Alain Morel

Somatic mRNA Analysis of BRCA1 Splice Variants Provides a Direct Theranostic Impact on PARP Inhibitors

The identification of pretherapeutic somatic BRCA variants can have considerable clinical impact given that they affect response to the new poly (ADP-ribose) polymerase (PARP)-targeted therapy. One major issue with this type of testing is the identification of splicing variants of uncertain significance (VUS) on degraded somatic messenger RNA. It is therefore important to be able to quickly characterize these splice variants. As part of PARP inhibitor targeted therapy, we have investigated a method for the direct confirmation of potential pathogenic somatic splice variants of BRCA1 found in fixed tumor samples. Previously these VUS have commonly only been tested by in silico analysis. Five BRCA1 variants affecting splicing were characterized from formalin-fixed, paraffin-embedded (FFPE) ovarian carcinoma tissues by next-generation sequencing (NGS). Three patient samples had already been functionally characterized and were used as controls. Total somatic RNA from samples was extracted, reverse-transcribed, and amplified with several primer pairs encompassing the target exon. The polymerase chain reaction (PCR) products were analyzed by capillary gel electrophoresis to assess possible changes in size due to splicing alterations. Finally, we confirmed our results by cloning, followed by Sanger sequencing, and analyzed the expression of the aberrant forms. Our molecular approach made it possible to visualize the splicing outcomes of three variants (c.5194-2A>G, c.5434C>G, and c.547+1G>A) already identified and present in databases and/or identified with prediction tools (ClinVar, UMD, ARUP Utah database, and Human Splice Finder splices sites prediction) and to confirm their exon skipping consequences, their expression in tumors, and thus their pathogenicity. The c.4484+5G>A variant was not found in databases and was predicted to have no impact on splicing, but was found to display altered processing in tumor tissue. This variant also had a major detrimental impact on transcriptional expression. In a break from purely in silico approaches, we propose a simple and rapid pretherapeutic functional analysis of somatic BRCA1 variants potentially involved in splicing alterations. This approach will allow more ovarian cancer patients to benefit from new therapies targeting PARP.

Functional pre-therapeutic evaluation by genome editing of variants of uncertain significance of essential tumor suppressor genes

AbstractBackgroundTargeted therapies in oncology are promising but variants of uncertain significance (VUS) limit their use for clinical management and necessitate functional testing in vitro. UsingBRCA1andBRCA2variants, which have consequences on PARP inhibitor sensitivity, andPOLEvariants, potential biomarkers of immunotherapy response, we developed a rapid functional assay based on CRISPR-Cas9 genome editing to determine the functional consequences of these variants having potentially direct implications on patients’ access to targeted therapies.MethodsWe first evaluated the functional impact of 26BRCA1and 7BRCA2variants by editing and comparing NGS results between the variant of interest and a silent control variant. Ten of these variants had already been classified as benign or pathogenic and were used as controls. Finally, we extended this method to the characterization ofPOLEVUS.ResultsFor the 23 variants that were unclassified or for which conflicting interpretations had been reported, 15 were classified as functionally normal and 6 as functionally abnormal. Another two variants were found to have intermediate consequences, both with potential impacts on splicing. We then compared these scores to the patients’ responses to PARP inhibitors when possible. Finally, to prove the application of our method to the classification of variants from other tumor suppressor genes, we exemplified with threePOLEVUS. Among them, two were classified with an intermediate functional impact and one was functionally abnormal. Eventually, fourPOLEvariants previously classified in databases were also evaluated. However, we found evidence of a discordance with the classification, variant p.Leu424Val being found here functionally normal.ConclusionsOur new rapid functional assay can be used to characterize the functional implication ofBRCA1andBRCA2variants, giving patients whose variants were evaluated as functionally abnormal access to PARP inhibitor treatment. Retrospective analysis of patients’ responses to PARP inhibitors, where accessible, was consistent with our functional score evaluation and confirmed the accuracy of our protocol. This method could potentially be extended to the classification of VUS from all essential tumor suppressor genes and can be performed within a timeframe compatible with clinical applications, thereby having a direct theranostic impact.