Dados do Trabalho

Título

Assessment of mutational signatures to classify variants of uncertain clinical significance in DNA repair genes in patients with colorectal or endometrial cancer.

Introdução

The most common genes associated to hereditary predisposition syndromes for colorectal cancer (CRC) and endometrial cancer (EC) are involved in DNA repair mechanisms, and when mutated, generate specific patterns of mutations known as mutational signatures. A significant percentage of genetic tests in suspected patients show variants of uncertain significance (VUS), hindering clinical diagnosis. The reclassification of VUS is essential in hereditary cancer genetic testing, and recent studies have shown that investigating the tumor mutation signatures can aid in variant classification.

Objetivo

To evaluate the use of tumor exome sequencing (WES) to determine mutational signatures and classify VUS in DNA repair genes in patients with CRC and EC.

Métodos

We will use three databases: data from previous group projects (600 patients), reports from the Laboratory of Genomic Diagnosis (LDG) at A.C.Camargo (2,500 patients), and the clinical database from the Department of Oncogenetics at A.C.Camargo (3,000 patients). We will select 10 to 15 patients with colorectal or endometrial cancer who have VUS detected in predisposition genes in previous genetic tests. We will select VUS in 8 DNA repair genes for which specific mutational signatures have been previously identified: {MLH1}, {MSH2}, {MSH6}, {PMS2}, {MUTYH}, {POLE}, {POLD1}, {NTHL1}. WES will be performed using samples of normal genomic DNA (leukocytes or saliva) and tumor DNA (fresh-frozen or formalin-fixed and paraffin-embedded tissue). Mutational signatures will be evaluated using the SigneR and Mutational Patterns tools, and they will be compared with the signatures from COSMIC Mutational Signatures v3. Additionally, we will investigate the presence of a second event in genes with VUS, such as single somatic mutations or loss of heterozygosity.

Resultados

So far, we have reviewed the results of more than 6,100 genetic tests from A.C.Camargo patients and identified 16 patients (11 females and 4 males) with Variants of Uncertain Significance (VUS) in the 8 selected genes. 14 patients presented CRC (Colorectal Cancer), 1 EC (Endometrial Cancer), and 1 GC (Gastric Cancer). With an average age of 44, a median of 45, and a standard deviation of ±8.45. The following respective number of VUS was found for each gene: {MLH1} (2), {MSH2} (2), {MSH6} (4), {PMS2} (2), {MUTYH} (3), {POLE} (3), {POLD1} (3), and {NTHL1} (2). Regarding the tumor location, 6 patients presented lesions in the right colon (ascending/transverse), 5 presented lesions in the left colon (descending, sigmoid, intraperitoneal and extraperitoneal rectum), and 5 showed no record. Only 1 patient showed MMRd with negative IHC for {MLH1}/{PMS2}. For genomic analysis, 1 patient showed mutated {BRAF}, 4 presented mutated {KRAS}, and 1 presented mutated {NRAS}. Lastly, 10 patients had family history of cancers associated with the digestive system. Tumor samples were requested to the biobank and we will proceed with WES of these samples.

Conclusões

In this project, we will establish and validate a set of genomic and experimental tools that will allow us to improve the reclassification of VUS in genes related to CRC and EC predisposition, resulting in more accurate diagnoses and with an impact on the management of cancer patients.

Palavras-chave

Colorectal cancer (CRC), Lynch syndrome, variants of uncertain significance (VUS).

Financiador do resumo

CNPq and FAPESP.