Safety and efficacy of low-dose sirolimus in the PIK3CA-Related Overgrowth Spectrum

Purpose PIK3CA-related overgrowth spectrum (PROS) encompasses a range of debilitating conditions defined by asymmetric overgrowth caused by mosaic activating PIK3CA variants. PIK3CA encodes the p110α catalytic subunit of phosphatidylinositol-3-kinase (PI3K), a critical transducer of growth factor signaling. As mTOR mediates the growth-promoting actions of PI3K, we hypothesized that the mTOR inhibitor sirolimus would slow pathological overgrowth. Methods Thirty-nine participants with PROS and progressive overgrowth were enrolled into open-label studies across three centers, and results were pooled. For the primary outcome, tissue volumes at affected and unaffected sites were measured by dual energy X-ray absorptiometry during 26 weeks of untreated run-in and 26 weeks of sirolimus therapy. Results Thirty participants completed the study. Sirolimus led to a change in mean percentage total tissue volume of –7.2% (SD 16.0, p = 0.04) at affected sites, but not at unaffected sites (+1.7%, SD 11.5, p = 0.48) (n = 23 evaluable). Twenty-eight of 39 (72%) participants had ≥1 adverse event related to sirolimus of which 37% were grade 3 or 4 in severity and 7/39 (18%) participants were withdrawn consequently. Conclusion This study suggests that low-dose sirolimus can modestly reduce overgrowth, but cautions that the side-effect profile is significant, mandating individualized risk–benefit evaluations for sirolimus treatment in PROS

Effects of eight neuropsychiatric copy number variants on human brain structure

Many copy number variants (CNVs) confer risk for the same range of neurodevelopmental symptoms and psychiatric conditions including autism and schizophrenia. Yet, to date neuroimaging studies have typically been carried out one mutation at a time, showing that CNVs have large effects on brain anatomy. Here, we aimed to characterize and quantify the distinct brain morphometry effects and latent dimensions across 8 neuropsychiatric CNVs. We analyzed T1-weighted MRI data from clinically and non-clinically ascertained CNV carriers (deletion/duplication) at the 1q21.1 (n = 39/28), 16p11.2 (n = 87/78), 22q11.2 (n = 75/30), and 15q11.2 (n = 72/76) loci as well as 1296 non-carriers (controls). Case-control contrasts of all examined genomic loci demonstrated effects on brain anatomy, with deletions and duplications showing mirror effects at the global and regional levels. Although CNVs mainly showed distinct brain patterns, principal component analysis (PCA) loaded subsets of CNVs on two latent brain dimensions, which explained 32 and 29% of the variance of the 8 Cohen’s d maps. The cingulate gyrus, insula, supplementary motor cortex, and cerebellum were identified by PCA and multi-view pattern learning as top regions contributing to latent dimension shared across subsets of CNVs. The large proportion of distinct CNV effects on brain morphology may explain the small neuroimaging effect sizes reported in polygenic psychiatric conditions. Nevertheless, latent gene brain morphology dimensions will help subgroup the rapidly expanding landscape of neuropsychiatric variants and dissect the heterogeneity of idiopathic conditions

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

Etude clinique et biologique d'une translocation t(X;Y)(p22.3;q11.2) déséquilibrée chez deux garçons non apparentés

BREST-BU Médecine-Odontologie (290192102) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Data-driven study on individual occupant comfort using heating setpoints and window openings in new low-energy apartments – preliminary insights

This work suggests a method to evaluate residential building occupants’ neutral temperature in winter based on their interaction with their heating system. This study applies the developed method on eight new, low-energy apartments in Copenhagen, Denmark. A set of indoor temperature, heating setpoint, window opening and floor heating valve opening data was collected from mid-January to the end of April, spanning through a large part of the Danish heating season. Semi-structured interviews were performed with occupants of three of the eight apartments in order to understand their use of their heating system. This preliminary study permits to highlight the potential and the current limitations of the proposed method, both for neutral temperature estimation as such and for applications in optimizing the energy flexibility provided by the building. This article suggests directions for further elaboration of the model. The main two influential factors highlighted here affecting setpoint adjustment are the occupants’ acceptability of temperature variation and their ability to control the heating system

FGF14 ‐related episodic ataxia: delineating the phenotype of Episodic Ataxia type 9

International audienceWe report four patients from two families who presented attacks of childhood-onset episodic ataxia associated with pathogenic mutations in the FGF14 gene. Attacks were triggered by fever, lasted several days, and had variable frequencies. Nystagmus and/or postural tremor and/or learning disabilities were noticed in individuals harboring FGF14 mutation with or without episodic ataxia. These cases and literature data delineate the FGF14-mutation-related episodic ataxia phenotype: wide range of age at onset (from childhood to adulthood), variable durations and frequencies, triggering factors including fever, and association to chronic symptoms. We propose to add FGF14-related episodic ataxia to the list of primary episodic ataxia as Episodic Ataxia type 9

uORF-creating mutations in Van der Woude syndrome: why it is important to study 5’UTRs

International audienceBackground/Objectives:Van der Woude syndrome (VWS, MIM 119300) is an autosomal dominant cleft lip and/or palate with typical lower lip pits. Most patients carry loss-of-function mutations in IRF6. Upstream open reading frame (uORF)-creating mutations have been reported in four VWS patients. Pathogenic uORFcreating mutations are mostly out-of-frame upstream start codons (uAUG) in the 5’UTR. We searched for IRF6 uORF mutations and assessed the ability to predict the pathogenicity of uORFcreating variations of 5 prediction tools.Methods:We analyzed IRF6 UTR and coding regions in 68 VWS probands. By using a set of 44 reference genes, we assessed 5 in silico tools predicting the probability of ATGs to initiate translation: NetStart, ATGpr, TIS Miner, AltORFev, TIS Predictor. We then assessed the potential pathogenicity of all the theoretical uORFs in IRF6 5’UTR.Results:We have identified two novel uORF-creating mutations (c.-141C>T and c.-162C>T), representing 3% (2/68) of the probands. The 7 carriers of the two families had typical VWS signs. Our in silico analyses revealed a higher accuracy for AI-based tools over those based on Kozak consensus scoring. There are 28 theoretical uAUG-creating SNVs in IRF6 5’UTR. With AI-based tools, the six uAUG identified in VWS patients have high translation initiation site scores; 3 to 4 of the theoretical uAUG-creating SNVs had high scores and could correspond to pathogenic mutations. For the dozen of theoretical SNVs with intermediate scores, predicting pathogenicity remains challenging.Conclusion:As untranslated regions are frequently understudied in NGS strategies, uORF-creating mutations may be underdiagnosed in VWS and in human pathology in general

uORF-creating-mutations in Van der Woude syndrome: why it is important to study 5’UTRs

International audienceThe Van der Woude syndrome (VWS, MIM 119300), is an autosomal dominant disorder characterized by cleft lip with or without cleft palate, or isolated cleft palate, due to loss-of-function mutations in IRF6 (Interferon Regulatory Factor-6) or GRHL3 (Grainyhead-Like Transcription Factor 3). Most patients show pits on their lower lips. In VWS, most IRF6 alterations are premature stop codons or missense mutations. Pathogenic upstream open reading frame (uORF) mutations are characterized by an out-of-frame upstream start codon (uAUG) located in the 5’UTR and leading to a premature stop codon. uORFs overlap the usual ATG start codon and have a minimum length of 9 nucleotides. We assessed the main features of six uORF-creating mutations identified in VWS patients (two in the lab and four previously described). We also determined all the theoretical SNVs located in IRF6 5’UTR (NM_006147.4) that could create an uORFs and we assessed their potential pathogenicity based on Kozak site in silico prediction.Only four uORF-creating mutations in IRF6 have been previously associated with VWS to date. We report here two novel mutations creating out-of-frame uAUGs (c.-141C>T p.? and c.-162C>T p.?) that probably reduce IRF6 expression. In our lab, IRF6 mutations are found in about 80% of families with VWS and uORFs-creating mutations represent of 3.2% of them (2/63). Previous studies identifying uORFs-creating mutations did not provide detailed phenotypic data. In our group, in the 6 heterozygotes for c.-141C>T, three had a cleft lip with or without cleft palate and three had only a bifid uvula. The patient heterozygote for c.-162C>T had a posterior cleft with an ankyloblepharon.Most genes naturally have uORFs in their 5’UTR region, nonetheless we observed that there were no physiological uORF in IRF6. All 6 uORFs identified in VWS had the same termination codon that occurs in exon 3 (56 nucleotides after the usual ATG). To go further, we searched for all potential uAUG-creating SNV in IRF6 5’UTR. We identified 41 of them, including the 6 identified in patients. Except one, none of them is present in the gnomAD control population. Using a machine-learning-based tool (TIS Predictor, biorxiv.org/content/10.1101/2021.08.17.456657v1, 0 to 1 score range), we then assessed each Kozak similarity score. All 6 uORFs identified in patients had high scores comprised between 0.71 and 0.83, compared to 0.81 for the usual ATG. Among the 35 theoretical SNVs creating an uAUG, 10 may create a potential but weak Kozak site (score range: 0.50-0.71).In conclusion, uORF-creating mutations can thus be responsible for typical VWS. As untranslated regions are not included in most captured regions in high throughput sequencing strategies, this category of variants may be underdiagnosed in VWS and in human pathology in general

Extending the prenatal Noonan's phenotype by review of ultrasound and autopsy data

Abstract Objectives The antenatal phenotypic spectrum of Noonan Syndrome (NS) requires better characterization. Methods This multicenter retrospective observational included 16 fetuses with molecularly confirmed NS admitted for fetopathological examination between 2009 and 2016. Results Among 12 pathogenic variants (PV) in PTPN11 (80%), 5 (42%) fell between position c.179 and c.182. Ultrasound showed increased nuchal translucency ( n = 13/16, 93%), increased nuchal fold after 15 weeks of gestation ( n = 12/16, 75%), pleural effusions ( n = 11/16, 69%), polyhydramnios ( n = 9/16, 56%), hydrops ( n = 7/16, 44%), cardiovascular ( n = 6/16, 38%) and cerebral ( n = 4/16, 25%) anomalies. Fetopathological examination found dysmorphic features in all cases, cardiovascular anomalies ( n = 12/15, 80%), pulmonary hypoplasia ( n = 10/15, 67%), effusions ( n = 7/15, 47%) and neuropathological anomalies ( n = 5/15, 33%). Hydrops was significantly ( p = 0.02) more frequent in the four fetuses with RIT1 , NRAS and RAF1 PV versus the 12 fetuses with PTPN11 PV. Conclusions Increased nuchal translucency and nuchal fold is common in NS. Noonan Syndrome antenatal phenotype showed high in utero fetal death, hydrops, prenatal pleural effusion and pulmonary hypoplasia, although the inclusion of only deceased fetuses will have selected more severe phenotypes. Non‐specific cardiovascular and neurological abnormalities should be added to NS antenatal phenotype. Next generation sequencing will help detect more genotypes, clarifying the prenatal phenotype and identifying genotype‐phenotype correlations