Two Novel Variants in YARS2 Gene Are Responsible for an Extended MLASA Phenotype with Pancreatic Insufficiency

Pathogenic variants in the mitochondrial tyrosyl-tRNA synthetase gene (YARS2) were associated with myopathy, lactic acidosis, and sideroblastic anemia (MLASA). However, patients can present mitochondrial myopathy, with exercise intolerance and muscle weakness, leading from mild to lethal phenotypes. Genes implicated in mtDNA replication were studied by Next Gener ation Sequencing (NGS) and whole exome sequence with the TruSeq Rapid Exome kit (Illumina, San Diego, CA, USA). Mitochondrial protein translation was studied following the Sasarman and Shoubridge protocol and oxygen consumption rates with Agilent Seahorse XF24 Analyzer Mi tostress Test, (Agilent, Santa Clara, CA, USA). We report two siblings with two novel compound heterozygous pathogenic variants in YARS2 gene: a single nucleotide deletion in exon 1, c.314delG (p.(Gly105Alafs*4)), which creates a premature stop codon in the amino acid 109, and a single nu cleotide change in exon 5 c.1391T>C (p.(Ile464Thr)), that cause a missense variant in amino acid 464. We demonstrate the pathogenicity of these new variants associated with reduced YARS2 mRNA transcript, reduced mitochondrial protein translation and dysfunctional organelle function. These pathogenic variants are responsible for late onset MLASA, herein accompanied by pancreatic insuf ficiency, observed in both brothers, clinically considered as Pearson's syndrome. Molecular study of YARS2 gene should be considered in patients presenting Pearson's syndrome characteristics and MLASA related phenotypes

Leigh syndrome associated with TRMU gene mutations

Insuficiència hepàtica aguda: Síndrome de Leigh; TRMUInsuficiencia hepática aguda; Síndrome de Leigh; TRMUAcute liver failure; Leigh syndrome; TRMUtRNA 5-methylaminomethyl-2-thiouridylate methyltransferase (TRMU) deficiency causes an early onset potentially reversible acute liver failure, so far reported in less than 30 patients. We describe two new unrelated patients with an acute liver failure and a neuroimaging compatible with Leigh syndrome (LS) due to TRMU deficiency, a combination not previously reported. Our report enlarges the phenotypical spectrum of TRMU disease.This work was partially supported by the Spanish Instituto de Salud Carlos III, Fondo de Investigaciones Sanitarias and cofounded with ERDF funds (Grant No. FIS PI15/01428, PI19/01772)

Configuración de una estrategia para la identificación genético-molecular de pacientes con enfermedad mitocondrial

Las enfermedades mitocondriales son un grupo de trastornos hereditarios de metabolismo caracterizados por la alteración de la función mitocondrial, que en la mayor parte de los casos derivan en una disfunción en el sistema de fosforilación oxidativa. Este grupo de enfermedades es muy heterogéneo tanto clínica como genéticamente, debido a su implicación multiorgánica y a su origen genético dual. Debido a que por lo general no hay correlación entre fenotipo y genotipo en los pacientes con sospecha de enfermedad mitocondrial, en la mayor parte de los casos es difícil realizar un diagnóstico molecular definitivo. La integración de las técnicas de secuenciación masiva en este diagnóstico permite mejorar su eficacia, así como asociar nuevos fenotipos a genes ya descritos como implicados en estas enfermedades o incluso asociar nuevos genes a fenotipos clínicos. Durante el desarrollo de este trabajo, se ha integrado la secuenciación masiva en el diagnóstico de pacientes con fenotipo clínico de enfermedad mitocondrial. En primer lugar, se ha puesto a punto la secuenciación del ADNmt completo, así como se ha diseñado y validado un panel de genes a la carta incluyendo aquellos genes implicados en el mantenimiento del ADNmt, para su posterior uso en el diagnóstico; además, junto a dos aproximaciones, se ha aplicado el exoma clínico y el exoma completo a este diagnóstico. Finalmente, se han caracterizado variantes potencialmente patogénicas no descritas anteriormente, y se han estudiado posibles variables modificadoras del fenotipo en pacientes con sordera neurosensorial no sindrómica portadores de la variante homoplasmica m.1555A>G. Se ha obtenido un alto rendimiento diagnostico incluyendo diferentes técnicas de secuenciación masiva en la rutina diagnóstica de pacientes con enfermedad mitocondrial, sobretodo en pacientes bien caracterizados clínicamente. La secuenciación del ADNmt ha permitido la detección de variantes patogénicas en muy bajo porcentaje de heteroplasmia, así como el diagnóstico de pacientes con variantes no asociadas comúnmente a sus fenotipos. La aplicación del panel de genes a la carta ha permitido realizar el diagnóstico genético de pacientes con deleciones múltiples en el ADNmt. Con la aplicación del exoma clínico y el exoma completo, hemos identificado variantes potencialmente patogénicas asociadas a pacientes con síndrome de Leigh y defectos en la actividad enzimática de los complejos OXPHOS; además, una de las variantes se ha encontrado en un gen donde no se han asociado mutaciones previamente a un fenotipo clínico, abriendo nuevas líneas de investigación. Además, se ha podido caracterizar la patogenicidad de las variantes patogénicas estudiadas, asociándolas a los fenotipos clínicos de los pacientes.The mitochondrial disorders (MD) are a group of inherited metabolic diseases characterized by an alteration in the correct function of the mitochondria, mainly due to deficiencies of the oxidative phosphorylation system. These diseases are genetically and clinical heterogenic, due to their dual genetic origin (they can be caused due to mutations in the nuclear and in the mitochondrial genome) and their great phenotypic variability (the disease can affect only one organ or it can be multisystemic). Many times this group of disorders lacks of a genotype-phenotype correlation, since the same mutation can generate different phenotypes, and one specific phenotype can be caused by mutations in different genes, and this fact hampers the genetic diagnose of these disorders. The hypothesis of this thesis proposes that the use of the next generation sequencing (NGS) technologies in the genetic diagnostic of the MD will improve its performance. The use of the NGS in the diagnostic of these diseases will allow the detection of new point mutations in genes already described. Furthermore, the diagnostic through NGS also will allow to associate genes related with a specific MD to new phenotypes, or even to discover new genes causing MD, thus expanding the genetic and phenotypic spectrum of MD and improving the performance of the genetic diagnostic. In the present work we have integrated massive sequencing analysis of mitochondrial and nuclear genes to the diagnostic of patients with MD. We have set up and validated the complete mitochondrial DNA (mtDNA) sequencing that has enabled us to detect low levels of mtDNA heteroplasmy. Furthermore, the covering homogeneity of the complete mtDNA molecule has been optimized. This methodology has allowed us to precisely determine the concrete deleted sequences in single mtDNA deletions. Additionally, we have designed à la carte and validated a panel of genes directly related to mtDNA maintenance for diagnostic purposes. In patients with MD the clinic (n=8) and complete (n=9) exomes have been studied and analyzed. In this regard, new potentially mutagenic variants in both nuclear and mitochondrial DNA genes have been completely characterized, as well as potential phenotypic modulator variants in Non-Syndromic Sensoryneural Hearing Loss patients carrying the homoplasmic m.1555A>G mutation in the MTRNR1 gene. The application of the massive sequencing analysis technique in the diagnosis of these MD has represented an increase in the diagnosis efficiency, specially in those patients that had been well characterized clinically. MtDNA sequencing has allowed the detection in peripheric blood samples of pathogenic variants with a very low degree of heteroplasmy that were not previously detected by the classic Sanger sequencing, reducing the necessity of performing a muscle biopsy. In the complete mtDNA sequencing study, we have detected pathogenic variants that had not been previously associated to the phenotype of the patients. Additionally, the application of the genes panel related with mtDNA maintenance has proven to be very efficient, specially in those patients with multiple mtDNA deletions, being the POLG and TK2 the most representative in those patients. The clinic exome study in patients with Leigh syndrome has allowed us to genetically diagnose 2 out of 6 patients studied. Finally, in two patients with multi-enzymatic deficit of the oxidative phosphorylation system, we have found new potentially pathogenic variants, one in a gene previously associated with the YARS2 clinical phenotype, while the other in a mitochondrial gene previously not associated to any MD