A Solve-RD ClinVar-based reanalysis of 1522 index cases from ERN-ITHACA reveals common pitfalls and misinterpretations in exome sequencing

Purpose Within the Solve-RD project (https://solve-rd.eu/), the European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies aimed to investigate whether a reanalysis of exomes from unsolved cases based on ClinVar annotations could establish additional diagnoses. We present the results of the “ClinVar low-hanging fruit” reanalysis, reasons for the failure of previous analyses, and lessons learned. Methods Data from the first 3576 exomes (1522 probands and 2054 relatives) collected from European Reference Network for Intellectual disability, TeleHealth, Autism and Congenital Anomalies was reanalyzed by the Solve-RD consortium by evaluating for the presence of single-nucleotide variant, and small insertions and deletions already reported as (likely) pathogenic in ClinVar. Variants were filtered according to frequency, genotype, and mode of inheritance and reinterpreted. Results We identified causal variants in 59 cases (3.9%), 50 of them also raised by other approaches and 9 leading to new diagnoses, highlighting interpretation challenges: variants in genes not known to be involved in human disease at the time of the first analysis, misleading genotypes, or variants undetected by local pipelines (variants in off-target regions, low quality filters, low allelic balance, or high frequency). Conclusion The “ClinVar low-hanging fruit” analysis represents an effective, fast, and easy approach to recover causal variants from exome sequencing data, herewith contributing to the reduction of the diagnostic deadlock

PDGF enhances IRES-mediated translation of Laminin B1 by cytoplasmic accumulation of La during epithelial to mesenchymal transition

The extracellular matrix protein Laminin B1 (LamB1) regulates tumor cell migration and invasion. Carcinoma cells acquire invasive properties by epithelial to mesenchymal transition (EMT), which is a fundamental step in dissemination of metastatic cells from the primary tumor. Recently, we showed that enhanced translation of LamB1 upon EMT of malignant hepatocytes is mediated by an internal ribosome entry site (IRES). We demonstrated that the IRES transacting factor La binds the minimal IRES motif and positively modulates IRES activity of LamB1. Here, we show that platelet-derived growth factor (PDGF) enhances IRES activity of LamB1 by the increasing cytoplasmic localization of La during EMT. Accordingly, cells expressing dominant negative PDGF receptor display reduced cytoplasmic accumulation of La and show no elevation of IRES activity or endogenous LamB1 levels after stimulation with PDGF. Furthermore, La-mediated regulation of LamB1 IRES activity predominantly depends on MAPK/ERK signaling downstream of PDGF. Notably, LamB1 expression is not significantly downregulated by the impairment of the translation initiation factor eIF4E. In vivo , knockdown of La associated with decreased LamB1 expression and reduced tumor growth. Together, these data suggest that PDGF is required for the cytoplasmic accumulation of La that triggers IRES-dependent translation of LamB1 during EMT.(VLID)458954

Identification of two homozygous mutations, in the male reproductive tract specific beta-defensin 126/128 genes, potentially underlie a severe sperm dysfunction

Introduction: Hereditary breast and ovarian cancer (HBOC) is estimated to represent 5-10% of all breast and ovarian cancer cases. Pathogenic germline variants in BRCA1 and BRCA2 account for 25% of familial cases. The identification of genetic defects in HBOC patients allows detection of carriers that can benefit from cancer risk management protocols, and predictive genetic testing to at-risk family members, after appropriate genetic counseling. Two female patients with a personal and family history of cancer were studied by next-generation sequencing (NGS). Methods: NGS using TruSight Cancer Panel (Illumina) followed by bioinformatic analysis of 18 genes associated with HBOC was performed. Pathogenic variants were confirmed by Sanger sequencing. Results: A rare event of double heterozigosity for pathogenic variants was identified in both patients: patient A was heterozygous for BRCA1:c.2037delinsCC, p.(Lys679Asn*4) and ATM:c.3802delG, p.(Val1268*) and patient B carried both BRCA2:c.6001dupT, p.(Ser2001Phefs*2) and ATM:3435_3436delTGinsA, p.(Asp1145Glufs*11). After genetic counseling, three relatives of patient A were analyzed: while one of her two healthy sons was heterozygous for the ATM variant, the other was a double heterozygote for BRCA1:c.2037delinsCC and ATM:c.3802delG; a female cousin, recently diagnosed with breast cancer, was a carrier of ATM:c.3802delG only. Conclusions: The identification of these two rare cases of double heterozigosity for pathogenic variants in BRCA1/BRCA2 and ATM genes, highlights the importance of using NGS-gene panel testing in HBOC. If molecular analysis had been restricted to BRCA genes only, the pathogenic ATM variants would have been missed in both families, depriving them of appropriate genetic counseling and cancer risk management.info:eu-repo/semantics/publishedVersio