Integration of functional assay data results provides strong evidence for classification of hundreds of BRCA1 variants of uncertain significance

Purpose

BRCA1 pathogenic variant heterozygotes are at a substantially increased risk for breast and ovarian cancer. The widespread uptake of testing has led to a significant increase in the detection of missense variants in BRCA1, the vast majority of which are variants of uncertain clinical significance (VUS), posing a challenge to genetic counseling. Here, we harness a wealth of functional data for thousands of variants to aid in variant classification.

Methods

We have collected, curated, and harmonized functional data for 2701 missense variants representing 24.5% of possible missense variants in BRCA1. Results were harmonized across studies by converting data into binary categorical variables (functional impact versus no functional impact). Using a panel of reference variants we identified a subset of assays with high sensitivity and specificity (≥80%) and apply the American College of Medical Genetics and Genomics/Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines to assign evidence criteria for classification.

Results

Integration of data from validated assays provided ACMG/AMP evidence criteria in favor of pathogenicity for 297 variants or against pathogenicity for 2058 representing 96.2% of current VUS functionally assessed. We also explore discordant results and identify limitations in the approach.

Conclusion

High quality functional data are available for BRCA1 missense variants and provide evidence for classification of 2355 VUS according to their pathogenicity.

Abstract 5883: Phosphodiesterase 7-A is a novel potential therapeutic target against ovarian cancer

Ovarian cancer (OC) is the leading cause of gynecologic cancer-related deaths due to late diagnosis and chemoresistance. RNA-seq data, conducted in collaboration with our group, compared the expression of transcription levels between normal Fallopian tube and high-grade serous ovarian carcinoma samples and revealed phosphodiesterase 7-A as a novel potential therapeutic target against the disease. Metabolic cell viability assays (MCV) were conducted following OC cells treatment with selective PDE7 inhibitor (BRL50481) in monotherapy or in association with paclitaxel (PTX). Mechanism of action of the drug was evaluated by cell cycle analysis, anexina V/PI assay, immunoblotting, real-time PCR and scanning/transmission electron microscopy. Data showed that the use of the BRL50481 in monotherapy reduced A2780 cells MCV by ~60% in a dose-dependent manner after 48h treatment, but nothing significant was observed in OVCAR3. On the other hand, the association of BRL50481 and PTX promoted inhibition of MCV in both cell lines analyzed. An increase in the potency of PTX was also observed, an aspect verified with the reduction of its IC50 in relation to monotherapy by 30% (p<0.01). Treatment chronology in cell survival was also verified. Thus, pretreatment of A2780 with BRL50481 200μM followed by its association with PTX promoted a reduction in cells MCV of ~70% (p<0.01) compared to treatment with PTX alone. With regard to OVCAR3, 400μM pretreatment of BRL50481 provided a VCM reduction of ~20% (p<0.001). Therefore, our results showed beneficial effect between the combination of PDE7 inhibitor and PTX, which allowed reduction of the PTX concentration used in A2780 and OVCAR3 by ~82.7 x 108 and 80.4 x 103uM, respectively. Moreover, the combination of BRL50481 and PTX promoted increased cell necrosis in OVCAR3. In addition, pretreatment of OVCAR3 with BRL50481 modulated the gene expression of the cytokines, as well as increased IL-6 secretion. The combination of BRL50481 and PTX further modulated negatively the PI3K/AKT/mTOR signaling pathway in both cell lines studied. Furthermore, the A2780-pretreated cells showed an increase in the expression of the pro-apoptotic Bax protein. Still, cell death may be related to the induction of autophagy seen in both by the increase of the expression of beclin. Moreover, BRL50481 promoted changes in OC cellular morphology, resembling the induction of cell death by BRL50481, as well as mitochondria and mitochondrial cristae modification. The association of the PDE7 inhibitor with PTX has been proved potentially beneficial in the fight against OC. The impressive additive effect between the drugs allows us to postulate a substantial decrease in PTX neurotoxicity caused in patients by the drug. Our current challenge is to synthesize less toxic BRL50481 analogues, which is only approved for experimental purposes, hence providing hope for better life quality to OC patients.

Citation Format: Nayara G. Tessarollo, Isabella S. Guimarães, Diandra Z. dos Santos, Taciane B. Henriques, Marcele LM Souza, Laura Maciel, João Carlos A. Almeida, Alan Branco, Ian V. Silva, Leticia BA Rangel. Phosphodiesterase 7-A is a novel potential therapeutic target against ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5883.

Association between serotonin 2C receptor gene (HTR2C) polymorphisms and psychopathological symptoms in children and adolescents

Serotonin 2C receptors (5HT2C) are involved in serotonin-driven dynamic equilibrium adjustments responsible for homeostatic stability in brain structures that modulate behavior and emotions. Single nucleotide polymorphisms (SNPs) from the serotonin 2C receptor gene (HTR2C) have been associated with several neurological and mental disorders, including abnormalities in cognitive and emotional processes. The aim of this study was to evaluate the association between the rs6318 SNP of the HTR2C gene and behavioral characteristics exhibited by children and adolescents based on the Child Behavior Checklist (CBCL/6-18) inventory. Eighty-five psychiatric outpatients between 8 and 18 years of age underwent genotyping of the rs6318 SNP. The CBCL/6-18 scale was administered to their caregivers. The chi-squared test was used to assess differences in the frequency of C and G alleles of the rs6318 SNP relative to the grouped CBCL/6-18 scores; significance level was 5%. The presence of the G allele of rs6318 was found to be associated with characteristics of aggressive behavior and social problems, and aggressive behavior was found to be associated with heterozygosis in females. These findings contribute to the identification of mental and behavioral phenotypes associated with gene expression.

NPHS2 mutations account for only 15% of nephrotic syndrome cases

Background

Nephrotic syndrome is traditionally classified on the basis of the response to standard steroid treatment. Mutations in more than 24 genes have been associated with nephrotic syndrome in children, although the great majority of steroid-resistant cases have been attributed to mutations in three main genes: NPHS1, NPHS2 and WT1. The aims of this study were to identify mutations in these genes more frequently reported as mutated and to characterize each variation using different in silico prediction algorithms in order to understand their biological functions.

Methods

We performed direct sequence analysis of exons 8 and 9 of WT1, 8 exons of NPHS2 and 29 exons of NPHS1, including NPHS2 and NPHS1 intron–exon boundary sequences, as well as 700 bp of the 5′ UTR from both genes in 27 steroid-resistant patients aged between 3 months and 18 years.

Results

Analysis of the NPHS2 gene revealed four missense mutations, one frameshift mutation and three variations in the 5′ UTR. Four patients presented compound heterozygosis, and four other patients presented one heterozygous alteration only. WT1 and NPHS1 gene analysis did not reveal any mutations.

Discussion

This is the first study focusing on genetics of SRNS in Brazilian children. Identification of mutations is important because it could influence physicians’ decision on patient treatment, as patients carrying mutations can be spared the side effects of immunosuppressive therapy and ultimately could be considered for kidney transplantation from a living donor.

Conclusions

After molecular analysis of the genes more frequently reported as mutated in 27 steroid-resistant nephrotic syndrome patients, we identified NPHS2 mutations confirming the hereditary character of the kidney disease in only 14.8 % of patients. Therefore, the next step is to perform a next generation sequencing based analysis of glomeluropathy-related panel of genes for the remaining patients in order to search for mutations in other genes related to steroid-resistant nephrotic syndrome.

Electronic supplementary material

The online version of this article (doi:10.1186/s12881-015-0231-9) contains supplementary material, which is available to authorized users.