MicroRNAs (miRNAs) are key regulators of gene expression in animals and plants. Studies in a variety of model organisms show that miRNAs modulate developmental processes. To our knowledge, the only ...hereditary condition known to be caused by a miRNA is a form of adult-onset non-syndromic deafness, and no miRNA mutation has yet been found to be responsible for any developmental defect in humans. Here we report the identification of germline hemizygous deletions of MIR17HG, encoding the miR-17∼92 polycistronic miRNA cluster, in individuals with microcephaly, short stature and digital abnormalities. We demonstrate that haploinsufficiency of miR-17∼92 is responsible for these developmental abnormalities by showing that mice harboring targeted deletion of the miR-17∼92 cluster phenocopy several key features of the affected humans. These findings identify a regulatory function for miR-17∼92 in growth and skeletal development and represent the first example of an miRNA gene responsible for a syndromic developmental defect in humans.
Hypopigmentation along Blaschko's lines is a hallmark of a poorly defined group of mosaic syndromes whose genetic causes are unknown. Here we show that postzygotic inactivating mutations of RHOA ...cause a neuroectodermal syndrome combining linear hypopigmentation, alopecia, apparently asymptomatic leukoencephalopathy, and facial, ocular, dental and acral anomalies. Our findings pave the way toward elucidating the etiology of pigmentary mosaicism and highlight the role of RHOA in human development and disease.
Nicolaides-Baraitser syndrome (NCBRS) is a neurodevelopmental disorder caused by pathogenic sequence variants in SMARCA2 which encodes the catalytic component of the chromatin remodeling BAF complex. ...Pathogenic variants in genes that encode epigenetic regulators have been associated with genome-wide changes in DNA methylation (DNAm) in affected individuals termed DNAm signatures.
Genome-wide DNAm was assessed in whole-blood samples from the individuals with pathogenic SMARCA2 variants and NCBRS diagnosis (n = 8) compared to neurotypical controls (n = 23) using the Illumina MethylationEPIC array. Differential methylated CpGs between groups (DNAm signature) were identified and used to generate a model enabling classification variants of uncertain significance (VUS; n = 9) in SMARCA2 as "pathogenic" or "benign". A validation cohort of NCBRS cases (n = 8) and controls (n = 96) demonstrated 100% model sensitivity and specificity.
We identified a DNAm signature of 429 differentially methylated CpG sites in individuals with NCBRS. The genes to which these CpG sites map are involved in cell differentiation, calcium signaling, and neuronal function consistent with NCBRS pathophysiology. DNAm model classifications of VUS were concordant with the clinical phenotype; those within the SMARCA2 ATPase/helicase domain classified as "pathogenic". A patient with a mild neurodevelopmental NCBRS phenotype and a VUS distal to the ATPase/helicase domain did not score as pathogenic, clustering away from cases and controls. She demonstrated an intermediate DNAm profile consisting of one subset of signature CpGs with methylation levels characteristic of controls and another characteristic of NCBRS cases; each mapped to genes with ontologies consistent with the patient's unique clinical presentation.
Here we find that a DNAm signature of SMARCA2 pathogenic variants in NCBRS maps to CpGs relevant to disorder pathophysiology, classifies VUS, and is sensitive to the position of the variant in SMARCA2. The patient with an intermediate model score demonstrating a unique genotype-epigenotype-phenotype correlation underscores the potential utility of this signature as a functionally relevant VUS classification system scalable beyond binary "benign" versus "pathogenic" scoring. This is a novel feature of DNAm signatures that could enable phenotypic predictions from genotype data. Our findings also demonstrate that DNAm signatures can be domain-specific, highlighting the precision with which they can reflect genotypic variation.
Treacher Collins syndrome (TCS) is a rare autosomal dominant mandibulofacial dysostosis, with a prevalence of 0.2–1/10,000. Features include bilateral and symmetrical malar and mandibular hypoplasia ...and facial abnormalities due to abnormal neural crest cell (NCC) migration and differentiation. To date, three genes have been identified: TCOF1, POLR1C, and POLR1D. Despite a large number of patients with a molecular diagnosis, some remain without a known genetic anomaly.
We performed exome sequencing for four individuals with TCS but who were negative for pathogenic variants in the known causative genes. The effect of the pathogenic variants was investigated in zebrafish.
We identified three novel pathogenic variants in POLR1B. Knockdown of polr1b in zebrafish induced an abnormal craniofacial phenotype mimicking TCS that was associated with altered ribosomal gene expression, massive p53-associated cellular apoptosis in the neuroepithelium, and reduced number of NCC derivatives.
Pathogenic variants in the RNA polymerase I subunit POLR1B might induce massive p53-dependent apoptosis in a restricted neuroepithelium area, altering NCC migration and causing cranioskeletal malformations. We identify POLR1B as a new causative gene responsible for a novel TCS syndrome (TCS4) and establish a novel experimental model in zebrafish to study POLR1B-related TCS.
Wiedemann-Steiner syndrome (WDSTS) is a Mendelian syndromic intellectual disability (ID) condition associated with hypertrichosis cubiti, short stature, and characteristic facies caused by pathogenic ...variants in the
gene. Clinical features can be inconclusive in mild and unusual WDSTS presentations with variable ID (mild to severe), facies (typical or not) and other associated malformations (bone, cerebral, renal, cardiac and ophthalmological anomalies). Interpretation and classification of rare
variants can be challenging. A genome-wide DNA methylation episignature for
-related syndrome could allow functional classification of variants and provide insights into the pathophysiology of WDSTS. Therefore, we assessed genome-wide DNA methylation profiles in a cohort of 60 patients with clinical diagnosis for WDSTS or Kabuki and identified a unique highly sensitive and specific DNA methylation episignature as a molecular biomarker of WDSTS. WDSTS episignature enabled classification of variants of uncertain significance in the
gene as well as confirmation of diagnosis in patients with clinical presentation of WDSTS without known genetic variants. The changes in the methylation profile resulting from
mutations involve global reduction in methylation in various genes, including homeobox gene promoters. These findings provide novel insights into the molecular etiology of WDSTS and explain the broad phenotypic spectrum of the disease.
Despite the availability of whole exome (WES) and genome sequencing (WGS), chromosomal microarray (CMA) remains the first-line diagnostic test in most rare disorders diagnostic workup, looking for ...copy number variations (CNVs), with a diagnostic yield of 10%-20%. The question of the equivalence of CMA and WES in CNV calling is an organisational and economic question, especially when ordering a WGS after a negative CMA and/or WES.
This study measures the equivalence between CMA and GATK4 exome sequencing depth of coverage method in detecting coding CNVs on a retrospective cohort of 615 unrelated individuals. A prospective detection of WES-CNV on a cohort of 2418 unrelated individuals, including the 615 individuals from the validation cohort, was performed.
On the retrospective validation cohort, every CNV detectable by the method (ie, a CNV with at least one exon not in a dark zone) was accurately called (64/64 events). In the prospective cohort, 32 diagnoses were performed among the 2418 individuals with CNVs ranging from 704 bp to aneuploidy. An incidental finding was reported. The overall increase in diagnostic yield was of 1.7%, varying from 1.2% in individuals with multiple congenital anomalies to 1.9% in individuals with chronic kidney failure.
Combining single-nucleotide variant (SNV) and CNV detection increases the suitability of exome sequencing as a first-tier diagnostic test for suspected rare Mendelian disorders. Before considering the prescription of a WGS after a negative WES, a careful reanalysis with updated CNV calling and SNV annotation should be considered.
Summary
Kabuki syndrome (KS) is now listed in the Human Inborn Errors of Immunity (IEI) Classification. It is a rare disease caused by KMT2D and KDM6A variants, dominated by intellectual disability ...and characteristic facial features. Recurrently, pathogenic variants are identified in those genes in patients examined for autoimmune cytopenia (AIC), but interpretation remains challenging. This study aims to describe the genetic diagnosis and the clinical management of patients with paediatric‐onset AIC and KS. Among 11 patients with AIC and KS, all had chronic immune thrombocytopenic purpura, and seven had Evans syndrome. All had other associated immunopathological manifestations, mainly symptomatic hypogammaglobinaemia. They had a median of 8 (5–10) KS‐associated manifestations. Pathogenic variants were detected in KMT2D gene without clustering, during the immunological work‐up of AIC in three cases, and the clinical strategy to validate them is emphasized. Eight patients received second‐line treatments, mainly rituximab and mycophenolate mofetil. With a median follow‐up of 17 (2–31) years, 8/10 alive patients still needed treatment for AIC. First‐line paediatricians should be able to recognize and confirm KS in children with ITP or multiple AIC, to provide early appropriate clinical management and specific long‐term follow‐up. The epigenetic immune dysregulation in KS opens exciting new perspectives.
From a cohort of 1802 patients with paediatric‐onset autoimmune cytopenia (AIC), 11 pathogenic variants in the KMT2D gene were identified, with three cases detected during this AIC genetic work‐up. Three patients had variants of unknown significance; this underscores challenges in NGS interpretation using both genetic and clinical data integration. Recognizing KS in paediatric or adult patients with AIC is crucial for appropriate management and follow‐up. Those rare patients may benefit from rituximab, mycophenolate mofetil or rapamycin.
Little is known about knowledge transfer with the public. We explored how citizens, physicians, and communication specialists understand knowledge transfer in public spaces such as libraries. The ...initial study aimed at evaluating the scaling up of a program on disseminating research findings on potentially inappropriate medication. Twenty-two citizen workshops were offered by 16 physicians and facilitated by 6 communication specialists to 322 citizens in libraries during spring 2019. We did secondary analysis using the recorded workshop discussions to explore the type of knowledge participants used. Participants described four kinds of knowledge: biomedical, sociocultural beliefs, value-based reasoning, and institutional knowledge. Biomedical knowledge included scientific evidence, research methods, clinical guidelines, and access to research outcomes. Participants discussed beliefs in scientific progress, innovative clinical practices, and doctors' behaviours. Participants discussed values related to reliability, transparency, respect for patient autonomy and participation in decision-making. All categories of participants used these four kinds of knowledge. However, their descriptions varied particularly for biomedical knowledge which was described by physician-speakers and communication specialists-facilitators as scientific evidence, epidemiological and clinical practice guidelines, and pathophysiological theories. Communication specialists-facilitators also described scientific journalistic sources and scientific journalistic reports as proxies of scientific evidence. Citizens described biomedical knowledge in terms of knowledge to make informed decisions. These findings offer insights for future scientific knowledge exchange interventions with the public.
Objective
This study involved very early post‐mortem (PM) examination of human fetal anatomy at 8 weeks of gestation (WG) using whole‐body multimodal micro‐imaging: micro‐CT and high‐field MRI ...(HF‐MRI). We discuss the potential place of this imaging in early first‐trimester virtual autopsy.
Methods
We performed micro‐CT after different contrast‐bath protocols including diffusible iodine‐based contrast‐enhanced (dice) and HF‐MRI with a 9.4 T machine with qualitative and quantitative evaluation and obtained histological sections.
Results
Nine fetuses were included: the crown–rump length was 10–24 mm and corresponded to 7 and 9 WG according to the Robinson formula. The Carnegie stages were 17–21. Dice micro‐CT and HF‐MRI presented high signal to noise ratio, >5, according to the Rose criterion, and for allowed anatomical phenotyping in these specimens. Imaging did not alter the histology, allowing immunostaining and pathological examination.
Conclusion
PM non‐destructive whole‐body multimodal micro‐imaging: dice micro‐CT and HF‐MRI allows for PM human fetal anatomy study as early as 8 WG. It paves the way to virtual autopsy in the very early first trimester. Obtaining a precision phenotype, even regarding miscarriage products, allows a reverse phenotyping to select variants of interest in genome‐wide analysis, offering potential genetic counseling for bereaved parents.
Key points
What's already known about this topic?
Autopsies considered too invasive are often refused by grieving couples after fetal loss.
Fetal virtual autopsy has developed with standard imaging (MRI and CT) used after 24 weeks of gestation (WG) and micro‐CT and high‐field MRI (HF‐MRI) used from 11 to 24 WG.
The current scientific literature on micro‐CT and HF‐MRI before 11 WG is weak.
Miscarriages are common and require further explorations and research.
What does this study add?
Iodine‐contrast micro‐CT and HF‐MRI allow for post‐mortem human fetal anatomy visualization as early as 8 WG and pave the way for virtual autopsy at very early first trimester and thus precise phenotyping of miscarriage products.
The choice of either technique will be based on cost, availability, ease of use, target organ of interest, preparation and acquisition duration.
Micro‐imaging does not appear to exclude subsequent histological examination.
Self-renewal and differentiation of pluripotent murine embryonic stem cells (ESCs) is regulated by extrinsic signaling pathways. It is less clear whether cellular metabolism instructs developmental ...progression. In an unbiased genome-wide CRISPR/Cas9 screen, we identified components of a conserved amino-acid-sensing pathway as critical drivers of ESC differentiation. Functional analysis revealed that lysosome activity, the Ragulator protein complex, and the tumor-suppressor protein Folliculin enable the Rag GTPases C and D to bind and seclude the bHLH transcription factor Tfe3 in the cytoplasm. In contrast, ectopic nuclear Tfe3 represses specific developmental and metabolic transcriptional programs that are associated with peri-implantation development. We show differentiation-specific and non-canonical regulation of Rag GTPase in ESCs and, importantly, identify point mutations in a Tfe3 domain required for cytoplasmic inactivation as potentially causal for a human developmental disorder. Our work reveals an instructive and biomedically relevant role of metabolic signaling in licensing embryonic cell fate transitions.
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•Genome-wide CRISPR/Cas9 screen for differentiation resistance in mouse ESCs•Lysosomal Rag GTPase signaling inactivates Tfe3 to license exit from self-renewal•Rag GTPase regulation in steady-state cells and starvation is distinct•Tfe3 inactivation mutations found in a human mosaic developmental disorder
Villegas et al. identify mouse embryonic stem cell differentiation drivers in a genome-wide CRISPR/Cas9 screen. The majority of these are part of a lysosomal signaling pathway that licenses differentiation by inactivating the transcription factor Tfe3. The authors discover lysosomal-signaling-insensitive Tfe3 mutations as potentially causal for a human developmental disorder.
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