Investigation of the role of tumor mutational signatures as an approach for VUS reclassification and to investigate high-risk patients for colorectal cancer

• Grant number: 24/15483-1
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• Start date: June 01, 2025
• End date: March 31, 2027
• Field of knowledge: Biological Sciences - Genetics - Human and Medical Genetics
• Principal Investigator: Giovana Tardin Torrezan
• Grantee: Anthony Vladimir Campos Segura
• Host Institution: A C Camargo Cancer Center. Fundação Antonio Prudente (FAP). São Paulo , SP, Brazil

Abstract

Aim: The most common genes associated with hereditary colorectal cancer (CRC) and endometrial cancer (EC) predisposition syndromes are involved in DNA repair mechanisms. When altered, these genes generate specific patterns of somatic mutations known as tumor mutational signatures (TMS). Recent pioneering studies in the literature illustrate how identifying TMS in high-risk CRC (HR-CRC) patients can provide evidence to improve the diagnosis of these cases, such as the reclassification of variants of uncertain significance (VUS) and the determination of the etiology of multiple tumors. Objectives: To explore the application of tumor mutational signatures in two scenarios: first, to support reclassification approaches for VUS in patients suspected of having hereditary colorectal or endometrial cancer; second, to investigate etiologies associated with the development of colorectal cancer in high-risk patients.Methods:We utilized four databases from previous projects within our group, totaling 6,100 records of patients who underwent germline genetic testing and 3,000 CRC patient records. For the VUS cohort, we included 17 patients with CRC or EC and VUS detected in 8 genes involved in DNA repair mechanisms. In the HR-CRC cohort, we separated two groups: G1, 8 patients with synchronous tumors and 1 with metachronous tumors; G2, 7 patients with unexplained polyposis. So far, we have performed whole-exome sequencing (WES) on 8 paired samples of normal and tumor DNA from the VUS cohort. Somatic variants were called using the Genome Analysis Toolkit (GATK), and TMS were assigned using "SIGPROFILER Assignment," "R," and "Python," followed by cosine similarity analysis with a threshold >0.90. As negative and positive controls for both cohorts, we will use the TCGA CRC cohort. Results: We observed the presence of MMR-deficiency signatures (SBS6, SBS20, ID2, and ID7) in a sample with a VUS in PMS2 and POLD1, as well as positivity for MLH1 promoter methylation. In a sample with a VUS in POLE, we identified a small contribution of the corresponding signature SBS10b (8.8%), combined with a low mutational burden. For the remaining samples analyzed so far, no TMS related to the investigated VUS were identified. Conclusions: The information obtained so far for the 8 VUS does not indicate pathogenicity. However, additional testing is needed to provide more robust evidence, including comparisons with TCGA controls. With the future stages of the study, we aim to establish and validate a set of genomic and experimental tools for analyzing and applying TMS to challenges relevant to the diagnosis of CRC patients.