Pathway analysis is an important task for gaining novel insights into the molecular architecture of many complex diseases. With the advancement of new sequencing technologies, a large amount of quantitative gene expression data have been continuously acquired. The springing up omics data sets such as proteomics has facilitated the investigation on disease relevant pathways. Although much work has previously been done to explore the single omics data, little work has been reported using multi-omics data integration, mainly due to methodological and technological limitations. While a single omic data can provide useful information about the underlying biological processes, multi-omics data integration would be much more comprehensive about the cause-effect processes responsible for diseases and their subtypes. This project investigates the combination of miRNAseq, proteomics, and RNAseq data on seven types of muscular dystrophies and control group. These unique multi-omics data sets provide us with the opportunity to identify disease-specific and most relevant biological pathways. We first perform t-test and OVEPUG test separately to define the differential expressed genes in protein and mRNA data sets. In multi-omics data sets, miRNA also plays a significant role in muscle development by regulating their target genes in mRNA dataset. To exploit the relationship between miRNA and gene expression, we consult with the commonly used gene library - Targetscan to collect all paired miRNA-mRNA and miRNA-protein co-expression pairs. Next, by conducting statistical analysis such as Pearson's correlation coefficient or t-test, we measured the biologically expected correlation of each gene with its upstream miRNAs and identify those showing negative correlation between the aforementioned miRNA-mRNA and miRNA-protein pairs. Furthermore, we identify and assess the most relevant disease-specific pathways by inputting the differential expressed genes and negative correlated genes into the gene-set libraries respectively, and further characterize these prioritized marker subsets using IPA (Ingenuity Pathway Analysis) or KEGG. We will then use Fisher method to combine all these p-values derived from separate gene sets into a joint significance test assessing common pathway relevance. In conclusion, we will find all negative correlated paired miRNA-mRNA and miRNA-protein, and identifying several pathophysiological pathways related to muscular dystrophies by gene set enrichment analysis. This novel multi-omics data integration study and subsequent pathway identification will shed new light on pathophysiological processes in muscular dystrophies and improve our understanding on the molecular pathophysiology of muscle disorders, preventing and treating disease, and make people become healthier in the long term. / Master of Science

Yes / Background: Understanding and countering the well-established negative health consequences of spaceflight remains a primary challenge preventing safe deep space exploration. Targeted/personalized therapeutics are at the forefront of space medicine strategies, and cross-species molecular signatures now define the 'typical' spaceflight response. However, a lack of direct genotype-phenotype associations currently limits the robustness and, therefore, the therapeutic utility of putative mechanisms underpinning pathological changes in flight. Methods: We employed the worm Caenorhabditis elegans as a validated model of space biology, combined with 'NemaFlex-S' microfluidic devices for assessing animal strength production as one of the most reproducible physiological responses to spaceflight. Wild-type and dys-1 (BZ33) strains (a Duchenne muscular dystrophy (DMD) model for comparing predisposed muscle weak animals) were cultured on the International Space Station in chemically defined media before loading second-generation gravid adults into NemaFlex-S devices to assess individual animal strength. These same cultures were then frozen on orbit before returning to Earth for next-generation sequencing transcriptomic analysis. Results: Neuromuscular strength was lower in flight versus ground controls (16.6% decline, p

Les terres rares (TRs) sont des métaux stratégiques du XXIe siècle dont la demande croissante résulte de leurs propriétés essentielles, notamment dans les domaines des énergies renouvelables, de la médecine et des hautes technologies. Ils sont classés en TR lourdes (HTRs), terres légères légères (LTRs) et non-lanthanides. Leur dissémination dans l'environnement, associée à une faible recyclabilité, fait des TRs des contaminants émergents pour lesquels les études de toxicité sont jusqu'à présent très disparates. Afin d’établir une base générale de la réponse cellulaire et moléculaire à un stress TRs, nous avons premièrement utilisé des stratégies complémentaires et à haut débit pour étudier la réponse, ainsi que l’absorption des TRs chez le modèle eucaryote Saccharomyces cerevisiae. Les deletome, transcriptome, protéome et ionome de la levure ont été analysés et approfondis par des analyses physiologiques ciblées. Bien que des réponses communes aux TRs et à d'autres métaux aient été mises en évidence, les réponses spécifiques aux TRs étaient prédominantes. La composition de la paroi cellulaire, la biosynthèse des sphingolipides, la voie ESCRT et l'endocytose sont des éléments clés de la réponse aux TRs. Deuxièmement, nous avons exploré les effets des TRs sur le transcriptome et le ionome du modèle végétal Arabidopsis thaliana. L'exposition des TRs a négativement impacté l'architecture racinaire, comme l'a révélé la modulation de gènes liés à l'auxine. De plus, le ionome a été modifié et les gènes liés à une carence en Fe largement représentés parmi les gènes les plus différentiellement exprimés. Afin d'identifier de nouvelles plantes modèles accumulant des TRs, des espèces de Phytolacca et de fougères ont été criblées. Malgré un trait d’accumulation des TRs conservé chez quelques genres de fougères et Phytolacca, un enrichissement en HTRs chez Phytolacca et en LTRs chez les fougères a été observé. Cependant, plusieurs espèces de Dryopteris présentent des teneurs contrastées en TRs dans les frondes et représentent de nouveaux modèles pertinents pour décrypter les mécanismes d’accumulation et de tolérance aux TRs. Globalement, des divergences ont été mises en évidence dans la réponse aux différentes TRs, en fonction de leur rayon ionique. La composition de la paroi cellulaire, la détoxification vacuolaire, mais aussi l’accumulation et le fractionnement des TRs ont souligné ces différences. Nous avons confirmé que les LTRs empruntaient les canaux calciques, tandis que de nouvelles preuves ont été données sur le rôle des transporteurs de Fe dans l'accumulation de HTRs. En conclusion, nous apportons ici de nouveaux éléments sur la toxicité et les spécificités des TRs, ainsi que des explications moléculaires pour certains effets déjà connus. Ce travail constitue un premier travail de base complet et multi-approches pour de futures études afin d’approfondir la compréhension de la toxicité des TRs chez les organismes vivants. / Rare earth elements (REEs) are strategic metals whose demand in the 21st century is increasing as a result of their essential properties useful to the fields of renewable energies, medicine, and high-technologies. They are classified as heavy REEs (HREEs), light REEs (LREEs) and non-lanthanides. Their dissemination in the environment, together with poor recyclability, leads REEs to be considered emerging contaminants, for which toxicity studies are currently very fragmented. To build a strong general foundation on the cellular and molecular response to REEs, we first adopted high-throughput and complementary strategies to study the REE stress response and their uptake in the unicellular eukaryotic model Saccharomyces cerevisiae. The deletome, transcriptome, proteome and ionome of yeast were analysed together with in-depth physiological experiments. Although common responses between REEs and other metals were highlighted, REE-specific responses were predominant. Cell wall composition, sphingolipid biosynthesis, the ESCRT pathway and endocytosis were emphasized as key elements in the cellular response to REEs. Second, we explored how REEs affect the transcriptome and ionome of the plant model Arabidopsis thaliana. REE exposure negatively affected the root architecture, as revealed by the modulation of auxin-related genes. REEs impaired the ionome, and Fe deficiency-related genes were largely represented among the most differentially expressed genes in both roots and leaves. Additionally, to identify new REE-accumulating plant models, collections of ferns and Phytolacca species were screened. Despite a conserved REE accumulation trait for Phytolacca and a few fern genera, HREE enrichment was observed in Phytolacca, while LREEs were preferentially transferred into the fronds of all fern species. However, several Dryopteris species harboured contrasting REE contents in the fronds. The latter species will be of great importance in deciphering the mechanisms of REE accumulation and tolerance. Overall, the response towards REEs differed according to their ionic radius. The cell wall composition, vacuolar detoxification, and the accumulation and fractionation of REEs notably accounted for these differences. Our findings support LREE-mediated entry through calcium channels, while new evidence was provided for the role of Fe transporters in the accumulation of HREEs. In conclusion, we have provided new insights into REE toxicity and specificities, together with the molecular elucidation of REE effects that have not previously been mechanistically explained. This work is a first multi-approach comprehensive groundwork that will be used for future studies to deepen the understanding and assessment of REE toxicity in organisms.

Die embryonale Gonade ist bei Säugetieren das einzige bipotente Organ, das sich während der Geschlechtsbestimmung in Hoden oder Eierstock differenziert. Nach der Spezifikation produziert sie geschlechtsspezifische Hormone, die wichtige morphologische, physiologische und Verhaltensänderungen auslösen und schließlich zu reifen Fortpflanzungsorganen führen, die für die Fortpflanzung der Art unerlässlich sind. Trotz der evolutionären Bedeutung der Gonadenfunktion gibt es erhebliche Entwicklungsunterschiede zwischen den Arten, deren molekulare Mechanismen weitgehend unerforscht sind. Zur Untersuchung dieser Mechanismen wurden Einzelzell-Omics-Techniken (scRNA- und scATAC-seq) an sich entwickelnden Gonaden eingesetzt, um molekulare Faktoren für interspezifische Unterschiede während der Geschlechtsdifferenzierung zu analysieren. Bekannte Zelltypen wurden in Hoden und Eierstöcken von Schweinen (mit medullären Strängen), Mäusen (ohne medulläre Stränge), Kaninchen (mit verzögerter Meiose der Keimzellen) und Maulwürfen (mit Ovotestes) zu geschlechtsdimorphen Zeitpunkten charakterisiert. Interartspezifische Vergleiche zeigten sowohl konservierte als auch artspezifische Ereignisse auf den Ebenen der dynamischen Genexpression, Co-Expressionsnetzwerke und zellulären Kommunikation. Expressionsdaten wurden mit epigenomischen Daten integriert, um genregulatorische Netzwerke (GRNs) abzuleiten und die regulatorischen Mechanismen zu klären. Analysen zeigten die Einbeziehung artenspezifischer Transkriptionsfaktoren in konservierte GRNs und identifizierten mutmaßliche cis-regulatorische Elemente, die mit artspezifisch exprimierten Genen verknüpft sind. Die Studie legt nahe, dass unterschiedliche Kontrollmechanismen die Meiose in ovariellen Keimzellen über Arten hinweg initiieren und dass der Metabolismus steroidogener Enzyme zu einzigartigen Entwicklungsmerkmalen bei Kaninchen beitragen könnte. / In mammals, the embryonic gonad is the only bipotential organ, differentiating into either testis or ovary during sex determination. Once specified, it produces sex-specific hormones that induce key morphological, physiological, and behavioral changes, leading to mature reproductive organs essential for species perpetuation. Despite the evolutionary importance of gonadal function, significant developmental plasticity exists across species, with underlying molecular mechanisms largely unexplored. To address this, single-cell omics techniques (scRNA- and scATAC-seq) were employed on developing gonads to investigate molecular contributors to interspecies differences during sex differentiation. Known cell types were characterized in testes and ovaries of pigs (exhibiting medullary cords), mice (lacking medullary cords), rabbits (displaying delayed meiosis of germ cells), and moles (forming ovotestes) at sexually dimorphic time points. Interspecies comparative analyses revealed both conserved and species-specific events at the levels of dynamic gene expression, co-expression networks, and cellular communication. Expression data were integrated with epigenomic data to infer gene regulatory networks (GRNs), clarifying regulatory mechanisms governing these events. Analyses revealed species-specific transcription factors in conserved GRNs and identified putative cis-regulatory elements linked with species-specific expressed genes. The study suggests diverse controls initiate meiosis in ovarian germ cells across species and that steroidogenic enzyme metabolism may contribute to unique developmental features in rabbits. Overall, this study advances the understanding of mammalian gonad differentiation and highlights how gene expression program evolution has contributed to mammalian phenotype diversity.

Einzelzell-Omics-Daten stehen derzeit im Fokus der Entwicklung computergestützter Methoden in der Molekularbiologie und Genetik. Einzelzellexperimenten lieferen dünnbesetzte, hochdimensionale Daten über zehntausende Gene oder hunderttausende regulatorische Regionen in zehntausenden Zellen. Diese Daten bieten den Forschenden die Möglichkeit, Gene und regulatorische Regionen zu identifizieren, welche die Bestimmung und Aufrechterhaltung der Zellidentität koordinieren. Die gängigste Strategie zur Identifizierung von Zellidentitätsmarkern besteht darin, die Zellen zu clustern und dann Merkmale zu finden, welche die Cluster unterscheiden, wobei davon ausgegangen wird, dass die Zellen innerhalb eines Clusters die gleiche Identität haben. Diese Annahme ist jedoch nicht immer zutreffend, insbesondere nicht für Entwicklungsdaten bei denen sich die Zellen in einem Kontinuum befinden und die Definition von Clustergrenzen biologisch gesehen potenziell willkürlich ist. Daher befasst sich diese Dissertation mit Clustering-unabhängigen Strategien zur Identifizierung von Markern aus Einzelzell-Omics-Daten. Der wichtigste Beitrag dieser Dissertation ist SEMITONES, eine auf linearer Regression basierende Methode zur Identifizierung von Markern. SEMITONES identifiziert (Gruppen von) Markern aus verschiedenen Arten von Einzelzell-Omics-Daten, identifiziert neue Marker und übertrifft bestehende Marker-Identifizierungsansätze. Außerdem ermöglicht die Identifizierung von regulatorischen Markerregionen durch SEMITONES neue Hypothesen über die Regulierung der Genexpression während dem Erwerb der Zellidentität. Schließlich beschreibt die Dissertation einen Ansatz zur Identifizierung neuer Markergene für sehr ähnliche, dennoch underschiedliche neurale Vorlauferzellen im zentralen Nervensystem von Drosphila melanogaster. Ingesamt zeigt die Dissertation, wie Cluster-unabhängige Ansätze zur Aufklärung bisher uncharakterisierter biologischer Phänome aus Einzelzell-Omics-Daten beitragen. / Single-cell omics approaches are the current frontier of computational method development in molecular biology and genetics. A single single-cell experiment provides sparse, high-dimensional data on tens of thousands of genes or hundreds of thousands of regulatory regions (i.e. features) in tens of thousands of cells (i.e. samples). This data provides researchers with an unprecedented opportunity to identify those genes and regulatory regions that determine and coordinate cell identity acquisition and maintenance. The most common strategy for identifying cell identity markers consists of clustering the cells and then identifying differential features between these clusters, assuming that cells within a cluster share the same identity. This assumption is, however, not guaranteed to hold, particularly for developmental data where cells lie along a continuum and inferring cluster boundaries becomes non-trivial and potentially biologically arbitrary. In response, this thesis presents clustering-independent strategies for marker feature identification from single-cell omics data. The primary contribution of this thesis is a linear regression-based method for marker feature identification from single-cell omics data called SEMITONES. SEMITONES can identify markers or marker sets from diverse single-cell omics data types, identifies novel markers, outperforms existing marker identification approaches. The thesis also describes how the identification of marker regulatory regions by SEMITONES enables the generation of novel hypotheses regarding gene regulation during cell identity acquisition. Lastly, the thesis describes the clustering-independent identification of novel marker genes for highly similar yet distinct neural progenitor cells in the Drosophila melanogaster central nervous system. Altogether, the thesis demonstrates how clustering-independent approaches aid the elucidation of yet uncharacterised biological patterns from single cell-omics data.

Les carcinoïdes pulmonaires, les carcinomes neuroendocriniens à grandes cellules (LCNEC) et les mésothéliomes malins sont des tumeurs thoraciques rares, dont l'incidence a augmenté au cours des dernières années. Le diagnostic de ces tumeurs est soumis à la variabilité inter-observateur et les opportunités thérapeutiques sont limitées. De grandes études génomiques visant à les caractériser au niveau moléculaire pourraient aider à mieux comprendre les mécanismes sous-jacents à leur développement et faciliter le diagnostic et le traitement de ces maladies. Mon projet de thèse visait à combler les lacunes dans la compréhension des carcinoïdes pulmonaires, des LCNEC et du mésothéliome péritonéal malin. À la suite des travaux entrepris au cours de ma thèse, nous avons constaté que (1) de la même manière que le mésothéliome pleural, les mésothéliomes péritonéaux sont également caractérisés par des mutations conduisant à la perte d'expression de BAP1, facteur de bon pronostic, (2) les patients atteints d’un LCNEC conservant une expression de RB1 présentent de meilleurs résultats lorsqu’ils sont traité avec une chimiothérapie du cancer du poumon non à petites cellules par rapport à une chimiothérapie du cancer du poumon à petites cellules, (3) les carcinoïdes pulmonaires peuvent être classés en trois groupes moléculaires pertinents sur le plan clinique, et (4) , l'identification de supra carcinoïdes confirme l'existence d'un lien moléculaire entre les néoplasmes neuroendocriniens pulmonaires de faible et de haut grade / Pulmonary carcinoids, large-cell neuroendocrine carcinomas (LCNEC), and malignant mesotheliomas are rare thoracic tumours, which incidence has been increasing over the past years. The diagnosis of these tumours is subjected to inter-observer variability and the therapeutic opportunities are limited. Large genomic studies to characterize them at a molecular level might help to better understand the mechanisms underlying their development, and to help the diagnosis and treatment of these diseases. My thesis project aimed to fill the gap in the understanding of pulmonary carcinoids, LCNEC, and malignant peritoneal mesothelioma. As result of the work undertaken during my thesis, we found that (1) similarly to pleural mesothelioma, peritoneal mesotheliomas are also characterised by mutations leading to the loss of expression of BAP1, which is a factor of good prognostic, (2) LCNEC patients with a remaining expression of RB1 have a better outcome when treated with non-small cell lung cancer chemotherapy in comparison to small-cell lung cancer chemotherapy, (3) pulmonary carcinoids can be classified in three clinically-relevant molecular groups, and (4), the identification of supra carcinoids supports a molecular link between the low and high-grade lung neuroendocrine neoplasms

In questa tesi di Dottorato, l’obiettivo era valutare l’impatto di diversi ingredienti alimentari sul metabolismo di alcuni batteri intestinali e viceversa, mediante l’applicazione di tecniche omiche. Utilizzando le tecniche di metabolomica e trascrittomica, è stata studiata la risposta all’acido linoleico del ceppo Bifidobacterium breve DSM 20213. Utilizzando un approccio combinato di metagenomica e metabolomica, è stato possibile studiare le modifiche a carico del microbiota intestinale, del profilo fenolico e degli acidi grassi, in biscotti senza glutine (a base di erba medica) durante digestione e fermentazione in vitro. Inoltre, è stato valutato come alcuni batteri potessero interferire negativamente su una terapia farmacologica a base di Diclofenac, un farmaco usato per alcune patologie intestinali. Per questo tipo di studio è stata utilizzata la spettrometria di massa ad alta risoluzione, che ha consentito di ipotizzare un coinvolgimento dell’enzima batterico β-glucuronidasi. Una sola tecnica omica, seppure di ultima generazione, non permette di valutare tutte le modificazioni del microbiota intestinale data la complessità dei fattori coinvolti. Per questa ragione, integrare più approcci omici potrebbe risultare una buona strategia per analizzare il reale impatto del microbiota sulla salute dell’ospite. Questo permetterebbe di valutare le interazioni microbiota-ospite, i principali metabolismi e le interconnessioni tra gruppi batterici coinvolti nella risposta ad uno stimolo esterno come l’assunzione di particolari ingredienti con l’alimentazione. / The aim of the present PhD thesis was to explore the metabolic response of intestinal bacteria to food components by using ‘omics’ approaches. In particular, the first part of this thesis was focused on the effect of linoleic acid on Bifidobacterium breve DSM 20213 strain. Firstly, an untargeted metabolomics-based approach was used to explore the primary changes in metabolic profile of this strain grown in presence of linoleic acid. Secondly, the gene expression of B. breve DSM 20213 induced by linoleic acid exposure was investigated. Integrated use of metabolomics/transcriptomics was applied to better understand the response mechanisms to linoleic acid stress. In the third part of the thesis, using a combination of metagenomics and metabolomics, the in vitro large intestine fermentation of gluten-free rice cookies containing alfalfa seed was investigated. In the last part of my PhD, the negative effect of β-glucuronidase producing bacteria was evaluated by means of qualitative high-resolution mass spectrometry. Based on my experience there is not a gold standard approach for evaluating a complex environment such as the gastrointestinal tract. For this reason, an integrated use of different techniques should be mandatory to have an accurate framework of gut microbiota composition, its potential metabolic network and the impact on the host physiology and health.

Drosophila suzukii est une drosophile invasive en Europe, Amérique du Nord et Amérique du Sud. Contrairement aux autres espèces de drosophiles, les femelles parasitent les fruits mûrs que les larves consomment, engendrant d’importants dégâts sur les cultures fruitières. Les stratégies mises en place par cette espèce pour tolérer les températures hivernales sous nos latitudes sont encore peu comprises. Par conséquent, l’objectif de ma thèse était d’acquérir des connaissances fondamentales sur la thermotolérance de cette espèce, en m’intéressant notamment à la plasticité de la tolérance au froid et aux mécanismes physiologiques sous-jacents à l’acclimatation. J’ai évalué la thermotolérance basale de D. suzukii en soumettant des adultes et des pupes à un large panel de températures (froides et chaudes). Ces expérimentations ont permis de confirmer que cette espèce était intolérante au froid et que des températures supérieures à 32°C impactaient grandement sa survie. Par la suite, j’ai évalué la plasticité de sa tolérance au froid. Mes travaux ont permis de confirmer que sa thermotolérance était effectivement plastique, puisque l’utilisation de températures fluctuantes ou l’acclimatation permettaient de réduire sa mortalité lors d’expositions aux basses températures. L’acclimatation chez D. suzukii était corrélée à de nombreuses modifications physiologiques, telles que l’accumulation de cryoprotecteurs, un réajustement de la composition des phospholipides membranaires et des réserves lipidiques, une régulation des gènes liés à l’activité des transporteurs ioniques ainsi qu’un maintien de l’homéostasie métabolique. Ces modifications, également observées chez d’autres espèces d’insectes, pourraient être liées à l’augmentation de la tolérance au froid de D. suzukii, jouant probablement un rôle important dans sa survie hivernale et donc dans le succès de son invasion. Ces connaissances acquises sur sa thermobiologie contribueront sans doute à mieux cerner les limites physiologiques de cette espèce et prédire l’évolution de son invasion, ainsi que sa phénologie et les variations de populations au cours des saisons dans les zones déjà envahies. Mes résultats ouvrent également des perspectives intéressantes pour la mise en place de techniques de lutte intégrée contre D. suzukii. / Drosophila suzukii is an invasive pest in Europe, North and South America. Unlike other drosophilids, females oviposit in ripe fruits that larvae consume, provoking important damages on fruit productions. The overwintering strategies of this fly are yet poorly understood. Therefore, the aim of my thesis was to acquire new fundamental knowledge about the thermal biology of this fly, and more specifically the plasticity of its thermal tolerance and the physiological mechanisms underpinning cold acclimation. In order to define its basal thermal tolerance, adults and pupae were subjected to a large set of high and low temperatures. My data confirmed that this pest was chill susceptible, and showed that survival was greatly compromised during exposures above 32°C. Next, I evaluated its thermal tolerance plasticity. My data confirmed the high plasticity of its cold tolerance, as fluctuating thermal regimes and acclimation were able to decrease the mortality due to cold exposures. Acclimation in this species was correlate with several physiological adjustments, such as: cryoprotectant accumulation, remodeling of membrane phospholipids and lipidic reserves, upregulation of genes linked with activity of ionic transporters and maintenance of metabolic homeostasis. Those modifications (which are shared among temperate insect species) are likely linked with cold tolerance increase provoked by acclimation. Therefore, these physiological adjustments could play an important role in its overwintering success in Europe and Canada, which can facilitate its invasion in these regions. These new data will participate to a better understanding of its physiological limits, and are thus of importance for predicting the evolution of its invasion front and its phenology and demographic variations in invaded areas. My results are also of interest regarding the set-up of integrated pest management strategies against this fly.

No description available.

INTRODUCTION: The legal and illicit use of cannabinoid-containing products is accelerating worldwide and is accompanied by increasing abuse problems. Due to legal issues, the USA will be entering a period of rapidly expanding recreational use of cannabinoids without the benefit of needed basic or clinical research. Most clinical cannabinoid research is focused on adults. However, the pediatric population is particularly vulnerable since the central nervous system is still undergoing developmental changes and is potentially susceptible to cannabinoid-induced alterations. RESEARCH DESIGN AND METHODS: This review focuses on the systems medicine of cannabinoids with emphasis on the need for future studies to include pediatric populations and mother-infant dyads. RESULTS AND CONCLUSION: Systems medicine integrates omics-derived data with traditional clinical medicine with the long-term goal of optimizing individualized patient care and providing proactive medical advice. Omics refers to large-scale data sets primarily derived from genomics, epigenomics, proteomics, and metabolomics.