Development of Sensitive Droplet Digital PCR Assays for Detecting Urinary TERT Promoter Mutations as Non-Invasive Biomarkers for Detection of Urothelial Cancer

Hosen, M.I.; Forey, N.; Durand, G.; Voegele, C.; Bilici, S.; Avogbe, P.H.; Delhomme, T.M.; Foll, M.; Manel, A.; Vian, E.; Meziani, S.; De Tilly, B.; Polo, G.; Lole, O.; Francois, P.; Boureille, A.; Pisarev, E.; Salas Andrei, R.O.; Monteiro-Reis, S.; Henrique, R.; Byrnes, G.; Jeronimo, C.; Scelo, G.; McKay, J.D.; Calvez-Kelm, F.L.; Zvereva, M.

Авторы: Hosen Md Ismail, Forey Nathalie, Durand Geoffroy, Voegele Catherine, Bilici Selin, Avogbe Patrice Hodonou, Delhomme Tiffany Myriam, Foll Matthieu, Manel Arnaud, Vian Emmanuel, Meziani Sonia, De Tilly Berengere, Polo Gilles, Lole Olesia, Francois Pauline, Boureille Antoine, Pisarev Eduard, Salas Andrei R.O.S.E, Monteiro-Reis Sara, Henrique Rui, Byrnes Graham, Jeronimo Carmen, Scelo Ghislaine, McKay James D., Calvez-Kelm Florence Le, Zvereva Maria
Журнал: Cancers
Том: 12
Номер: 12
Год издания: 2020
Издательство: MDPI
Местоположение издательства: Basel, Switzerland
Первая страница: 3541
Последняя страница: 3541
DOI: 10.3390/cancers12123541
Аннотация: Somatic mutations in the telomerase reverse transcriptase (TERT) promoter regions are frequent events in urothelial cancer (UC) and their detection in urine (supernatant cell-free DNA or DNA from exfoliated cells) could serve as putative non-invasive biomarkers for UC detection and monitoring. However, detecting these tumor-borne mutations in urine requires highly sensitive methods, capable of measuring low-level mutations. In this study, we developed sensitive droplet digital PCR (ddPCR) assays for detecting TERT promoter mutations (C228T, C228A, CC242-243TT, and C250T). We tested the C228T and C250T ddPCR assays on all samples with sufficient quantity of urinary DNA (urine supernatant cell-free DNA (US cfDNA) or urine pellet cellular DNA (UP cellDNA)) from the DIAGURO (n = 89/93 cases and n = 92/94 controls) and from the IPO-PORTO (n = 49/50 cases and n = 50/50 controls) series that were previously screened with the UroMuTERT assay and compared the performance of the two approaches. In the DIAGURO series, the sensitivity and specificity of the ddPCR assays for detecting UC using either US cfDNA or UP cellDNA were 86.8% and 92.4%. The sensitivity was slightly higher than that of the UroMuTERT assay in the IPO-PORTO series (67.4% vs. 65.3%, respectively), but not in the DIAGURO series (86.8% vs. 90.7%). The specificity was 100% in the IPO-PORTO controls for both the UroMuTERT and ddPCR assays, whereas in the DIAGURO series, the specificity dropped for ddPCR (92.4% versus 95.6%). Overall, an almost perfect agreement between the two methods was observed for both US cfDNA (n = 164; kappa coefficient of 0.91) and UP cellDNA (n = 280; kappa coefficient of 0.94). In a large independent series of serial urine samples from DIAGURO follow-up BC cases (n = 394), the agreement between ddPCR and UroMuTERT was (i) strong (kappa coefficient of 0.87), regardless of urine DNA types (kappa coefficient 0.89 for US cfDNA and 0.85 for UP cellDNA), (ii) the highest for samples with mutant allelic fractions (MAFs) > 2% (kappa coefficient of 0.99) and (iii) only minimal for the samples with the lowest MAFs (< 0.5%; kappa coefficient 0.32). Altogether, our results indicate that the two methods (ddPCR and UroMuTERT) for detecting urinary TERT promoter mutations are comparable and that the discrepancies relate to the detection of low-allelic fraction mutations. The simplicity of the ddPCR assays makes them suitable for implementation in clinical settings.
Добавил в систему: Писарев Эдуард Константинович

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Development of Sensitive Droplet Digital PCR Assays for Detecting Urinary TERT Promoter Mutations as Non-Invasive Biomarkers for Detection of Urothelial Cancerстатья

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