Neuromuscular disease genetics in under-represented populations: increasing data diversity

Neuromuscular diseases (NMDs) affect ∼15 million people globally. In high income settings DNA-based diagnosis has transformed care pathways and led to gene-specific therapies. However, most affected families are in low-to-middle income countries (LMICs) with limited access to DNA-based diagnosis. Most (86%) published genetic data is derived from European ancestry. This marked genetic data inequality hampers understanding of genetic diversity and hinders accurate genetic diagnosis in all income settings. We developed a cloud-based transcontinental partnership to build diverse, deeply-phenotyped and genetically characterized cohorts to improve genetic architecture knowledge, and potentially advance diagnosis and clinical management. We connected 18 centres in Brazil, India, South Africa, Turkey, Zambia, Netherlands and the UK. We co-developed a cloud-based data solution and trained 17 international neurology fellows in clinical genomic data interpretation. Single gene and whole exome data were analysed via a bespoke bioinformatics pipeline and reviewed alongside clinical and phenotypic data in global webinars to inform genetic outcome decisions. We recruited 6001 participants in the first 43 months. Initial genetic analyses ‘solved’ or ‘possibly solved’ ∼56% probands overall. In-depth genetic data review of the four commonest clinical categories (limb girdle muscular dystrophy, inherited peripheral neuropathies, congenital myopathy/muscular dystrophies and Duchenne/Becker muscular dystrophy) delivered a ∼59% ‘solved’ and ∼13% ‘possibly solved’ outcome. Almost 29% of disease causing variants were novel, increasing diverse pathogenic variant knowledge. Unsolved participants represent a new discovery cohort. The dataset provides a large resource from under-represented populations for genetic and translational research. In conclusion, we established a remote transcontinental partnership to assess genetic architecture of NMDs across diverse populations. It supported DNA-based diagnosis, potentially enabling genetic counselling, care pathways and eligibility for gene-specific trials. Similar virtual partnerships could be adopted by other areas of global genomic neurological practice to reduce genetic data inequality and benefit patients globally

Bir rekombinant kromozom 4 olgusunun klinik özelliklerinin ayrıntılı tanımlanması

Recombinant chromosome 4 is a very rare chromosomal aberration with eighteen cases reported in the literature up to date. Here we report a five years old male patient with de novo rec(4) dup(4p) del(4q). The physical examination findings were as follows: caput quadratum, flat occiput, low frontal hairline, hypertelorism, ptosis, blepharophimosis, high arched eyebrows, flat nasal root with anteverted nostrils and short nose, long and smooth philtrum, thin upper lip with triangular mouth, microretrognathia, high arched palate, dental anomalies, large low-set ears, short neck, broad chest with widely spaced nipples, micropenis, cryptorchidism. Conventional cytogenetic analysis revealed the karyotype as 46,XY,rec(4)dup(4p14p16.3)del(4q34.3q35). Flourescence insitu hybridization (FISH) analysis with sub-telomeric probes for 4p and 4q showed duplication of 4p and deletion of 4q in recombinant chromosome 4. His parents’ chromosomal analysis and sub-telomeric FISH analysis were both normal. The patient’s final karyotype was reported as 46,XY,rec(4)dup(4p16.3p14)del(4q34.4q35).arr[h g19]4p16.3p14(68,345-36,018)x3,4q34.3q35(177,676,319-190,957,460)x1 detected by Microarray. According the literature all cases with recombinant chromosome 4 have similar clinical findings. Except for our case only one case in the literature has been reported to be de novo. In conclusion, we reported a very rare case of recombinant chromosome 4, which has the largest deletion and duplication in the literature. Further cases with similar findings would help the delineation of the findings associated with this chromosomal abnormality.Rekombinant kromozom 4, literatürde bugüne kadar bildirilen 18 vakayla birlikte ender görülen bir kromozomal anormalidir. Bu yazıda de novo rec (4)dup(4p)del(4q) karyotipine sahip 5 yaşında bir erkek hastayı bildirdik. Hastanın fizik muayenesinde kaput kuadratum, yassı oksiput, düşük frontal saç çizgisi, hipertelorizm, pitozis, blefarofimozis, yüksek kemerli kaşlar, antevert burun delikleri ile düz burun kökü, kısa burun, uzun ve pürüzsüz filtrum, üçgen ince üst dudak, mikroretrognati, yüksek kemerli damak, diş anomalileri, geniş, düşük kulaklar, kısa boyun, geniş aralıklı meme uçları, mikropenis, kriptorşidizm saptanmıştır. Konvansiyonel sitogenetik analiz sonucunda karyotipin 46,XY,rec(4)dup(4p14p16.3)del(4q34.3q35) karyotipi saptanmıştır. 4p ve 4q için subtelomerik problarla yapılan floresan in-situ hibridizasyon (FISH) analizi, rekombinant kromozom 4'te 4p'nin duplikasyonunu ve 4q'nun delesyonunu göstermiştir. Yapılan microarray analizi sonrası hastanın son karyotipi 46,XY, rec (4) dup (4p16.3p14) del (4q34.4q35) .arr [hg19] 4p16.3p14 (68.345-36.018) x3,4q34.3q35 (177,676,319-190,957,460) olarak rapor edilmiştir. Literatüre göre rekombinant kromozom 4 olan tüm olgular benzer klinik bulgulara sahiptir. Bizim olgumuz dışında literatürde sadece bir olgunun de novo olduğu bildirilmiştir. Sonuç olarak, bu yazıda nadir bir rekombinant kromozom 4 olgusu bildirilmiştir. Benzer bulgulara sahip bildirilecek diğer vakalar, nadir görülen bu rekombinasyonun daha iyi tanımlanmasına yardımcı olacaktır

De novo mutations of the ATP6V1A gene cause developmental encephalopathy with epilepsy

none25V-type proton (H +) ATPase (v-ATPase) is a multi-subunit proton pump that regulates pH homeostasis in all eukaryotic cells; in neurons, v-ATPase plays additional and unique roles in synapse function. Through whole exome sequencing, we identified de novo heterozygous mutations (p.Pro27Arg, p.Asp100Tyr, p.Asp349Asn, p.Asp371Gly) in ATP6V1A, encoding the A subunit of v-ATPase, in four patients with developmental encephalopathy with epilepsy. Early manifestations, observed in all patients, were developmental delay and febrile seizures, evolving to encephalopathy with profound delay, hypotonic/dyskinetic quadriparesis and intractable multiple seizure types in two patients (p.Pro27Arg, p.Asp100Tyr), and to moderate delay with milder epilepsy in the other two (p.Asp349Asn, p.Asp371Gly). Modelling performed on the available prokaryotic and eukaryotic structures of v-ATPase predicted p.Pro27Arg to perturb subunit interaction, p.Asp100Tyr to cause steric hindrance and destabilize protein folding, p.Asp349Asn to affect the catalytic function and p.Asp371Gly to impair the rotation process, necessary for proton transport. We addressed the impact of p.Asp349Asn and p.Asp100Tyr mutations on ATP6V1A expression and function by analysing ATP6V1A-overexpressing HEK293T cells and patients' lymphoblasts. The p.Asp100Tyr mutant was characterized by reduced expression due to increased degradation. Conversely, no decrease in expression and clearance was observed for p.Asp349Asn. In HEK293T cells overexpressing either pathogenic or control variants, p.Asp349Asn significantly increased LysoTracker® fluorescence with no effects on EEA1 and LAMP1 expression. Conversely, p.Asp100Tyr decreased both LysoTracker® fluorescence and LAMP1 levels, leaving EEA1 expression unaffected. Both mutations decreased v-ATPase recruitment to autophagosomes, with no major impact on autophagy. Experiments performed on patients' lymphoblasts using the LysoSensor™ probe revealed lower pH of endocytic organelles for p.Asp349Asn and a reduced expression of LAMP1 with no effect on the pH for p.Asp100Tyr. These data demonstrate gain of function for p.Asp349Asn characterized by an increased proton pumping in intracellular organelles, and loss of function for p.Asp100Tyr with decreased expression of ATP6V1A and reduced levels of lysosomal markers. We expressed p.Asp349Asn and p.Asp100Tyr in rat hippocampal neurons and confirmed significant and opposite effects in lysosomal labelling. However, both mutations caused a similar defect in neurite elongation accompanied by loss of excitatory inputs, revealing that altered lysosomal homeostasis markedly affects neurite development and synaptic connectivity. This study provides evidence that de novo heterozygous ATP6V1A mutations cause a developmental encephalopathy with a pathomechanism that involves perturbations of lysosomal homeostasis and neuronal connectivity, uncovering a novel role for v-ATPase in neuronal development.noneFassio A.; Esposito A.; Kato M.; Saitsu H.; Mei D.; Marini C.; Conti V.; Nakashima M.; Okamoto N.; Olmez Turker A.; Albuz B.; Semerci Gunduz C.N.; Yanagihara K.; Belmonte E.; Maragliano L.; Ramsey K.; Balak C.; Siniard A.; Narayanan V.; Ohba C.; Shiina M.; Ogata K.; Matsumoto N.; Benfenati F.; Guerrini R.Fassio, A.; Esposito, A.; Kato, M.; Saitsu, H.; Mei, D.; Marini, C.; Conti, V.; Nakashima, M.; Okamoto, N.; Olmez Turker, A.; Albuz, B.; Semerci Gunduz, C. N.; Yanagihara, K.; Belmonte, E.; Maragliano, L.; Ramsey, K.; Balak, C.; Siniard, A.; Narayanan, V.; Ohba, C.; Shiina, M.; Ogata, K.; Matsumoto, N.; Benfenati, F.; Guerrini, R

Clinical and molecular evaluation of MEFV gene variants in the Turkish population: a study by the National Genetics Consortium

Familial Mediterranean fever (FMF) is a monogenic autoinflammatory disorder with recurrent fever, abdominal pain, serositis, articular manifestations, erysipelas-like erythema, and renal complications as its main features. Caused by the mutations in the MEditerranean FeVer (MEFV) gene, it mainly affects people of Mediterranean descent with a higher incidence in the Turkish, Jewish, Arabic, and Armenian populations. As our understanding of FMF improves, it becomes clearer that we are facing with a more complex picture of FMF with respect to its pathogenesis, penetrance, variant type (gain-of-function vs. loss-of-function), and inheritance. In this study, MEFV gene analysis results and clinical findings of 27,504 patients from 35 universities and institutions in Turkey and Northern Cyprus are combined in an effort to provide a better insight into the genotype-phenotype correlation and how a specific variant contributes to certain clinical findings in FMF patients. Our results may help better understand this complex disease and how the genotype may sometimes contribute to phenotype. Unlike many studies in the literature, our study investigated a broader symptomatic spectrum and the relationship between the genotype and phenotype data. In this sense, we aimed to guide all clinicians and academicians who work in this field to better establish a comprehensive data set for the patients. One of the biggest messages of our study is that lack of uniformity in some clinical and demographic data of participants may become an obstacle in approaching FMF patients and understanding this complex disease