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Опыт исследования образцов уротелиальной карциномы с помощью панели секвенирования нового поколения на 523 гена
© ООО «КОНСИЛИУМ МЕДИКУМ», 2024 г.
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Gridneva YaV, Khmelkova DN, Volkova MI, Blagodatskikh KA, Zheludkevich AA, Semenova AB, Veshchevailov AA, Babkina AV, Bondarev SA, Galkin VN. Experience of Next-Generation Sequencing in urothelial carcinoma specimens with panel for 523 genes. Journal of Modern Oncology. 2024;26(4):489–494. DOI: 10.26442/18151434.2024.4.203018
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Цель. Оценить профиль мутаций опухолевых образцов УК с помощью панели секвенирования нового поколения (NGS) на 523 гена.
Материалы и методы. Изучены фиксированные в формалине и залитые в парафин образцы УК 36 пациентов. Carcinoma in situ без папиллярной опухоли верифицирована у 1 (2,9%), Ta – у 14 (38,8%), T1 – у 19 (52,7%), T>T1 – у 2 (5,6%) больных; УК high-grade имела место у 14 (38,9%) пациентов. Из парафиновых блоков выделяли ДНК и РНК, готовили библиотеки с помощью панели Illumina TruSight Oncology 500, после чего проводили NGS с последующей биоинформатической обработкой данных.
Результаты. Медиана мутационной нагрузки (tumor mutation burden – TMB) составила 14,1 (1,6–102,9) мутации/Мб: TMB≥20 мутаций/Мб – 6 (16,7%). Во всех случаях уровень микросателлитной нестабильности являлся низким. В 36 образцах выявлена 181 терапевтически значимая и онкогенная мутация в 62 генах: медиана – 5 (1–16) мутаций в образце. В структуре мутаций доминировали SNV: 123 (68%); наибольшая частота – G>A 36 (29,3%). Выявлено 47 (26,0%) indel-мутаций, 10 (5,5%) амплификаций и 1 (0,6%) транслокация. Клинически значимые мутации обнаружены во всех образцах. Наибольшая частота клинически значимых мутаций отмечена в генах FGFR3 – 22 (61,1%) образца с мутациями в данном гене, KDM6A – 22 (61,1%), STAG2 – 13 (36,1%), PIK3CA – 9 (25,0%) и ARID1A – 9 (25,0%). Патогенные мутации 1–2-го уровня, обеспечивающие потенциальные терапевтические мишени, обнаружены в 29 (80,6%) из 36 образцов и включали альтерации 13 генов (AKT1, ATM, BRAF, СHEK2, ERBB2, FGFR3, IDH1, MLH1, NF1, NRAS, PIK3CA, PTEN и TSC1). Частыми мутациями 3–4-го уровня терапевтической значимости являлись KDM6A (61,6%), ARID1A (25,0%) и CDKN2A (11,4%).
Заключение. Исследование с помощью панели NGS на 523 гена подтвердило высокую TMB и низкую частоту микросателлитной нестабильности в опухолевых клетках УК. Наиболее частыми патогенными мутациями, ассоциированными с потенциальными терапевтическими мишенями при УК, являются альтерации FGFR3, PIK3CA и ERBB2.
Ключевые слова: уротелиальная карцинома, секвенирование нового поколения, профиль мутаций
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Background. Genomic alterations in urothelial carcinoma (UC) cells range from point DNA mutations to complex chromosomal rearrangements and changes in the number of chromosomes in the tumor cell. The UC genetic profile is highly heterogeneous, leading to significant variability in the natural history of the disease, prognosis, and responses to treatment. To evaluate the genetic alterations of Russian patients with bladder cancer is of great interest.
Aim. To evaluate the mutation profile in UC specimens with the next-generation sequencing (NGS) panel for 523 genes.
Materials and methods. Thirty-six patients' UC samples fixed in formalin and embedded in paraffin were studied. Carcinoma in situ without papillary tumor was verified in 1 (2.9%), Ta in 14 (38.8%), T1 in 19 (52.7%), T>T1 in 2 (5.6%) patients. High-grade UC was verified in 14 (38.9%) specimens. DNA and RNA were isolated from the paraffin blocks, libraries were prepared with the Illumina TruSight Oncology 500 panel, and then NGS was performed, followed by bioinformatics data processing.
Results. The median tumor mutation burden (TMB) was 14.1 (1.6-102.9) mutations/Mb: TMB≥20 mutations/Mb – 6 (16.7%). In all cases, the level of microsatellite instability was low. In 36 specimens, 181 therapeutically significant and oncogenic mutations were identified in 62 genes; the median was 5 (1–16) mutations per specimen. Single nucleotide variants prevailed in the mutation structure: 123 (68%); G>A had the highest frequency 36 (29.3%). There were 47 (26.0%) indel mutations, 10 (5.5%) amplifications, and 1 (0.6%) translocation. Clinically significant mutations were detected in all specimens. The highest frequency of clinically significant mutations was observed in the FGFR3 genes – 22 (61.1%) specimens with mutations in this gene, KDM6A – 22 (61.1%), STAG2 – 13 (36.1%), PIK3CA – 9 (25.0%), and ARID1A – 9 (25.0%). Pathogenic level 1-2 mutations providing potential therapeutic targets were detected in 29 (80.6%) of 36 specimens and included alterations of 13 genes (AKT1, ATM, BRAF, CHEK2, ERBB2, FGFR3, IDH1, MLH1, NF1, NRAs, PIK3CA, PTEN, and TSC1). Frequent mutations of level 3-4 therapeutic significance were in KDM6A (61.6%), ARID1A (25.0%), and CDKN2A (11.4%) genes.
Conclusion. A 523-gene NGS panel study confirmed the high TMB and low rate of microsatellite instability in UC tumor cells. The most common pathogenic mutations associated with potential therapeutic targets in UC were FGFR3, PIK3CA, and ERBB2 alterations.
Keywords: urothelial carcinoma, next-generation sequencing, mutation profile
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8. Alexandrov LB, Nik-Zainal S, Wedge DC, et al. Signatures of mutational processes in human cancer. Nature. 2013;500(7463):415-21.
9. Chalmers ZR, Connelly CF, Fabrizio D, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9(1):34.
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11. Chandran EBA, Iannantuono GM, Atiq SO, et al. Mismatch repair deficiency and microsatellite instability in urothelial carcinoma: a systematic review and meta-analysis. BMJ Oncol. 2024;3(1):e000335.
12. Kang HW, Kim WJ, Yun SJ. The therapeutic and prognostic implications of molecular biomarkers in urothelial carcinoma. Transl Cancer Res. 2020;9(10):6609-23.
13. Hurst CD, Alder O, Platt FM, et al. Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency. Cancer Cell. 2017;32(5):701-15.e7. DOI:10.1016/j.ccell.2017.08.005
14. Ascione CM, Napolitano F, Esposito D, et al. Role of FGFR3 in bladder cancer: Treatment landscape and future challenges. Cancer Treat Rev. 2023;115:102530.
15. Wysocki PJ, Jung KH, Oh DY, et al. Efficacy and safety of trastuzumab deruxtecan (T-DXd) in patients (pts) with HER2-expressing solid tumors: Results from the bladder cohort of the DESTINY-PanTumor02 (DP-02) study. J Clin Oncol. 2024;42(16):4565.
16. Shariati M, Meric-Bernstam F. Targeting AKT for cancer therapy. Expert Opin Investig Drugs. 2019;28(11):977-88.
17. Carmona FJ, Montemurro F, Kannan S, et al. AKT signaling in ERBB2-amplified breast cancer. Pharmacol Ther. 2016;158:63-70.
18. André F, Ciruelos E, Rubovszky G, et al. Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer. N Engl J Med. 2019;380(20):1929-40.
19. Marqués M, Corral S, Sánchez-Díaz M, et al. Tumor and Stromal Cell Targeting with Nintedanib and Alpelisib Overcomes Intrinsic Bladder Cancer Resistance. Mol Cancer Ther. 2023;22(5):616-29.
20. Maio M, Ascierto PA, Manzyuk L, et al. Pembrolizumab in microsatellite instability high or mismatch repair deficient cancers: updated analysis from the phase II KEYNOTE-158 study. Ann Oncol. 2022;33(9):929-38.
21. Wicks AJ, Krastev DB, Pettitt SJ, et al. Opinion: PARP inhibitors in cancer-what do we still need to know? Open Biol. 2022;12(7):220118.
22. Hertzman JC, Egyhazi BS. BRAF inhibitors in cancer therapy. Pharmacol Ther. 2014;142(2):176-82.
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24. Farnsworth DA, Inoue Y, Johnson FD, et al. MEK inhibitor resistance in lung adenocarcinoma is associated with addiction to sustained ERK suppression. NPJ Precis Oncol. 2022;6(1):88.
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1. Gladkov OA, Bulychkin PV, Volkova MI, et al. Prakticheskie rekomendatsii po lekarstvennomu lecheniiu raka mochevogo puzyria. Prakticheskie rekomendatsii RUSSCO, ch. 1. Zlokachestvennye Opukholi. 2023;13(#3s2):620-39 (in Russian).
2. Hurst CD, Cheng G, Platt FM, et al. Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight. Cell Rep Med. 2021;2(12):100472.
3. Illumina, Inc. Available at: https://support.illumina.com. Accessed: 15.06.2024.
4. Gudmundsson S, Singer-Berk M, Watts NA, et al. Variant interpretation using population databases: Lessons from gnomAD. Human Mutation. 2021;43(8):1012-30.
5. ClinVar. Available at: https://www.ncbi.nlm.nih.gov/clinvar/ Accessed: 12.01.2024.
6. Li MM, Datto M, Duncavage EJ, et al. Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017;19(1):4-23. DOI:10.1016/j.jmoldx.2016.10.002
7. Chakravarty D, Gao J, Phillips SM, et al. OncoKB: A Precision Oncology Knowledge Base. JCO Precis Oncol. 2017;2017:PO.17.00011. DOI:10.1200/PO.17.00011
8. Alexandrov LB, Nik-Zainal S, Wedge DC, et al. Signatures of mutational processes in human cancer. Nature. 2013;500(7463):415-21.
9. Chalmers ZR, Connelly CF, Fabrizio D, et al. Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden. Genome Med. 2017;9(1):34.
10. Marabelle A, Fakih M, Lopez J, et al. Association of tumour mutational burden with outcomes in patients with advanced solid tumours treated with pembrolizumab: prospective biomarker analysis of the multicohort, open-label, phase 2 KEYNOTE-158 study. Lancet Oncol. 2020;21(10):1353-65.
11. Chandran EBA, Iannantuono GM, Atiq SO, et al. Mismatch repair deficiency and microsatellite instability in urothelial carcinoma: a systematic review and meta-analysis. BMJ Oncol. 2024;3(1):e000335.
12. Kang HW, Kim WJ, Yun SJ. The therapeutic and prognostic implications of molecular biomarkers in urothelial carcinoma. Transl Cancer Res. 2020;9(10):6609-23.
13. Hurst CD, Alder O, Platt FM, et al. Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency. Cancer Cell. 2017;32(5):701-15.e7. DOI:10.1016/j.ccell.2017.08.005
14. Ascione CM, Napolitano F, Esposito D, et al. Role of FGFR3 in bladder cancer: Treatment landscape and future challenges. Cancer Treat Rev. 2023;115:102530.
15. Wysocki PJ, Jung KH, Oh DY, et al. Efficacy and safety of trastuzumab deruxtecan (T-DXd) in patients (pts) with HER2-expressing solid tumors: Results from the bladder cohort of the DESTINY-PanTumor02 (DP-02) study. J Clin Oncol. 2024;42(16):4565.
16. Shariati M, Meric-Bernstam F. Targeting AKT for cancer therapy. Expert Opin Investig Drugs. 2019;28(11):977-88.
17. Carmona FJ, Montemurro F, Kannan S, et al. AKT signaling in ERBB2-amplified breast cancer. Pharmacol Ther. 2016;158:63-70.
18. André F, Ciruelos E, Rubovszky G, et al. Alpelisib for PIK3CA-Mutated, Hormone Receptor-Positive Advanced Breast Cancer. N Engl J Med. 2019;380(20):1929-40.
19. Marqués M, Corral S, Sánchez-Díaz M, et al. Tumor and Stromal Cell Targeting with Nintedanib and Alpelisib Overcomes Intrinsic Bladder Cancer Resistance. Mol Cancer Ther. 2023;22(5):616-29.
20. Maio M, Ascierto PA, Manzyuk L, et al. Pembrolizumab in microsatellite instability high or mismatch repair deficient cancers: updated analysis from the phase II KEYNOTE-158 study. Ann Oncol. 2022;33(9):929-38.
21. Wicks AJ, Krastev DB, Pettitt SJ, et al. Opinion: PARP inhibitors in cancer-what do we still need to know? Open Biol. 2022;12(7):220118.
22. Hertzman JC, Egyhazi BS. BRAF inhibitors in cancer therapy. Pharmacol Ther. 2014;142(2):176-82.
23. Thomas J, Sonpavde G. Molecularly Targeted Therapy towards Genetic Alterations in Advanced Bladder Cancer. Cancers (Basel). 2022;14(7):1795.
24. Farnsworth DA, Inoue Y, Johnson FD, et al. MEK inhibitor resistance in lung adenocarcinoma is associated with addiction to sustained ERK suppression. NPJ Precis Oncol. 2022;6(1):88.
25. Li BT, Skoulidis F, Falchook G, et al. CodeBreaK 100: Registrational Phase 2 Trial of Sotorasib in KRAS p.G12C Mutated Non-small Cell Lung Cancer. Presented at: International Association for the Study of Lung Cancer 2020 World Conference on Lung Cancer; January 28-31, 2021; virtual. Abstract PS01.07.
26. Tian W, Zhang W, Wang Y, et al. Recent advances of IDH1 mutant inhibitor in cancer therapy. Front Pharmacol. 2022;13:982424.
27. Ali ES, Mitra K, Akter S, et al. Recent advances and limitations of mTOR inhibitors in the treatment of cancer. Cancer Cell Int. 2022;22(1):284.
1ГБУЗ «Городская клиническая больница им. С.С. Юдина» Департамента здравоохранения г. Москвы, Москва, Россия;
2ФГАОУ ВО «Первый Московский государственный медицинский университет им. И.М. Сеченова» Минздрава России (Сеченовский Университет), Москва, Россия;
3ПАО «Центр генетики и репродуктивной медицины “ГЕНЕТИКО”», Москва, Россия;
4ООО «АйТиДжен Лабс», Москва, Россия;
5ФГБОУ ДПО «Российская медицинская академия непрерывного профессионального образования» Минздрава России, Москва, Россия
*mivolkova@rambler.ru
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Yana V. Gridneva1,2, Darya N. Khmelkova3,4, Maria I. Volkova*1,5, Konstantin A. Blagodatskikh3, Anna A. Zheludkevich3, Anna B. Semenova1, Alexander A. Veshchevailov1, Alexandra V. Babkina1, Sergey A. Bondarev1, Vsevolod N. Galkin1,2
1Moscow City Hospital named after S.S. Yudin, Moscow Healthcare Department, Moscow, Russia;
2Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia;
3Center of Genetics and Reproductive Medicine Genetico PJSC, Moscow, Russia;
4ITGen Labs LLC, Moscow, Russia;
5Russian Medical Academy of Continuous Professional Education, Moscow, Russia
*mivolkova@rambler.ru