Exome-wide molecular insights from blood and urine liquid biopsies in genitourinary cancers

Abstract

Background: Liquid biopsy has emerged as a non-invasive method for real-time cancer monitoring especially in genitourinary (GU) oncology. Most current studies utilize a panel-based molecular profiling ranging from 50-600 genes; however, a comprehensive exome-wide profiling of real-world patient samples has been lacking.

Methods: Over 2000 liquid biopsy samples were analyzed in this study, including urine samples from early-stage bladder cancer and plasma samples from prostate, lung, breast, esophageal, head and neck cancers, among others. Cell-free DNA (cfDNA) was extracted from these samples and analyzed using PredicineWES+^TM, a boosted comprehensive whole-exome sequencing (WES) assay with an in-depth coverage of 600 cancer-related genes derived from the PredicineATLAS^TM panel. Data analysis was conducted in-house using Predicine's DeepSea bioinformatics software.

Results: The PredicineWES+^TM assay demonstrated high sensitivity for detecting somatic mutations across the exome and showed comparable tumor mutational burden (TMB) estimates with the PredicineATLAS^TM panel. Interestingly, the highest tumor TMB score was observed in bladder cancer among the analyzed cancers, which is consistent with literature using tissue-based genomic profiling. The most common cancer variants include TP53, ERBB2, KRAS, PIK3CA, FGFR3, APC, among others.

Conclusion: Liquid biopsy-based genomic profiling across various cancer types provides an in-depth analysis of biomarker discovery for personalized cancer care, setting the foundation for improved cancer diagnosis and personalized treatment strategies for urological diseases.

Keywords

cell free DNA / genitourinary oncology / liquid biopsy / next-generation sequencing (NGS)

References

[1] Alix-Panabières C , Marchetti D , Lang JE . Liquid biopsy:from concept to clinical application. Sci Rep. 2023; 13 (1): 21685.

[2] Bronkhorst AJ , Ungerer V , Oberhofer A , Gabriel S , Polatoglou E , Randeu H , et al. New perspectives on the importance of cell-free DNA biology. Diagnostics. 2022; 12 (9): 2147.

[3] Fonseca NM , Maurice-Dror C , Herberts C , Tu W , Fan W , Murtha AJ , et al. Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer. Nat Commun. 2024; 15 (1): 1828.

[4] García-Pardo M , Makarem M , Li JJN , Kelly D , Leighl NB . Integrating circulating-free DNA (cfDNA) analysis into clinical practice:opportunities and challenges. Br J Cancer. 2022; 127 (4): 592- 602.

[5] Ignatiadis M , Sledge GW , Jeffrey SS . Liquid biopsy enters the clinic -implementation issues and future challenges. Nat Rev Clin Oncol. 2021; 18 (5): 297- 312.

[6] Tivey A , Church M , Rothwell D , Dive C , Cook N . Circulating tumour DNA-looking beyond the blood. Nat Rev Clin Oncol. 2022; 19 (9): 600- 12.

[7] Zang J , Zhang R , Jin D , Xie F , Shahatiaili A , Wu G , et al. Integrated longitudinal circulating tumor DNA profiling predicts immunotherapy response of metastatic urothelial carcinoma in the POLARIS-03 trial. J Pathol. 2023; 261 (2): 198- 209.

[8] Sivakumar S , Jin DX , Tukachinsky H , Murugesan K , McGregor K , Danziger N , et al. Tissue and liquid biopsy profiling reveal convergent tumor evolution and therapy evasion in breast cancer. Nat Commun. 2022; 13 (1): 7495.

[9] Ye L , Chu X , Ni J , Chu L , Yang X , Zhu Z . NGS-based tissue-blood TMB comparison and blood-TMB monitoring in stage-III non-small cell lung cancer treated with concurrent chemoradiotherapy. Cancer Invest. 2024; 42 (2): 165- 75.

[10] Ji H , Long X , Gu J , Jin J , Mao X , Wang Z , et al. Longitudinal monitoring of plasma circulating tumour DNA enables the prediction of early relapse in patients with non-Hodgkin lymphoma: a case series. Diagnostics. 2021; 11 (11): 2055.

[11] Lee H , Han J , Choi YL . Real-world analysis of the EGFR mutation test in tissue and plasma samples from non-small cell lung cancer. Diagnostics. 2021; 11 (9): 1695.

[12] Haselmann V , Hedtke M , Neumaier M , Haselmann V , Hedtke M , Neumaier M . Liquid profiling for cancer patient stratification in precision medicine-current status and challenges for successful implementation in standard care. Diagnostics. 2022; 12 (3): 748- 236.

[13] Roldan Ruiz J , Fuentes Gago MG , Chinchilla Tabora LM , Gonzalez Morais I , Sayagues JM , Abad Hernández M , et al. The impact of liquid biopsies positive for EGFR mutations on overall survival in non-small cell lung cancer patients. Diagnostics. 2023; 13 (14): 2347.

[14] Llueca A , Canete-Mota S , Jaureguí A , Barneo M , Ibañez MV , Neef A , et al. The impact of liquid biopsy in advanced ovarian cancer care. Diagnostics. 2024; 14 (17): 1868.

[15] Shitara K , Muro K , Watanabe J , Yamazaki K , Ohori H , Shiozawa M , et al. Baseline ctDNA gene alterations as a biomarker of survival after panitumumab and chemotherapy in metastatic colorectal cancer. Nature Med. 2024; 30 (3): 730- 9.

[16] Bailey MH , Meyerson WU , Dursi LJ , Wang LB , Dong G , Liang WW , et al. Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples. Nat Commun. 2020; 11 (1): 4748.

[17] Jiang Y , Dong Y , Zhao S , Liu D , Zhang J , Xu X , et al. Multiregion WES of metastatic pancreatic neuroendocrine tumors revealed heterogeneity in genomic alterations, immune microenvironment and evolutionary patterns. Cell Commun Signaling. 2024; 22 (1): 164.

[18] Menzel M , Ossowski S , Kral S , Metzger P , Horak P , Marienfeld R , et al. Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients. npj Precis Oncol. 2023; 7 (1): 106.

[19] Van Hout CV , Tachmazidou I , Backman JD , Hoffman JD , Liu D , Pandey AK , et al. Exome sequencing and characterization of 49,960 individuals in the UK Biobank. Nature. 2020; 586 (7831): 749- 56.

[20] Yu L , Zhang Y , Wang D , Li L , Zhang R , Li J . Harmonizing tumor mutational burden analysis:Insights from a multicenter study using in silico reference data sets in clinical whole-exome sequencing (WES). Am J Clin Path. 2024; 162 (4): 408- 19.

[21] Zhang H , He X , Wang Y , Li C , Jiang H , Hou S , et al. Simultaneous CNV-seq and WES: An effective strategy for molecular diagnosis of unexplained fetal structural anomalies. Heliyon. 2024; 10 (20): e39392.

[22] Choi Y , Dharia NV , Jun T , Chang J , Royer-Joo S , Yau KK , et al. Circulating tumor DNA dynamics reveal KRAS G12C mutation heterogeneity and response to treatment with the KRAS G12C inhibitor divarasib in solid tumors. Clin Cancer Res. 2024; 30 (17): 3788- 97.

[23] Zhang R , Zang J , Jin D , Xie F , Shahatiaili A , Wu G , et al. Urinary tumor DNA MRD analysis to identify responders to neoadjuvant immunotherapy in muscle-invasive bladder cancer. Clin Cancer Res. 2023; 29 (20): 4040- 6.

[24] Sacher A , LoRusso P , Patel MR , Miller WH , Garralda E , Forster MD , et al. Single-agent divarasib (GDC-6036) in solid tumors with a KRAS G12C mutation. N Engl J Med. 2023; 389 (8): 710- 21.

[25] Davis AA , Luo J , Zheng T , Dai C , Dong X , Tan L , et al. Genomic complexity predicts resistance to endocrine therapy and CDK4/6 inhibition in hormone receptor-positive (HR+)/HER2-negative metastatic breast cancer. Clin Cancer Res. 2023; 29 (9): 1719- 29.

[26] Desai J , Alonso G , Kim SH , Cervantes A , Karasic T , Medina L , et al. Divarasib plus cetuximab in KRAS G12C-positive colorectal cancer: a phase 1b trial. Nature Med. 2024; 30 (1): 271- 8.

[27] Singh H , Lowder KE , Kapner K , Kelly RJ , Zheng H , McCleary NJ , et al. Clinical outcomes and ctDNA correlates for CAPOX BETR: a phase II trial of capecitabine, oxaliplatin, bevacizumab, trastuzumab in previously untreated advanced HER2+ gastroesophageal adenocarcinoma. Nat Commun. 2024; 15 (1): 6833.

[28] Gu Z , Eils R , Schlesner M . Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016; 32 (18): 2847- 9.

[29] Gandara DR , Paul SM , Kowanetz M , Schleifman E , Zou W , Li Y , et al. Blood-based tumor mutational burden as a predictor of clinical benefit in non-small-cell lung cancer patients treated with atezolizumab. Nature Med. 2018; 24 (9): 1441- 8.

[30] Kim ES , Velcheti V , Mekhail T , Yun C , Shagan SM , Hu S , et al. Blood-based tumor mutational burden as a biomarker for atezolizumab in non-small cell lung cancer: the phase 2 B-F1RST trial. Nature Med. 2022; 28 (5): 939- 45.

[31] Peters S , Dziadziuszko R , Morabito A , Felip E , Gadgeel SM , Cheema P , et al. Atezolizumab versus chemotherapy in advanced or metastatic NSCLC with high blood-based tumor mutational burden:primary analysis of BFAST cohort C randomized phase 3 trial. Nature Med. 2022; 28 (9): 1831- 9.

[32] Aparicio J . Precision medicine in metastatic colorectal cancer: targeting KRAS G12C mutation. Transl Gastroenterol Hepatol. 2024; 9: 53.

[33] Luo FX , Arter ZL . Adagrasib in KRYSTAL-12 has broken the KRAS (G12C) enigma code in non-small cell lung carcinoma. Lung Cancer (Auckland, N.Z.). 2024; 15: 161- 7.

[34] Schmidt JF , Entz D , Brasch F , Goerner M . Sotorasib in KRAS p.G12C-mutated pulmonary sarcomatoid carcinoma: Therapeutic efficacy of a KRAS inhibitor in symptomatic brain metastases. Case Rep Oncol. 2024; 17 (1): 1019- 24.

[35] Turner NC , Im SA , Saura C , Juric D , Loibl S , Kalinsky K , et al. Inavolisib-based therapy in PIK3CA-mutated advanced breast cancer. N Engl J Med. 2024; 391 (17): 1584- 96.

[36] André F , Ciruelos E , Rubovszky G , Campone M , Loibl S , Rugo HS , et al. Alpelisib for PIK3CA-mutated, hormone receptor-positive advanced breast cancer. N Engl J Med. 2019; 380 (20): 1929- 40.

[37] Turner NC , Oliveira M , Howell SJ , Dalenc F , Cortes J , Gomez Moreno HL , et al. Capivasertib in hormone receptor-positive advanced breast cancer. N Engl J Med. 2023; 388 (22): 2058- 70.

[38] Loriot Y , Matsubara N , Park SH , Huddart RA , Burgess EF , Houede N , et al. Erdafitinib or chemotherapy in advanced or metastatic urothelial carcinoma. N Engl J Med. 2023; 389 (21): 1961- 71.

[39] Loriot Y , Necchi A , Park SH , Garcia-Donas J , Huddart R , Burgess E , et al. Erdafitinib in locally advanced or metastatic urothelial carcinoma. N Engl J Med. 2019; 381 (4): 338- 48.

[40] Goyal L , Meric-Bernstam F , Hollebecque A , Valle JW , Morizane C , Karasic TB , et al. Futibatinib for FGFR2-rearranged intrahepatic cholangiocarcinoma. N Engl J Med. 2023; 388 (3): 228- 39.

[41] Zhu K , Yang X , Tai H , Zhong X , Luo T , Zheng H . HER2. Biomark Res. 2024; 12 (1): 16.

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The Author(s). UroPrecision published by John Wiley & Sons Australia, Ltd on behalf of Higher Education Press.