Functional analysis of rare variants in mismatch repair proteins augments results from computation-based predictive methods

Abstract

The cancer-predisposing Lynch Syndrome (LS) arises from germline mutations in DNA mismatch repair (MMR) genes, predominantly MLH1, MSH2, MSH6, and PMS2. A major challenge for clinical diagnosis of LS is the frequent identification of variants of uncertain significance (VUS) in these genes, as it is often difficult to determine variant pathogenicity, particularly for missense variants. Generic programs such as SIFT and PolyPhen-2, and MMR gene-specific programs such as PON-MMR and MAPP-MMR, are often used to predict deleterious or neutral effects of VUS in MMR genes. We evaluated the performance of multiple predictive programs in the context of functional biologic data for 15 VUS in MLH1, MSH2, and PMS2. Using cell line models, we characterized VUS predicted to range from neutral to pathogenic on mRNA and protein expression, basal cellular viability, viability following treatment with a panel of DNA-damaging agents, and functionality in DNA damage response (DDR) signaling, benchmarking to wild-type MMR proteins. Our results suggest that the MMR gene-specific classifiers do not always align with the experimental phenotypes related to DDR. Our study highlights the importance of complementary experimental and computational assessment to develop future predictors for the assessment of VUS.

Germline variants in DNA repair genes associated with hereditary breast and ovarian cancer syndrome: analysis of a 21 gene panel in the Brazilian population

“…3c), but differently to p.Arg18Lys, there is no report of this variant in other studies, and it is characterized as possibly pathogenic by two prediction tools. Recently, a study encompassing the functional characterization of 44 PALB2 missense variants evidenced that both variants are not affecting the evaluated PALB2 protein functions [96].…”

Caracterização molecular da Síndrome Hereditária do Câncer de Mama e/ou Ovário

“…The p.Asp792Asn (c.2374G>A)variant was identified in a gastric diffuse cancer case that deceased three year after the diagnosis. It has been described as presenting a moderate decrease in mismatch repair activity [97], which corroborates our analysis association. Due to it, we suggest that those variants may be related to increased risk to HBOC, but segregation studies and functional characterization are mandatory to access the contribution of those variants to HBOC etiology.…”

“…Já a variante p.Asp792Asn, c.2374G>A (rs587781265) (p=2.2e-16 ), foi identificada em um paciente com câncer de estômago que veio a óbito. Esta variante já foi descrita nos tópicos acima, sendo relacionada a um comprometimento moderado do sistema de reparo MMR(ARORA et al, 2017). Representação esquemática da proteína PMS2 e variantes encontradas no estudo e associadas ao risco para HBOC.…”

Predicting treatable traits for long-acting bronchodilators in patients with stable COPD

“… 23 The SIFT score, which indicates the degree of damage of the individual variant, has already been shown in many studies to be indicative of the degree of damage to the gene. 24 – 26 The method of using the damaged-gene score has been used in a previous study on drug responsiveness to damaged genes. 27 …”