scholarly journals Functional assay-based classification of PMS2 variants in Lynch Syndrome

Author(s):  
Emily Rayner ◽  
Yvonne Tiersma ◽  
Cristina Fortuno ◽  
Sandrine van Hees-Stuivenberg ◽  
Mark Drost ◽  
...  

The large majority of germline alterations identified in the DNA mismatch repair (MMR) gene PMS2, a low-penetrance gene for the cancer predisposition Lynch Syndrome (LS, OMIM 120435), represent variants of unknown significance (VUS). The inability to assess pathogenicity of such VUS interferes with personalized healthcare. The complete in vitro MMR activity (CIMRA) assay, that only requires sequence information on the VUS, provides a functional analysis-based tool suited for VUS classification. To derive a formula that translates CIMRA assay results for PMS2 VUS into the odds of pathogenicity (OddsPath), we used a set of clinically classified PMS2 variants, supplemented by inactivating variants generated by an in cellulo genetic screen, as proxies for pathogenic variants. Validation of this OddsPath revealed very high predictive values for PMS2 VUS. We conclude that this OddsPath provides an integral metric that, similar to the other, higher penetrance, MMR proteins MSH2, MLH1 and MSH6, can be incorporated into the upcoming criteria for MMR gene VUS classification of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP). This will represent a seminal step forward in enabling personalized healthcare for individuals suspected of LS and their relatives.

Genes ◽  
2020 ◽  
Vol 11 (3) ◽  
pp. 325
Author(s):  
Gašper Klančar ◽  
Ana Blatnik ◽  
Vita Šetrajčič Dragoš ◽  
Vesna Vogrič ◽  
Vida Stegel ◽  
...  

The diagnostics of Lynch syndrome (LS) is focused on the detection of DNA mismatch repair (MMR) system deficiency. MMR deficiency can be detected on tumor tissue by microsatellite instability (MSI) using molecular genetic test or by loss of expression of one of the four proteins (MLH1, MSH2, MSH6, and PMS2) involved in the MMR system using immunohistochemistry (IHC) staining. According to the National Comprehensive Cancer Network (NCCN) guidelines, definitive diagnosis of LS requires the identification of the germline pathogenic variant in one of the MMR genes. In the report, we are presenting interesting novel MLH1 in-frame deletion LRG_216t1:c.2236_2247delCTGCCTGATCTA p.(Leu746_Leu749del) associated with LS. The variant appears to be associated with uncommon isolated loss of PMS2 immunohistochemistry protein staining (expression) in tumor tissue instead of MLH1 and PMS2 protein loss, which is commonly seen with pathogenic variants in MLH1. The variant was classified as likely pathogenic, based on segregation analysis and molecular characterization of blood and tumor samples. According to the American College of Medical Genetics (ACMG) guidelines, the following evidence categories of PM1, PM2, PM4, and PP1 moderate have been used for classification of the novel variant. By detecting and classifying the novel MLH1 variant as likely pathogenic, we confirmed the LS in this family.


2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Raffaella Liccardo ◽  
Marina De Rosa ◽  
Paola Izzo ◽  
Francesca Duraturo

About 10% of total colorectal cancers are associated with known Mendelian inheritance, as Familial Adenomatous Polyposis (FAP) and Lynch syndrome (LS). In these cancer types the clinical manifestations of disease are due to mutations in high-risk alleles, with a penetrance at least of 70%. The LS is associated with germline mutations in the DNA mismatch repair (MMR) genes. However, the mutation detection analysis of these genes does not always provide informative results for genetic counseling of LS patients. Very often, the molecular analysis reveals the presence of variants of unknown significance (VUSs) whose interpretation is not easy and requires the combination of different analytical strategies to get a proper assessment of their pathogenicity. In some cases, these VUSs may make a more substantial overall contribution to cancer risk than the well-assessed severe Mendelian variants. Moreover, it could also be possible that the simultaneous presence of these genetic variants in several MMR genes that behave as low risk alleles might contribute in a cooperative manner to increase the risk of hereditary cancer. In this paper, through a review of the recent literature, we have speculated a novel inheritance model in the Lynch syndrome; this could pave the way toward new diagnostic perspectives.


2020 ◽  
Vol 18 (5) ◽  
pp. 1112-1120.e1 ◽  
Author(s):  
Anne Goverde ◽  
Ellis L. Eikenboom ◽  
Ellemieke L. Viskil ◽  
Marco J. Bruno ◽  
Michael Doukas ◽  
...  

2016 ◽  
Vol 113 (15) ◽  
pp. 4128-4133 ◽  
Author(s):  
Hellen Houlleberghs ◽  
Marleen Dekker ◽  
Hildo Lantermans ◽  
Roos Kleinendorst ◽  
Hendrikus Jan Dubbink ◽  
...  

Single-stranded DNA oligonucleotides can achieve targeted base-pair substitution with modest efficiency but high precision. We show that “oligo targeting” can be used effectively to study missense mutations in DNA mismatch repair (MMR) genes. Inherited inactivating mutations in DNA MMR genes are causative for the cancer predisposition Lynch syndrome (LS). Although overtly deleterious mutations in MMR genes can clearly be ascribed as the cause of LS, the functional implications of missense mutations are often unclear. We developed a genetic screen to determine the pathogenicity of these variants of uncertain significance (VUS), focusing on mutator S homolog 2 (MSH2). VUS were introduced into the endogenous Msh2 gene of mouse embryonic stem cells by oligo targeting. Subsequent selection for MMR-deficient cells using the guanine analog 6-thioguanine allowed the detection of MMR-abrogating VUS. The screen was able to distinguish weak and strong pathogenic variants from polymorphisms and was used to investigate 59 Msh2 VUS. Nineteen of the 59 VUS were identified as pathogenic. Functional assays revealed that 14 of the 19 detected variants fully abrogated MMR activity and that five of the detected variants attenuated MMR activity. Implementation of the screen in clinical practice allows proper counseling of mutation carriers and treatment of their tumors.


2020 ◽  
Author(s):  
Xiaoyan Jia ◽  
Bala Bharathi Burugula ◽  
Victor Chen ◽  
Rosemary M. Lemons ◽  
Sajini Jayakody ◽  
...  

AbstractThe lack of functional evidence for the majority of missense variants limits their clinical interpretability, and poses a key barrier to the broad utility of carrier screening. In Lynch Syndrome (LS), one of the most highly prevalent cancer syndromes, nearly 90% of clinically observed missense variants are deemed “variants of uncertain significance” (VUS). To systematically resolve their functional status, we performed a massively parallel screen in human cells to identify loss-of-function missense variants in the key DNA mismatch repair factor MSH2. The resulting functional effect map is substantially complete, covering 94% of the 17,746 possible variants, and is highly concordant (96%) with existing functional data and expert clinicians’ interpretations. The large majority (89%) of missense variants were functionally neutral, perhaps unexpectedly in light of its evolutionary conservation. These data provide ready-to-use functional evidence to resolve the ∼1,300 extant missense VUSs in MSH2, and may facilitate the prospective classification of newly discovered variants in the clinic.


2017 ◽  
Vol 42 (5) ◽  
pp. 2021-2029 ◽  
Author(s):  
Chuanchau J. Jou ◽  
Cammon B. Arrington ◽  
Spencer Barnett ◽  
Jiaxiang Shen ◽  
Scott Cho ◽  
...  

Background/Aims: Congenital Sick Sinus Syndrome (SSS) is a disorder associated with sudden cardiac death due to severe bradycardia and prolonged pauses. Mutations in HCN4, the gene encoding inward Na+/K+ current (If), have been described as a cause of congenital SSS. The objective of this study is to develop an SSS model in embryonic zebrafish, and use zebrafish as a moderate-throughput assay to functionally characterize HCN4 variants. Methods: To determine the function of hcn4 in zebrafish, embryos were either bathed in the If -specific blocker (ZD-7288), or endogenous hcn4 expression was knocked down using splice-blocking morpholinos. To assess whether the zebrafish model discriminates benign from pathogenic variants, we tested four HCN4 mutations known to cause human SSS and four variants of unknown significance (VUS). Results: Pharmacological blockade and knockdown of hcn4 in zebrafish phenocopied human SSS, displaying bradycardia and cardiac pauses in intact embryos and explanted hearts. The zebrafish assay correctly identified all disease-causing variants. Of the VUS, the assay predicted 2 as benign and 2 as hypomorphic variants. Conclusions: We conclude that our embryonic zebrafish assay is a novel and effective tool to functionally characterize human HCN4 variants, which can be translated into important clinical prognostic information.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kerstin Hoppe ◽  
Karin Jurkat-Rott ◽  
Stefanie Kranepuhl ◽  
Scott Wearing ◽  
Sebastian Heiderich ◽  
...  

AbstractMalignant hyperthermia (MH) is a pharmacogenetic disorder of skeletal muscle metabolism characterized by generalized muscle rigidity, increased body temperature, rhabdomyolysis, hyperkalemia and severe metabolic acidosis. The underlying mechanism of MH involves excessive Ca2+ release from myotubes via the ryanodine receptor type 1 (RYR1) and the voltage-dependent L-type calcium channel (CACNA1S). As more than 300 variants of unknown significance have been detected to date, we examined whether freely available pathogenicity prediction tools are able to detect relevant MH causing variants. In this diagnostic accuracy study, blood samples from 235 individuals with a history of a clinical malignant hyperthermia or their close relatives were genetically screened for RYR1 variants of all 106 RYR1 exons and additionally for known variants of CACNA1S. In vitro contracture tests were conducted on muscle biopsies obtained from all individuals, independently of whether a pathogenic variant, a variant of unknown significance or no variant was detected. Comparisons were made to three established bioinformatic pathogenicity detection tools to identify the clinical impact of the variants of unknown significance. All detected genetic variants were tested for pathogenicity by three in silico approaches and compared to the in vitro contracture test. Sensitivity and specificity of exon screening of all individuals listed in our MH database was analyzed. Exon screening identified 97 (41%) of the 235 individuals as carriers of pathogenic variants. Variants of unknown significance were detected in 21 individuals. Variants of unknown significance were subdivided into 19 malignant-hyperthermia-susceptible individuals and 2 non-malignant-hyperthermia-susceptible individuals. All pathogenic variants as well as the malignant-hyperthermia-suspectible variants were correctly identified by the bioinformatic prediction tools. Sensitivity of in silico approaches ranged between 0.71 and 0.98 (Polyphen 0.94 [CI 95% 0.75; 0.99]; Sift 0.98 [CI 95% 0.81; 0.99]; MutationTaster 0.92 [CI 95% 0.75; 0.99]). Specificity differed depending on the used tool (Polphen 0.98 [CI 95% 0.32; 0.99]; Sift 0.98 [CI 95% 0.32; 0.99]; MutationTaster 0.00 [CI 95% 0.00; 0.60]). All pathogenic variants and variants of unknown significance were scored as probably damaging in individuals, demonstrating a high sensitivity. Specificity was very low in one of the three tested programs. However, due to potential genotype–phenotype discordance, bioinformatic prediction tools are currently of limited value in diagnosing pathogenicity of MH-susceptible variants.


2021 ◽  
Vol 12 ◽  
Author(s):  
Irene Gómez Delgado ◽  
Fernando Corvillo ◽  
Pilar Nozal ◽  
Emilia Arjona ◽  
Álvaro Madrid ◽  
...  

Haemolytic Uraemic Syndrome associated with Streptococcus pneumoniae infections (SP-HUS) is a clinically well-known entity that generally affects infants, and could have a worse prognosis than HUS associated to E. coli infections. It has been assumed that complement genetic variants associated with primary atypical HUS cases (aHUS) do not contribute to SP-HUS, which is solely attributed to the action of the pneumococcal neuraminidase on the host cellular surfaces. We previously identified complement pathogenic variants and risk polymorphisms in a few Hungarian SP-HUS patients, and have now extended these studies to a cohort of 13 Spanish SP-HUS patients. Five patients presented rare complement variants of unknown significance, but the frequency of the risk haplotypes in the CFH-CFHR3-CFHR1 region was similar to the observed in aHUS. Moreover, we observed desialylation of Factor H (FH) and the FH-Related proteins in plasma samples from 2 Spanish and 4 Hungarian SP-HUS patients. To analyze the functional relevance of this finding, we compared the ability of native and “in vitro” desialylated FH in: (a) binding to C3b-coated microtiter plates; (b) proteolysis of fluid-phase and surface-bound C3b by Factor I; (c) dissociation of surface bound-C3bBb convertase; (d) haemolytic assays on sheep erythrocytes. We found that desialylated FH had reduced capacity to control complement activation on sheep erythrocytes, suggesting a role for FH sialic acids on binding to cellular surfaces. We conclude that aHUS-risk variants in the CFH-CFHR3-CFHR1 region could also contribute to disease-predisposition to SP-HUS, and that transient desialylation of complement FH by the pneumococcal neuraminidase may have a role in disease pathogenesis.


2020 ◽  
Vol 40 (6) ◽  
Author(s):  
Komal Saleem ◽  
Tahir Zaib ◽  
Wei Ji ◽  
Chunhui Zhang ◽  
Qian Qin ◽  
...  

Abstract Colorectal cancer (CRC) is the third most developing cancer worldwide and Lynch syndrome (LS) accounts for 3–4% of CRC. Genetic alteration in any of DNA mismatch repair (MMR) gene is the major cause of LS that disrupt the normal upstream and downstream MMR events. Germline mutation of MLH1 in heterozygous state have an increased risk for CRC. Defective MMR pathway mostly results in microsatellite instability (MSI) that occurs in high percentage of CRC associated tumors. Here, we reported a patient with LS like metastatic CRC (mCRC) associated with other related cancers. Whole exome sequencing (WES) of the proband was performed to identify potential causative gene. Genetic screening validated by Sanger sequencing identified a heterozygous missense mutation in exon 12 of MLH1 (c.1151T>A, p.V384D). The clinical significance of identified variant was elucidated on the basis of clinicopathological data, computational predictions and various in vitro functional analysis. In silico predictions classified the variant to be deleterious and evolutionary conserved. In vitro functional studies revealed a significant decrease in protein expression because of stability defect leading to loss of MMR activity. Mutant residue found in MutL transducer domain of MLH1 that localized in the nucleus but translocation was not found to be significantly disturbed. In conclusion, our study give insight into reliability of combinatorial prediction approach of in silico and in vitro expression analysis. Hence, we highlighted the pathogenic correlation of MLH1 variant with LS associated CRC as well as help in earlier diagnosis and surveillance for improved management and genetic counselling.


Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 153-153
Author(s):  
Lucia Wolgast ◽  
Xiao Xuan Wu ◽  
Jessica Niakan ◽  
Alan Arslan ◽  
Jacob Rand

Abstract Abstract 153 Background: The antiphospholipid (aPL) syndrome (APS) is an autoimmune, thrombotic condition reported to be responsible for approximately 10% of patients with thromboembolic disease. APS is characterized by autoantibodies against phospholipids or plasma proteins bound to phospholipids that inhibit phospholipid-dependent coagulation reactions in vitro. The diagnostic criteria for APS are defined by the presence of an aPL antibody and the occurrence of one or more thrombotic events, including arterial or venous thromboses, multiple fetal losses and thrombocytopenia. The current assays for diagnosing APS are empirically-derived and include the lupus anticoagulant assay and aPL immunoassays for anticardiolipin and anti-ß2 glycoprotein-I antibodies. These assays do not test report on disease mechanisms and have poor specificities, sensitivities and predictive values. To date, several different mechanisms have been proposed for APS, including aPL antibody-mediated disruption of a potent anticoagulant protein, annexin A5. Annexin A5 forms two-dimensional crystal shields over membranes that expose anionic phospholipids; the crystallization and shielding of phospholipid from availability for coagulation reactions is disrupted by aPL antibodies. Therefore, we investigated the prevalence of evidence for this mechanism in blood samples from aPL-positive and negative patients. Methods: Clinical histories and laboratory data were obtained from adult patients with histories for venous thromboembolism (n=223), stroke (n=73) and pregnancy complications (n=178) that were evaluated for thrombophilia and from patients who were free of known disease (n=76). A novel mechanistic assay was performed for “annexin A5 resistance” (A5R), an assay that detects antibody-mediated interference with annexin A5 anticoagulant activity. Results were expressed as a percent prolongation of coagulation times by annexin A5. Differences between groups were compared using nonparametric Kruskal-Wallis test. Result: At a cut off A5R value at 210% - the lowest quartile value of A5R - 48% (72 out of 150) of patients in the aPL-positive thrombosis/stroke/pregnancy complication group had A5R values within the lowest quartile, in contrast to 15% (33 out of 221) of the aPL-negative thrombosis patients and 8% (6 out of 76) of the disease-free control. In aPL-positive patients, the A5R values (median±SD: 208±58%, n=196) were found to be significantly lower than in aPL-negative patients (247±46%, n=284, p<0.001). Furthermore, aPL-positive patients with any thrombotic event, including histories for venous thromboembolism, stroke and pregnancy complications, had significantly lower A5R values (213±57%, n=150) than aPL-negative patients with any thrombotic event (258±42%, n=221; p<0.001) and from patients who were free of known disease (275±42%, n=76; p<0.001). Specifically, aPL-positive patients with a history of either venous thromboembolism (185±59, n=40) or pregnancy complications (233±73, n=25) had significantly lower A5R values than aPL-negative patients with either venous thromboembolism (250±62, n=62; p<0.01) or pregnancy complications (245±91, n=91; p<0.001). Conclusion: This novel mechanistic assay identifies a significant subset of patients currently defined as aPL-positive as having evidence for aPL antibody-mediated resistance to annexin A5 anticoagulant activity. A5R may mark patients who have a propensity for venous thromboembolism and/or pregnancy complications. The identification of specific thrombogenic mechanisms in patients with APS through mechanistic assays opens the possibilities of improved diagnosis and targeted therapies for patients with this condition. Disclosures: No relevant conflicts of interest to declare.


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