2 and PMS2 genes in endometrial tumors. 2 of the 41 colorectal tumors (Case4, Case16) were in the MSI-High category. No variants were detected in the MMR genes in 19 tumors.
Conclusion: Although frame-shift and stop-gain mutations were detected in 23 tumors that would cause protein deficiency in MMR genes, MSI-H was not detected, as expected, except for two colorectal tumors. Therefore, the results of our study emphasise the need to define new predictive biomarkers clinically within the framework of algorithms to predict response to immunotherapy and determine prognosis.

Kaynakça

  • Pardoll D. Cancer and the immune system: basic concepts and targets for intervention. Semin Oncol. 2015;42:523–538.
  • Oiseth SJ, Aziz MS. Cancer immunotherapy: a brief review of the history, possibilities, and challenges ahead. J Cancer Metastasis Treat. 2017;3:250–261.
  • Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144:646–674.
  • Chen DS, Mellman I. Oncology meets immunology: the cancer-immunity cycle. Immunity. 2013;39:1–10.
  • Gasparri ML, Ruscito I, Taghavi K, Farooqi AA, Papadia A, Foraccetti C, et al. Molecular oncology: underlying mechanisms and translational advancements. Switzerland: Springer; 2017. p. 193–204. ISBN: 978-3-319-53081-9.
  • Couzin-Frankel J. Cancer immunotherapy. Science. 2013;324:1432–1433.
  • Palomaki GE, McClain MR, Melillo S, Hampel HL, Thibodeau SN. EGAPP supplementary evidence review: DNA testing strategies aimed at reducing morbidity and mortality from Lynch syndrome. Genet Med. 2009;11:42–65.
  • Latham A., Srinivasan P., Kemel Y., Shia J., Bandlamudi C., Mandelker D., Middha S., Hechtman J., Zehir A., Dubard-Gault M., et al. Microsatellite Instability Is Associated with the Presence of Lynch Syndrome Pan-Cancer. J. Clin. Oncol. 2019;37:286–295.
  • Li X., Liu G., Wu W. Recent advances in Lynch syndrome. Exp. Hematol. Oncol. 2021;10:37.
  • Dominguez-Valentin M., Sampson J.R., Seppälä T.T., ten Broeke S.W., Plazzer J.-P., Nakken S., Engel C., Aretz S., Jenkins M.A., Sunde L., et al. Cancer risks by gene, age, and gender in 6350 carriers of pathogenic mismatch repair variants: Findings from the Prospective Lynch Syndrome Database. Genet. Med. 2020;22:15–25
  • Guan J, Lim KS, Mekhail T, Chang CC. Programmed death ligand-1 (PDL1) expression in the programmed death receptor-1 (PD-1)/PD-L1 blockade: a key player against various cancers. Arch Pathol Lab Med. 2017;141:851–861.
  • Topalian SL, Hodi FS, Brahmer JR, Gettinger SN, Smith DC, McDermott DF, et al. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N Engl J Med. 2012;366:2443–2454.
  • Brahmer JR, Tykodi SS, Chow LQ, Hwu WJ, Topalian SL, Hwu P, et al. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N Engl J Med. 2012;366:2455–2465.
  • Lipson EJ, Forde PM, Hammers HJ, Emens LA, Taube JM, Topalian SL. Antagonists of PD-1 and PD-L1 in cancer treatment. Semin Oncol. 2015;42:587–600.
  • Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348:124–128.
  • Snyder A, Makarov V, Merghoub T, Yuan J, Zaretsky JM, Desrichard A, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med. 2014;371:2189–2199.
  • Van Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L, et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015;350:207–211.
  • Chalmers ZR, Connelly CF, Fabrizio D, Gay L, Ali SM, Ennis R, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9:34.
  • Jamieson NB, Maker AV. Gene-expression profiling to predict responsiveness to immunotherapy. Cancer Gene Ther. 2017;24:134–140.
  • Palmieri G, Colombino M, Cossu A, Marchetti A, Botti G, Ascierto PA. Genetic instability and increased mutational load: which diagnostic tool best direct patients with cancer to immunotherapy? J Transl Med. 2017;15:17.
  • Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, et al. PD-1 Blockade in tumors with mismatch-repair deficiency. N Engl J Med. 2015;372:2509–2520.
  • Dudley JC, Lin MT, Le DT, Eshleman JR. Microsatellite instability as a biomarker for PD-1 blockade. Clin Cancer Res. 2016;22:813–820.
  • Naboush A, Roman CA, Shapira I. Immune checkpoint inhibitors in malignancies with mismatch repair deficiency: a review of the state of the current knowledge. J Investig Med. 2017;65:754–758.
  • Samowitz WS, Curtin K, Ma KN, Schaffer D, Coleman LW, Leppert M, et al. Microsatellite instability in sporadic colon cancer is associated with an improved prognosis at the population level. Cancer Epidemiol Biomarkers Prev. 2001;10:917–923.
  • Hiroyuki Y, Yoshiyuki W, Tadateru M, Kohzoh I, Fumio I. Microsatellite instability in cancer: a novel landscape for diagnostic and therapeutic approach. Arch Toxicol. 2020;94:3349–3357.
  • Keitaro S. Concordance analysis of microsatellite instability status between polymerase chain reaction based testing and next generation sequencing for solid tumors. Sci Rep. 2021;11:20003.
  • Hirotsu Y, Nagakubo Y, Amemiya K, Shinozaki E, Mochizuki H, Omata Masao. Microsatellite instability status is determined by targeted sequencing with MSIcall in 25 cancer types. Clin Chim Acta. 2020;502:207–213.
  • Yamamoto H, Imai K. An updated review of microsatellite instability in the era of next-generation sequencing and precision medicine. Semin Oncol. 2019;46:261–270.
  • Palomaki GE, McClain MR, Melillo S, Hampel HL, Thibodeau SN, Schaefer G. EGAPP supplementary evidence review: DNA testing strategies aimed at reducing morbidity and mortality from Lynch syndrome. Genet Med. 2009;11:42–65.
  • Shia J, Ellis NA, Klimstra DS. The utility of immunohistochemical detection of DNA mismatch repair gene proteins. Virchows Arch. 2004;445:431–441.
  • Shia J. Immunohistochemistry versus microsatellite instability testing for screening colorectal cancer patients at risk for hereditary nonpolyposis colorectal cancer syndrome. Part I. The utility of immunohistochemistry. J Mol Diagn. 2008;10:293–300.
  • Lynch HT, Synder CL, Shaw TG. Milestones of Lynch syndrome: 1895–2015. Nat Rev Cancer. 2015;15:181–194.
  • Boland CR, Goel A. Microsatellite instability in colorectal cancer. Gastroenterology. 2010;138:2073–2087.
  • Liisa C. Microsatellite instability: a predictive biomarker for cancer immunotherapy. Appl Immunohistochem Mol Morphol. 2018;26:e15–e21.
  • Haraldsdottir S, Hampel H, Tomsic J, Frankel WL, Pearlman R, de la Chapelle A, et al. Colon and endometrial cancers with mismatch repair deficiency can arise from somatic, rather than germline, mutations. Gastroenterology. 2014;147:1308-1316.e1.
  • Gelsomino F, Barbolini M, Spallanzani A, Pugliese G, Cascinu S. The evolving role of microsatellite instability in colorectal cancer: a review. Cancer Treat Rev. 2016;51:19-26.
  • Mensenkamp AR, Vogelaar IP, van Zelst-Stams WA, Goossens M, Ouchene H, Hendriks-Cornelissen SJ, et al. Somatic mutations in MLH1 and MSH2 are a frequent cause of mismatch-repair deficiency in Lynch syndrome-like tumors. Gastroenterology. 2014;146:643-646.e8.
  • McCarthy AJ, Capo-Chichi JM, Spence T, Grenier S, Stockley T, Kamel-Reid S, et al. Heterogenous loss of mismatch repair (MMR) protein expression: a challenge for immunohistochemical interpretation and microsatellite instability (MSI) evaluation. J Pathol Clin Res. 2019;5:115-129.
  • Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2019;47:D941-D947.

Solid Tümörlerde DNA Yanlış Eşleşme Onarım Genleri ile Mikrosatellit İnstabilite Arasındaki İlişkinin Araştırılması

Yıl 2024, Cilt: 34 Sayı: 5, 689 - 695, 31.10.2024
https://doi.org/10.54005/geneltip.1510108

Öz

Amaç: Bu çalışmada kolorektal, endometrium ve over kanseri tanısı almış toplam 55 solid tümörün MSI durumunu ve MMR genlerindeki (MSH2, MSH6, MLH1, PMS2) somatik mutasyonları NGS yöntemi ile tespit etmeyi ve aralarındaki ilişkiyi ortaya koymayı amaçladık.
Gereç ve Yöntem: Kolorektal, endometrium ve yumurtalık kanseri tanısı almış 55 solid tümör örneklerinden 10 mikronluk kesitler alınarak DNA izolasyonu gerçekleştirilmiş ve dizi analizi için Kapa NGS DNA ekstraksiyon kiti kullanılmıştır. Elde edilen DNA’nın saflığı ve konsantrasyonu Qubit floremetre ile ölçülmüş, yüksek kalitede kütüphane hazırlanması için NadPrep DNA Universal Library Preparation Kit kullanılmıştır. Biyoinformatik analizler Genomize Seq platformunda gerçekleştirilmiştir. MSI değeri Roche Navify Mutation Caller yazılımı ile analiz edilmiş ve yüzde MSI değerleri NGS’nin ikincil analizi için MSIsensor2 boru hattı kullanılarak belirlenmiştir.
Bulgular: Tüm yumurtalık tümörleri MSI-Stabil kategorisindeydi. Ortalama MSI değeri 2,01 idi. Bir örneğin MSI değeri sıfırdı. Ayrıca, yumurtalık tümörlerinin hiçbirinde MSH2 ve MLH1 genlerinde mutasyon tespit edilmemiştir. 4 endometriyal tümörün 3’ü MSI-Stabil kategorisinde ve 1 tümör MSI-düşük (MSI değeri: 13,2) kategorisindeydi. Endometriyal tümörlerde MSH2 ve PMS2 genlerinde herhangi bir varyant tespit edilmemiştir. 41 kolorektal tümörün 2’si (Vaka4, Vaka16) MSI-Yüksek kategorisindeydi. MMR genlerinde 19 tümörde herhangi bir varyant tespit edilmemiştir.
Sonuç: MMR genlerinde protein eksikliğine neden olabilecek çerçeve kayması ve stop-gain mutasyonları 23 tümörde tespit edilmesine rağmen, iki kolorektal tümör dışında beklendiği gibi MSI-H tespit edilmemiştir. Bu nedenle, çalışmamızın sonuçları, immünoterapiye yanıtı öngörmek ve prognozu belirlemek için algoritmalar çerçevesinde klinik olarak yeni öngörücü biyobelirteçlerin tanımlanması gerektiğini vurgulamaktadır.

Kaynakça

  • Pardoll D. Cancer and the immune system: basic concepts and targets for intervention. Semin Oncol. 2015;42:523–538.
  • Oiseth SJ, Aziz MS. Cancer immunotherapy: a brief review of the history, possibilities, and challenges ahead. J Cancer Metastasis Treat. 2017;3:250–261.
  • Hanahan D, Weinberg RA. Hallmarks of cancer: the next generation. Cell. 2011;144:646–674.
  • Chen DS, Mellman I. Oncology meets immunology: the cancer-immunity cycle. Immunity. 2013;39:1–10.
  • Gasparri ML, Ruscito I, Taghavi K, Farooqi AA, Papadia A, Foraccetti C, et al. Molecular oncology: underlying mechanisms and translational advancements. Switzerland: Springer; 2017. p. 193–204. ISBN: 978-3-319-53081-9.
  • Couzin-Frankel J. Cancer immunotherapy. Science. 2013;324:1432–1433.
  • Palomaki GE, McClain MR, Melillo S, Hampel HL, Thibodeau SN. EGAPP supplementary evidence review: DNA testing strategies aimed at reducing morbidity and mortality from Lynch syndrome. Genet Med. 2009;11:42–65.
  • Latham A., Srinivasan P., Kemel Y., Shia J., Bandlamudi C., Mandelker D., Middha S., Hechtman J., Zehir A., Dubard-Gault M., et al. Microsatellite Instability Is Associated with the Presence of Lynch Syndrome Pan-Cancer. J. Clin. Oncol. 2019;37:286–295.
  • Li X., Liu G., Wu W. Recent advances in Lynch syndrome. Exp. Hematol. Oncol. 2021;10:37.
  • Dominguez-Valentin M., Sampson J.R., Seppälä T.T., ten Broeke S.W., Plazzer J.-P., Nakken S., Engel C., Aretz S., Jenkins M.A., Sunde L., et al. Cancer risks by gene, age, and gender in 6350 carriers of pathogenic mismatch repair variants: Findings from the Prospective Lynch Syndrome Database. Genet. Med. 2020;22:15–25
  • Guan J, Lim KS, Mekhail T, Chang CC. Programmed death ligand-1 (PDL1) expression in the programmed death receptor-1 (PD-1)/PD-L1 blockade: a key player against various cancers. Arch Pathol Lab Med. 2017;141:851–861.
  • Topalian SL, Hodi FS, Brahmer JR, Gettinger SN, Smith DC, McDermott DF, et al. Safety, activity, and immune correlates of anti-PD-1 antibody in cancer. N Engl J Med. 2012;366:2443–2454.
  • Brahmer JR, Tykodi SS, Chow LQ, Hwu WJ, Topalian SL, Hwu P, et al. Safety and activity of anti-PD-L1 antibody in patients with advanced cancer. N Engl J Med. 2012;366:2455–2465.
  • Lipson EJ, Forde PM, Hammers HJ, Emens LA, Taube JM, Topalian SL. Antagonists of PD-1 and PD-L1 in cancer treatment. Semin Oncol. 2015;42:587–600.
  • Rizvi NA, Hellmann MD, Snyder A, Kvistborg P, Makarov V, Havel JJ, et al. Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science. 2015;348:124–128.
  • Snyder A, Makarov V, Merghoub T, Yuan J, Zaretsky JM, Desrichard A, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med. 2014;371:2189–2199.
  • Van Allen EM, Miao D, Schilling B, Shukla SA, Blank C, Zimmer L, et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science. 2015;350:207–211.
  • Chalmers ZR, Connelly CF, Fabrizio D, Gay L, Ali SM, Ennis R, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9:34.
  • Jamieson NB, Maker AV. Gene-expression profiling to predict responsiveness to immunotherapy. Cancer Gene Ther. 2017;24:134–140.
  • Palmieri G, Colombino M, Cossu A, Marchetti A, Botti G, Ascierto PA. Genetic instability and increased mutational load: which diagnostic tool best direct patients with cancer to immunotherapy? J Transl Med. 2017;15:17.
  • Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, et al. PD-1 Blockade in tumors with mismatch-repair deficiency. N Engl J Med. 2015;372:2509–2520.
  • Dudley JC, Lin MT, Le DT, Eshleman JR. Microsatellite instability as a biomarker for PD-1 blockade. Clin Cancer Res. 2016;22:813–820.
  • Naboush A, Roman CA, Shapira I. Immune checkpoint inhibitors in malignancies with mismatch repair deficiency: a review of the state of the current knowledge. J Investig Med. 2017;65:754–758.
  • Samowitz WS, Curtin K, Ma KN, Schaffer D, Coleman LW, Leppert M, et al. Microsatellite instability in sporadic colon cancer is associated with an improved prognosis at the population level. Cancer Epidemiol Biomarkers Prev. 2001;10:917–923.
  • Hiroyuki Y, Yoshiyuki W, Tadateru M, Kohzoh I, Fumio I. Microsatellite instability in cancer: a novel landscape for diagnostic and therapeutic approach. Arch Toxicol. 2020;94:3349–3357.
  • Keitaro S. Concordance analysis of microsatellite instability status between polymerase chain reaction based testing and next generation sequencing for solid tumors. Sci Rep. 2021;11:20003.
  • Hirotsu Y, Nagakubo Y, Amemiya K, Shinozaki E, Mochizuki H, Omata Masao. Microsatellite instability status is determined by targeted sequencing with MSIcall in 25 cancer types. Clin Chim Acta. 2020;502:207–213.
  • Yamamoto H, Imai K. An updated review of microsatellite instability in the era of next-generation sequencing and precision medicine. Semin Oncol. 2019;46:261–270.
  • Palomaki GE, McClain MR, Melillo S, Hampel HL, Thibodeau SN, Schaefer G. EGAPP supplementary evidence review: DNA testing strategies aimed at reducing morbidity and mortality from Lynch syndrome. Genet Med. 2009;11:42–65.
  • Shia J, Ellis NA, Klimstra DS. The utility of immunohistochemical detection of DNA mismatch repair gene proteins. Virchows Arch. 2004;445:431–441.
  • Shia J. Immunohistochemistry versus microsatellite instability testing for screening colorectal cancer patients at risk for hereditary nonpolyposis colorectal cancer syndrome. Part I. The utility of immunohistochemistry. J Mol Diagn. 2008;10:293–300.
  • Lynch HT, Synder CL, Shaw TG. Milestones of Lynch syndrome: 1895–2015. Nat Rev Cancer. 2015;15:181–194.
  • Boland CR, Goel A. Microsatellite instability in colorectal cancer. Gastroenterology. 2010;138:2073–2087.
  • Liisa C. Microsatellite instability: a predictive biomarker for cancer immunotherapy. Appl Immunohistochem Mol Morphol. 2018;26:e15–e21.
  • Haraldsdottir S, Hampel H, Tomsic J, Frankel WL, Pearlman R, de la Chapelle A, et al. Colon and endometrial cancers with mismatch repair deficiency can arise from somatic, rather than germline, mutations. Gastroenterology. 2014;147:1308-1316.e1.
  • Gelsomino F, Barbolini M, Spallanzani A, Pugliese G, Cascinu S. The evolving role of microsatellite instability in colorectal cancer: a review. Cancer Treat Rev. 2016;51:19-26.
  • Mensenkamp AR, Vogelaar IP, van Zelst-Stams WA, Goossens M, Ouchene H, Hendriks-Cornelissen SJ, et al. Somatic mutations in MLH1 and MSH2 are a frequent cause of mismatch-repair deficiency in Lynch syndrome-like tumors. Gastroenterology. 2014;146:643-646.e8.
  • McCarthy AJ, Capo-Chichi JM, Spence T, Grenier S, Stockley T, Kamel-Reid S, et al. Heterogenous loss of mismatch repair (MMR) protein expression: a challenge for immunohistochemical interpretation and microsatellite instability (MSI) evaluation. J Pathol Clin Res. 2019;5:115-129.
  • Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 2019;47:D941-D947.
Toplam 39 adet kaynakça vardır.

Ayrıntılar

Birincil Dil İngilizce
Konular Tıbbi Genetik (Kanser Genetiği hariç)
Bölüm Original Article
Yazarlar

Ozkan Bagci 0000-0002-9896-6764

Erken Görünüm Tarihi 27 Ekim 2024
Yayımlanma Tarihi 31 Ekim 2024
Gönderilme Tarihi 3 Temmuz 2024
Kabul Tarihi 2 Eylül 2024
Yayımlandığı Sayı Yıl 2024 Cilt: 34 Sayı: 5

Kaynak Göster

Vancouver Bagci O. Investigation of the Relationship Between DNA Mismatch Repair Genes and Microsatellite Instability in Solid Tumors. Genel Tıp Derg. 2024;34(5):689-95.