A-type lamin mutations are associated with degenerative disorders causing dilated cardiomyopathy, Charcot-Marie-Tooth neuropathy and Limb-Girdle Muscular Dystrophy. Our lab has identified MLIP; a novel protein that interacts with lamin A/C. Knocked down MLIP expression in C2C12 myoblasts down regulates myogenic regulatory factors, MyoD and Myogenin, which delays myogenic differentiation. We hypothesize that MLIP is essential for myogenic differentiation. Our goal is to define the MLIP associated pathways involved in myogenic programming. Gene expression profiling of MLIP stably knocked down C2C12 cells, identified 30 genes implicated in human disease. Mutations in five of those genes (DMPK, HSPB8, LMNB2, NEFL and SGCD) cause muscular dystrophy, neuropathies, and lipodystrophies that have phenotypic overlap with laminopathies. Further studies involving the MLIP knocked down cell lines demonstrated that in the absence of puromycin, MLIP protein expression returns to normal. This in turn affects the interpretation of the gene expression data and attempted MLIP recovery experiments.

A-type lamin mutations are associated with degenerative disorders causing dilated cardiomyopathy, Charcot-Marie-Tooth neuropathy and Limb-Girdle Muscular Dystrophy. Our lab has identified MLIP; a novel protein that interacts with lamin A/C. Knocked down MLIP expression in C2C12 myoblasts down regulates myogenic regulatory factors, MyoD and Myogenin, which delays myogenic differentiation. We hypothesize that MLIP is essential for myogenic differentiation. Our goal is to define the MLIP associated pathways involved in myogenic programming. Gene expression profiling of MLIP stably knocked down C2C12 cells, identified 30 genes implicated in human disease. Mutations in five of those genes (DMPK, HSPB8, LMNB2, NEFL and SGCD) cause muscular dystrophy, neuropathies, and lipodystrophies that have phenotypic overlap with laminopathies. Further studies involving the MLIP knocked down cell lines demonstrated that in the absence of puromycin, MLIP protein expression returns to normal. This in turn affects the interpretation of the gene expression data and attempted MLIP recovery experiments.

A-type lamin mutations are associated with degenerative disorders causing dilated cardiomyopathy, Charcot-Marie-Tooth neuropathy and Limb-Girdle Muscular Dystrophy. Our lab has identified MLIP; a novel protein that interacts with lamin A/C. Knocked down MLIP expression in C2C12 myoblasts down regulates myogenic regulatory factors, MyoD and Myogenin, which delays myogenic differentiation. We hypothesize that MLIP is essential for myogenic differentiation. Our goal is to define the MLIP associated pathways involved in myogenic programming. Gene expression profiling of MLIP stably knocked down C2C12 cells, identified 30 genes implicated in human disease. Mutations in five of those genes (DMPK, HSPB8, LMNB2, NEFL and SGCD) cause muscular dystrophy, neuropathies, and lipodystrophies that have phenotypic overlap with laminopathies. Further studies involving the MLIP knocked down cell lines demonstrated that in the absence of puromycin, MLIP protein expression returns to normal. This in turn affects the interpretation of the gene expression data and attempted MLIP recovery experiments.

A-type lamin mutations are associated with degenerative disorders causing dilated cardiomyopathy, Charcot-Marie-Tooth neuropathy and Limb-Girdle Muscular Dystrophy. Our lab has identified MLIP; a novel protein that interacts with lamin A/C. Knocked down MLIP expression in C2C12 myoblasts down regulates myogenic regulatory factors, MyoD and Myogenin, which delays myogenic differentiation. We hypothesize that MLIP is essential for myogenic differentiation. Our goal is to define the MLIP associated pathways involved in myogenic programming. Gene expression profiling of MLIP stably knocked down C2C12 cells, identified 30 genes implicated in human disease. Mutations in five of those genes (DMPK, HSPB8, LMNB2, NEFL and SGCD) cause muscular dystrophy, neuropathies, and lipodystrophies that have phenotypic overlap with laminopathies. Further studies involving the MLIP knocked down cell lines demonstrated that in the absence of puromycin, MLIP protein expression returns to normal. This in turn affects the interpretation of the gene expression data and attempted MLIP recovery experiments.

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With the immense increase in the computational power available for the material science community in recent years, a range of new discoveries were made possible. Accurate investigations of large scale atomic systems, however, still come with an extremely high computational demand. While the recent development of Graphics Processing Unit (GPU) accelerated supercomputing might offer a solution to some extent, most well known electronic structure codes have yet to be fully ported to utilize this new power. With a soaring demand for new and better materials from both science and industry, a more efficient approach for the investigation of material properties needs to be implemented. The use of Machine Learning (ML) to obtain Interatomic Potentials (IP) which far outperform the classical potentials has increased greatly in recent years. With successful implementation of ML methods utilizing neural networks or Gaussian basis functions, the accuracy of ab-initio methods can be achieved at the demand of simulations with empirical potentials. Most ML approaches, however, require high accuracy data sets to be trained sufficiently. If no such data is available for the system of interest, the immense cost of creating a viable data set from scratch can quickly negate the benefit of using ML. In this diploma project, the elastic and thermodynamic properties of the Ti0.5Al0.5N random alloy at elevated temperature are therefore investigated using an Active Learning (AL) approach with the Machine Learning Interatomic Potentials (MLIP) package. The obtained material properties are found to be in good agreement with results from computationally demanding ab-initio studies of Ti0.5Al0.5N, at a mere fraction of the demand. The AL approach requires no high accuracy data sets or previous knowledge about the system, as the model is initially trained on low accuracy data which is removed from the training set (TS) at a later stage. This allows for an iterative process of improving and expanding the data set used to train the IP, without the need for large amounts of data.

Les myopathies héréditaires représentent un large groupe de pathologies neuromusculaires progressives affectant l’intégrité générale, structurelle et fonctionnelle du muscle squelettique. Elles engendrent une myriade de symptômes, ternissant qualité de vie et autonomie, et pouvant même s’avérer mortelles. La pose d’un diagnostic juste peut être difficile, entravée notamment par une faible prévalence de certaines myopathies, l’importante hétérogénéité clinique existante, et le chevauchement symptomatique des diverses formes. Malgré les avancées récentes faites dans le domaine des techniques de séquençage qui contribuent grandement au dépistage, au moins 25% des individus atteints de myopathies demeurent sans diagnostic génétique. Suivant l’investigation clinique d’un patient (Z46) atteint d’une myopathie distale à apparition tardive, l’analyse par séquençage ARN (RNA-seq) a révélé un variant non-sens homozygote de signification inconnue (VUS) à la fin de l’exon 5 du gène MLIP. Les niveaux d’expression génique altérés de « Protéine musculaire interagissant avec LMNA » (MLIP) et son partenaire « Lamine de type A » (LMNA) ont poussé à approfondir l’investigation. Davantage d’altérations -omiques furent identifiées par les techniques de RT-PCR, qPCR et WB, renforçant l’effet pathogénique du variant. Consolidant tous les résultats, le séquençage de longues lectures (LRS) a révélé un mécanisme d’épissage alternatif compensatoire de MLIP, qui tend à contourner et minimiser la production de transcrits arborant l’exon 5 muté. La présente étude vise à : 1) apporter un diagnostic génétique définitif au patient Z46, posant le variant MLIP comme causatif de la myopathie distale; 2) démontrer le pouvoir diagnostique du RNA-seq dans la résolution de ce cas complexe par l’identification et l’élucidation du VUS; 3) témoigner de l’étendue de la caractérisation transcriptomique offerte par les longues lectures du LRS. Couplé à cela, la modélisation du variant pathogénique par CRISPR/Cas9 dans une lignée cellulaire de myoblastes humains immortalisés permettra l’évaluation des impacts morpho-fonctionnels; conférant un supplément d’informations relatives aux fonctions musculaires normales et pathologiques de MLIP, faiblement caractérisées jusqu’à présent. / Hereditary myopathies represent a large group of progressive neuromuscular disorders affecting the general, structural and functional integrity of skeletal muscle. They cause a myriad of symptoms, impairing quality of life and autonomy, and can even be fatal. Making an accurate diagnosis can be difficult, hampered in particular by the low prevalence of certain myopathies, the significant clinical heterogeneity that exists, and the symptomatic overlap of the various forms. Despite recent advances in sequencing techniques that greatly assist in screening, at least 25% of individuals with myopathies remain without a genetic diagnosis. Following the clinical investigation of a patient (Z46) with a late-onset distal myopathy, RNA-sequencing (RNA-seq) analysis revealed a homozygous nonsense variant of unknown significance (VUS) at the end of exon 5 of the MLIP gene. Altered gene expression levels of ‘’Muscular LMNA-Interacting Protein’’ (MLIP) and its partner ‘’A-type Lamin’’ (LMNA) prompted further investigation. More -omic alterations were identified by RT-PCR, qPCR and WB technics, reinforcing the pathogenic effect of the variant. Consolidating all results, Long-Read Sequencing (LRS) revealed a compensatory alternative splicing mechanism of MLIP, which tends to bypass and minimize the production of transcripts carrying the mutated exon 5. The present study aims to: 1) provide a formal genetic diagnosis for patient Z46, positing the MLIP variant as causative of the distal myopathy; 2) demonstrate the diagnostic power of RNA-seq in resolving this complex case through identification and elucidation of the VUS; 3) testify to the breadth of transcriptomic characterization afforded by the long reads of LRS. Coupled with this, CRISPR/Cas9 modeling of the pathogenic variant in an immortalized human myoblast cell line will allow assessment of morpho-functional impacts; conferring additional information related to the normal and pathological muscles functions of MLIP, poorly characterized thus far.

Les myopathies héréditaires sont des maladies affectant les fibres musculaires, résultant d’un variant génétique pathogénique transmis par un ou les deux parents. Le diagnostic de ces maladies est complexe en raison de la similarité de certains symptômes avec d’autres maladies neuromusculaires et de leur hétérogénéité. Malgré les progrès des connaissances sur les maladies musculaires héréditaires, de nombreux patients ne reçoivent toujours pas de diagnostic moléculaire malgré les divers tests et le dépistage génétique. Actuellement, 13 variants dans le gène MLIP ont été rapportés chez 15 patients atteints d’une myopathie récessive. Les symptômes, les atteintes et l’âge au début de la maladie varient grandement entre ces patients. Ces variant sont suspectés d’entraîner une perte de fonction ou une altération majeure de la fonction protéique de MLIP et/ou de provoquer des dysfonctionnements dans les voies biologiques associées avec MLIP. De plus, les variants sont localisés autour de l’exon 4 contenant la séquence de localisation nucléaire et autour de l’exon 9 contenant, avec l’exon 10, un crochet AT permettant une interaction avec la chromatine. Pour comprendre la fonction de MLIP dans le muscle et expliquer la variabilité phénotypique, trois objectifs ont été définis : 1) définir le patron d’expression des transcrits chez trois patients; 2) modéliser le variant du patient adulte Z46 par CRISPR-Cas9 dans des myoblastes humains immortalisés; 3) analyser l’impact fonctionnel et pathologique des variants des trois patients. Le séquençage à longue lecture a révélé une architecture transcriptomique différente selon le groupe d’âge et a permis de répertorier 11 nouveaux transcrits non connus chez MLIP. De plus, les techniques de qRT-PCR et de Western Blot ont montré qu’uniquement le patient adulte Z46 présente un mécanisme compensatoire des niveaux de LMNA lors d’une diminution ou une perte de MLIP dans le noyau. Ce mécanisme serait spécifique au tissu ou au type cellulaire, car il n’est retrouvé dans les myoblastes porteurs du variant du patient. En analysant tous les résultats, la variabilité phénotypique semble être liée à la perte de la séquence de localisation nucléaire, mais aussi à l’intensité et l’efficacité de l’interaction entre MLIP et la chromatine. / Hereditary myopathies are diseases affecting muscle fibers, resulting from a pathogenic genetic variant transmitted by one or both parents. The diagnosis of these diseases is complex due to the similarity of some symptoms with other neuromuscular diseases and their heterogeneity. Despite advances in knowledge of hereditary muscle diseases, many patients still do not receive molecular diagnosis despite various tests and genetic screening. Currently, 13 variants in the MLIP gene have been reported in 15 patients with recessive myopathy. Symptoms, conditions, and age at the beginning of the disease vary greatly between these patients. These variants are suspected to cause loss of function or major impairment of MLIP protein function and/or to cause dysfunctions in the biological pathways associated with MLIP. Moreover, the variants are located around exon 4 containing the nuclear localization sequence, and around exon 9 containing, with exon 10, an AT-hook allowing an interaction with chromatin. To understand the function of MLIP in muscle and explain phenotypic variability, three objectives were defined: 1) to define the pattern of expression of transcripts in three patients; 2) to model the variant of adult patient Z46 by CRISPR-Cas9 in immortalized human myoblasts; 3) analyze the functional and pathological impact of the variants of the three patients. Long-Read Sequencing revealed a different transcriptomic architecture according to the age group and identified 11 new transcripts not known in MLIP. In addition, qRT-PCR and Western Blot techniques have shown that only the adult Z46 patient has a compensatory mechanism for LMNA levels during a decrease or loss of MLIP in the nucleus. This mechanism would be specific to tissue or cell type because it is not found in myoblasts carrying the variant of the same patient. By analyzing all the results, phenotypic variability seems to be related to the loss of the nuclear localization sequence, but also to the intensity and efficiency of the interaction between MLIP and chromatin.