Comprehensive RNA and protein functional assessments contribute to the clinical interpretation of MSH2 variants causing in-frame splicing alterations.

BACKGROUND: Spliceogenic variants in disease-causing genes are often presumed pathogenic since most induce frameshifts resulting in loss of function. However, it was recently shown in cancer predisposition genes that some may trigger in-frame anomalies that preserve function. Here, we addressed this question by using MSH2, a DNA mismatch repair gene implicated in Lynch syndrome, as a model system. METHODS: Eighteen MSH2 variants, mostly localised within canonical splice sites, were analysed by using minigene splicing assays. The impact of the resulting protein alterations was assessed in a methylation tolerance-based assay. Clinicopathological characteristics of variant carriers were collected. RESULTS: Three in-frame RNA biotypes were identified based on variant-induced spliceogenic outcomes: exon skipping (E3, E4, E5 and E12), segmental exonic deletions (E7 and E15) and intronic retentions (I3, I6, I12 and I13). The 10 corresponding protein isoforms exhibit either large deletions (49-93 amino acids (aa)), small deletions (12 or 16 aa) or insertions (3-10 aa) within different functional domains. We showed that all these modifications abrogate MSH2 function, in agreement with the clinicopathological features of variant carriers. CONCLUSION: Altogether, these data demonstrate that MSH2 function is intolerant to in-frame indels caused by the spliceogenic variants analysed in this study, supporting their pathogenic nature. This work stresses the importance of combining complementary RNA and protein approaches to ensure accurate clinical interpretation of in-frame spliceogenic variants.

Clinical and genetic findings in children with central nervous system arteriovenous fistulas.

OBJECTIVE: To assess the spectrum of genetic anomalies in a cohort of children presenting at least one cerebral or spinal pial arteriovenous fistula (AVF), and to describe their clinical characteristics. METHODS: From 1988 to 2016, all consecutive patients with at least one cerebral or spinal pial AVF were screened for genetic disease. All patients aged <18 years were included. Symptoms associated with AVF were recorded: heart failure, neurological deficit/seizure, and hemorrhage. The outcome was assessed using the modified Rankin Scale and school performance in children with cerebral AVF and the American Spinal Injury Association impairment scale in children with spinal AVF. RESULTS: Forty-three children were included. Twenty-five children were male and 18 were female. A germline mutation was identified in 23 probands (53.5 ± 14.9%): 8 in ENG (34.8 ± 14.2%), 1 in ACVRL1 (4.3 ± 6%) leading to a diagnosis of HHT, and 14 in RASA1 (60.9 ± 14.4%) leading to a diagnosis of capillary malformation/arteriovenous malformation type 1. No EphB4 gene mutation was identified. HHT patients presented a significantly lower rate of heart failure at diagnosis (p = 0.047). A trend toward an increased bleeding rate at presentation was observed in HHT (p = 0.069) and an increased rate of giant venous pouch in children in whom no mutation was identified (p = 0.097). Finally, an association with RASA1 mutation was observed in children with associated skin capillary hemangioma (p < 0001). INTERPRETATION: These results highlight the importance of genetic testing in this setting in view of the high frequency of gene mutations in pediatric cerebrospinal AVFs, and show the predominance of RASA1 over HHT mutations. Ann Neurol 2017;82:972-980.

NUP98-NSD1 fusion by insertion in acute myeloblastic leukemia.

A case of NUP98-NSD1 gene fusion resulting from the insertion of a subtelomeric part of chromosome 11p15.4 within the subtelomeric part of 5q35 was detected in a child with acute myeloblastic leukemia. This new case illustrates the importance of using fluorescence in situ hybridization followed by reverse transcriptase-polymerase chain reaction techniques to detect abnormalities involving subtelomeric chromosomal regions.

Identical abnormality of the short arm of chromosome 18 in two Philadelphia-positive chronic myelocytic leukemia patients with erythroblastic transformation, resulting in duplication of BCR-ABL1 fusion.

Two patients with Ph-positive chronic myelocytic leukemia in erythroblastic transformation and rearrangement of the short arm of chromosome 18 are reported. Fluorescence in situ hybridization studies showed that the 18p rearrangement resulted from translocation of the main part of chromosome 22 long arm to 18p, including BCR-ABL1 fusion. The 18p abnormality resulted, thus, in loss of 18p and duplication of BCR-ABL1 in both patients. The possible relation to the erythroblastic type of blastic phase is briefly discussed. In addition an apparently intact germline ABL1 gene was duplicated and inserted into chromosome 6 at band p21 in one of these patients.

Molecular characterisation of a prenatally diagnosed 5q15q21.3 deletion and review of the literature.

BACKGROUND: Ultrasound examination performed on a 32-year old woman at 30 weeks' gestation showed the presence of fetal malformations. Amniocentesis was performed. METHODS AND RESULTS: Cytogenetic analysis of cultured amniocytes revealed an interstitial deletion of the long arm of chromosome 5. Molecular studies confirmed that the deletion included the 5q15-21.3 region and was 14 Mb in size. Therefore, the karyotype was: 46,XY,del(5)(q15q21.3). In addition, analysis of polymorphic DNA markers showed that the deletion was of paternal origin. CONCLUSIONS: The pregnancy was terminated at 34 weeks' gestation. At autopsy, the fetus displayed dysmorphic features, thin limbs and renal abnormalities. The clinical findings observed in the fetus as well as in 20 cases reported previously allowed us to further delineate the phenotype of such interstitial 5q15q21.3 deletions.