Adenomas from individuals with pathogenic biallelic variants in the MUTYH and NTHL1 genes demonstrate base excision repair tumour mutational signature profiles similar to colorectal cancers, expanding potential diagnostic and variant classification applications

• Published in: medRxiv : the preprint server for health sciences
• Main Authors: Walker, Romy, Joo, Jihoon E, Mahmood, Khalid, Clendenning, Mark, Como, Julia, Preston, Susan G, Joseland, Sharelle, Pope, Bernard J, Medeiros, Ana B D, Murillo, Brenely V, Pachter, Nicholas, Sweet, Kevin, Spigelman, Allan D, Groves, Alexandra, Gleeson, Margaret, Bernatowicz, Krzysztof, Poplawski, Nicola, Andrews, Lesley, Healey, Emma, Gallinger, Steven, Grant, Robert C, Win, Aung K, Hopper, John L, Jenkins, Mark A, Torrezan, Giovana T, Rosty, Christophe, Macrae, Finlay A, Winship, Ingrid M, Buchanan, Daniel D, Georgeson, Peter
• Format: Journal Article
• Language: English
• Published: United States 09.08.2024
• Subjects: SBS30; hereditary cancer predisposition; adenoma; NTHL1; Colorectal cancer; SBS36; SBS18; variant of uncertain clinical significance; MUTYH; mutational signature

Colorectal cancers (CRCs) from people with biallelic germline likely pathogenic/pathogenic variants in or exhibit specific single base substitution (SBS) mutational signatures, namely combined SBS18 and SBS36 (SBS18+SBS36), and SBS30, respectively. The aim was to determine if adenomas from biallelic cases demonstrated these mutational signatures at diagnostic levels. Whole-exome sequencing of FFPE tissue and matched blood-derived DNA was performed on 9 adenomas and 15 CRCs from 13 biallelic cases, on 7 adenomas and 2 CRCs from 5 biallelic cases and on 27 adenomas and 26 CRCs from 46 non-hereditary (sporadic) participants. All samples were assessed for COSMIC v3.2 SBS mutational signatures. In biallelic cases, SBS18+SBS36 signature proportions in adenomas (mean±standard deviation, 65.6%±29.6%) were not significantly different to those observed in CRCs (76.2%±20.5%, =0.37), but were significantly higher compared with non-hereditary adenomas (7.6%±7.0%, =3.4×10 ). Similarly, in biallelic cases, SBS30 signature proportions in adenomas (74.5%±9.4%) were similar to those in CRCs (78.8%±2.4%) but significantly higher compared with non-hereditary adenomas (2.8%±3.6%, =5.1×10 ). Additionally, a compound heterozygote with the c.1187G>A p.(Gly396Asp) pathogenic variant and the c.533G>C p.(Gly178Ala) variant of unknown significance (VUS) in demonstrated high levels of SBS18+SBS36 in four adenomas and one CRC, providing evidence for reclassification of the VUS to pathogenic. SBS18+SBS36 and SBS30 were enriched in adenomas at comparable proportions observed in CRCs from biallelic and biallelic cases, respectively. Therefore, testing adenomas may improve the identification of biallelic cases and facilitate variant classification, ultimately enabling opportunities for CRC prevention.