Lipoxygenases (LOXs), cytochromes P450 (CYPs) and cyclooxygenases (COXs) catalyze peroxidation of unsaturated fatty acids. In humans they convert arachidonic acid into a variety of eicosanoids, which play a role in all inflammatory responses, cardiovascular and kidney diseases, Alzheimer's, cancer and other ailments. Blocking one pathway can prompt the body to switch to the available alternatives. In contrast to CYP and COX, LOX has a non-heme iron co-factor. Several LOXs are produced or stress-induced in the human body. They share the same mechanism, but differ in sequence causing catalysis on the same substrate to be regio- and stereospecific. The action of 15-LOXs could be pro- or anti-inflammatory, and pro- or anti-carcinogenic. Depending on the dose, LOXs inhibitors can induce or inhibit other oxygenases. Inhibition of these enzymes presents a great challenge in solving the problem of how to control their action and treat diseases, without causing severe side effects and maintaining/restoring a delicate equilibrium between them. Research on CYPs and COXs is more advanced, while studies of LOXs are lagging behind. This article presents a brief review about LOX structures and inhibition, their involvement in human diseases, and their interplay with other oxidoreductases.

<p dir="ltr">Systems biology dynamic models, which are based on differential equations, offer a flexible and accurate framework to explain physiological properties emerging from complex biochem- ical or biological systems. These models enable explicit quantification and interpretation, allowing for simulation and perturbation analysis to study biological features and their inter- actions, as well as understanding system progression and convergence under various initial conditions. However, their application in human disease systems is limited due to unknown kinetics parameters under disease conditions and a reductionist paradigm that fails to cap- ture the complexity of diseases. Meanwhile, the advent of omics technologies provides high- resolution molecular measurements from single cells and spatially resolved samples, as well as comprehensive disease-specific molecular signatures from large patient cohorts. This wealth of data holds the promise for characterizing complex biological systems, necessitating ad- vanced systems biology models and computational tools that can harness multi-omics data to reliably depict biological processes. However, this endeavor faces the challenge of nonlinear relationships between omics data and the system’s dynamic properties, such as the global or local low-rank gene expression patterns across cell types and the nonlinear complexities within transcriptional regulatory networks revealed by single-cell RNA sequencing.</p><p dir="ltr">The overall goal of this report is to develop new computational frameworks, AI-empowered methods, and related mathematical theories to explicitly represent and approximate the dy- namics of complex biological systems by using biological omics data. Our aim is to unravel the intricacies of context-specific dynamic systems using multi-Omics data. Specifically, we solved two different but related computational tasks and enabled the first-of-its-kind methods to (1) identify local low-rank matrices from large omics data, and (2) a robust optimization strategy to approximate metabolic flux. Subsequently, we delve into the realm of data-driven and AI-powered systems biology, harnessing the power of statistical learning and artificial intelligence to approximate differential equations or their representations. This research en- deavor not only contributes to the advancement of subspace modeling but also offers insights into a wide array of complex phenomena across diverse domains, with profound implications for computational biology and beyond.</p>

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2002. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2002. / Härtill 4 uppsatser.

Diss. (sammanfattning) Uppsala : Sveriges lantbruksuniv., 2007. / Härtill 4 uppsatser.

Recent technological advances and remarkable successes have led to genome-wide association studies (GWAS) becoming a tool of choice for investigating the genetic basis of common complex human diseases. These studies typically involve samples from thousands of individuals, scanning their DNA at up to a million loci along the genome to discover genetic variants that affect disease risk. Hundreds of such variants are now known for common diseases, nearly all discovered by GWAS over the last three years. As a result, many new studies are planned for the future or are already underway. In this thesis, I present analysis results from actual studies and some developments in theory and methodology. The Wellcome Trust Case Control Consortium (WTCCC) published one of the first large-scale GWAS in 2007. I describe my contribution to this study and present the results from some of my follow-up analyses. I also present results from a GWAS of a bipolar disorder sub-phenotype, and a recent and on-going fine mapping experiment. Building on methods developed as part of the WTCCC, I describe a Bayesian approach to GWAS analysis and compare it to widely used frequentist approaches. I do so both theoretically, by interpreting each approach from the perspective of the other, and empirically, by comparing their performance in the context of replicated GWAS findings. I discuss the implications of these comparisons on the interpretation and analysis of GWAS generally, highlighting the advantages of the Bayesian approach. Finally, I examine the effect of linkage disequilibrium on the detection and estimation of various types of genetic effects, particularly non-additive effects. I derive a theoretical result showing how the power to detect a departure from an additive model at a marker locus decays faster than the power to detect an association.

La méthylation de l'ADN est un processus vital pour le développement des mammifères. Sa distribution anormale,notamment au niveau des régions répétées du génome, est une signature pathologique. La découverte de maladies héréditaires touchant la stabilité du génome a permis des avancées considérables dans l'identification des acteurs et des mécanismes. Nous avons choisi d'étudier le syndrome ICF (Immunodéficience, instabilité Centromérique et anomalies Faciales), première maladie génétique identifiée avec des défauts de la méthylation de l’ADN, liés à une instabilité chromosomique. Lorsque j'ai commencé ma thèse, des mutations dans les gènes DNMT3B et ZBTB24 avaient été décrites comme causes génétiques du syndrome. Cependant, d'autres causes génétiques restaient inconnues. Nos travaux ont permis d'identifier deux nouveaux gènes, CDCA7 et HELLS, dont les mutations sont responsables du syndrome. J'ai montré que leur perte de fonction dans les cellules somatiques entraîne un défaut de méthylation des répétitions centromériques, suggérant leur rôle dans le maintien de la méthylation de l'ADN. Par conséquent, l'étude de l'étiologie d'une maladie génétique rare a permis d'identifier de nouveaux « gardiens » de la stabilité du génome, avec des fonctions jusqu'alors insoupçonnées dans les processus de méthylation de l'ADN et dans le développement. Au cours de mon doctorat, j'ai établi des cartes de méthylation des cellules de patients ICF afin d'identifier les cibles communes et distinctes de ces facteurs, ainsi que leurs caractéristiques génomiques et épigénomiques. Contrairement aux mutations de DNMT3B,celles de ZBTB24, CDCA7 et HELLS affectent la méthylation dans des régions pauvres en CpG, dans des régions intergéniques et dans des répétitions d'ADN intercalées. Plus généralement, ce sont les régions d'hétérochromatine qui sont les plus touchées et en particulier des clusters des gènes codants et non codants, dont certains sont exprimés de manière monoallélique. Pour mieux caractériser le rôle de ZBTB24 dans le développement et la méthylation de l'ADN,nous avons généré un modèle murin mutant qui nous a permis de monter que ZBTB24 était essentielle pour le développement embryonnaire précoce. De plus, ZBTB24 jouerait un rôle dans l'établissement de la méthylation des séquences répétées de l'ADN, à la fois en tandem ou intercalé. Fait intéressant, ZBTB24 semble être également impliqué dans l'établissement de la marque répressive H3K9me3, suggérant un rôle de la protéine dans le "dialogue" entre la méthylation de l'ADN et celle des histones. Dans l'ensemble, mon travail met l'accent sur la façon dont la méthylation de l'ADN et les marques d'hétérochromatine sont établies et maintenues à des gènes uniques et des répétitions de l'ADN, et fournit de nouveaux acteurs et mécanismes à considérer dans les études sur le maintien de la stabilité du génome. / DNA methylation is an essential process for the development of mammals. Its abnormal distribution, particularly at the level of the repeated regions of the genome, is a pathological signature. The discovery of hereditary diseases affecting DNA methylation and the stability of the genome allowed a considerable progress in the identification of their actors and mechanisms. We chose to study the ICF (Immunodeficiency, Centromeric Instability and Facial Abnormalities) syndrome, the first genetic disorder identified with defects in the distribution of DNA methylation, linked to chromosomal instability. When I started my PhD, mutations in two genes had been described to cause the ICF syndrome: DNMT3B and ZBTB24. However, the genetic origin of a subset of ICF patients remained unknown. We identified mutations in CDCA7 and HELLS as causative of the ICF syndrome. I showed that their loss of function in somatic cells results in the loss of DNA methylation at centromeric repeats, strongly suggestive of a role DNA methylation maintenance. Hence, the study of the aetiology of a genetic disease provided new candidate “guardians” of DNA repeats and genome stability, with virtually unknown functions but with exciting potential roles in the DNA methylation machinery and in development. During my PhD, I established methylation maps in ICF patients cells to identify common and distinct targets of these factors, as well as their genomic and epigenomic characteristics. In contrast to DNMT3B mutations, those in ZBTB24, CDCA7 and HELLS affect methylation at CpG-poor regions in intergenic genomic locations and at interspersed DNA repeats, and more generally, at genomic locations with heterochromatic features. Their integrity is required for the methylated status of coding and non-coding clusters of genes, some of which are expressed in a monoallelic manner. To better characterize the role of ZBTB24 in development and DNA methylation pathways, we generated a mouse model carrying mutations in ZBTB24. We showed that ZBTB24 is essential for early development, while it seemed to be dispensable for in vitro differentiation of murine ES cells. We implicated ZBTB24 in the establishment of DNA methylation at DNA repeats, both in tandem or interspersed, in differentiating ES cells. Interestingly, ZBTB24 seems to be also implicated in the establishment of the repressive mark H3K9me3 suggesting that ZBTB24 may indirectly control DNA methylation through an interplay with histone marks. As a whole, our work sheds light on how DNA methylation and heterochromatin marks are established and maintained at unique genes and DNA repeats, and provides new actors and mechanisms to consider in studies of the maintenance of genome stability.

La méiose est un processus de ségrégation des chromosomes essentiel pour la gamétogenèse chez tous les organismes qui présentent une reproduction sexuée. Ce mécanisme nécessite des connections entre chromosomes homologues et des structures intermédiaires d’ADN appelées Jonction de Holliday. Ces jonctions sont résolues principalement par complexe MutLγ (Mlh1-Mlh3). Des mutations sur les gènes impliqués en méiose s’accompagnent chez l’homme de problèmes allant de la stérilité à des réarrangements chromosomiques comme la trisomie. Mlh1-Mlh3 joue aussi un rôle dans la voie de réparation des mésappariements de l’ADN (MisMatch Repair - MMR). Notre laboratoire a révélé la première structure cristalline de la région C-terminale du complexe MutLα (Mlh1-Pms1) qui est l’endonucléase majeure de la voie MMR. Mon projet de thèse s’insère dans le cadre de l’étude des différentes fonctions des MutL eucaryotes et plus particulièrement sur le mécanisme moléculaire de MutLγ (Mlh1-Mlh3). Au cours de ma thèse, nous avons déterminé la structure cristalline du domaine C-terminale du complexe Mlh1-Mlh3 qui contient le site d’endonucléase et caractérisé 3 états du site actif. Nous avons montré le rôle de Mlh1 dans le site endonucléase. Nous avons caractérisé la spécificité de ce domaine pour les Jonctions de Holliday et proposé un modèle du site de fixation de l’ADN sur le complexe entier. Ce modèle a permis de proposer un nouveau mutant de séparation de fonction de Mlh1-Mlh3, appelé KERE, qui a été analysé par gel retard et génétique. / Meiosis is key process in sexual reproduction, where chromosomes are segregated. During this process, a parental diploid cell divides into haploid gametes. This mechanism requires connections between homologous chromosomes and intermediate DNA structures called Holliday Junctions. These junctions are mainly resolved by MutLγ (Mlh1-Mlh3) complex. Mutations of genes involved in meiosis are associated with human diseases including sterility and chromosomal rearrangements such as trisomy. Mlh1-Mlh3 plays also a role in DNA mismatch repair (MMR). Our laboratory has characterized the first crystal structure of the C-terminal region of the MutLα complex (Mlh1-Pms1) which is the major endonuclease in MMR. My thesis aims at understanding the molecular mechanism of MutLγ (Mlh1-Mlh3) mainly involved in meiosis and to compare it with Mlh1-Pms1 mainly involved in MMR.We determined the crystal structure of the C-terminal domain of the MutLγ complex which contains the endonuclease site. We characterized the structure of three different states of the active site. We showed how Mlh1 is an integral part of the Mlh3 endonuclease site. We characterized the specificity of this domain for Holliday Junctions and proposed a model of the full-length complex and its DNA binding sites. Finally, we design new separation of function allele of Mlh1-Mlh3, called KERE, which was analyzed by EMSA and genetic experiments.

Diss. (sammanfattning) Stockholm : Karol, inst., 2002. / Härtill 4 uppsatser.

Diss. (sammanfattning) Stockholm : Karol. inst., 2003. / Härtill 6 uppsatser.