Lubica Dudakova Doctoral Thesis ABSTRACT Keratoconus (KC) is a non-inflammatory disease of the cornea, in which ectasia and thinning occur probably due to defects in the collagen fibers binding. It is one of the most common indications for corneal transplantation. KC is a complex disorder with the involvement of both genetic and environmental factors; however the exact pathogenic mechanisms leading to the disease development have not been elucidated. The main aim of our work was to compare the presence and enzyme activity of cross- linking enzymes lysyl oxidases (LOX and LOX-like enzymes), in control human cornea samples and explanted cornea gained from patients with KC. We also focused on diseases previously described to be associated with KC with the aim to identify common signs among them. Furthermore, we replicated association of single nucleotide polymorphisms (SNPs) in LOX and hepatocyte growth factor (HGF) with KC risk. We attempted to link all pathophysiological disturbances observed in KC into one common pathway. We have used a wide spectrum of methods (cell culturing, immunohisto- and immunocytochemistry, microscopy, fluorimetric enzyme activity measurement, genotyping and direct sequencing, statistical analysis). We demonstrated the presence of entire family of LOX enzymes in control and in KC...

La lysyl oxydase (LOX) est une enzyme extracellulaire dont le rôle canonique est de catalyser la réticulation des fibres de collagènes et de l’élastine, assurant ainsi l’intégrité des tissus conjonctifs. La LOX agit également dans plusieurs types cellulaires comme régulateur de différents processus biologiques, soulignant des fonctions à la fois extra et intracellulaires. Ces travaux de thèse ont contribué à améliorer la compréhension du rôle de LOX dans l’épiderme, et plus précisément au cours de la différenciation des kératinocytes. Le développement d’un modèle de culture en monocouche à confluence, et d’un modèle tridimensionnel d’épiderme reconstruit ont permis d’aborder l’étude de LOX au cours de l’induction du programme de différenciation des kératinocytes et du processus de différenciation terminale conduisant à la formation d’un épiderme pluristratifié, cornifié et fonctionnel. L’expression de LOX est induite au cours des premières étapes de la différenciation de kératinocytes primaires ainsi que d’une lignée de kératinocytes immortalisés. Grâce à l’établissement de lignées de kératinocytes éteignant l’expression de LOX de façon stable, nous avons mis en évidence l’implication de la protéine LOX, indépendamment de son activité enzymatique, dans la régulation des premières étapes de différenciation des kératinocytes. En absence de LOX, l’initiation du programme de différenciation est perturbée, affectant la différenciation terminale et fonctionnelle des épidermes reconstruits. Ainsi, une régulation fine de l’expression de LOX est nécessaire au déroulement normal du processus de différenciation des kératinocytes, et donc au maintien de l’homéostasie épidermique / Lysyl oxidase (LOX) is an extracellular enzyme that catalyzes the cross-linking of fibrillar collagens or elastin, thereby regulating the structural integrity of connective tissues. Moreover, LOX displays multiple roles in different cell types, acting as a regulator of various biological processes at both extra and intracellular levels. The aim of the present work was to shed light on LOX functions in the epidermis, especially during keratinocyte differentiation. The development of culture models, consisting of confluent monolayers or reconstructed-epidermis allowed us to study LOX functions during the induction of the differentiation program, and furthermore during the terminal differentiation process leading to the formation of a pluristratified, cornified and functional epidermis. LOX expression is induced at the onset of the commitment to differentiation, both in primary and immortalized keratinocytes. Stable silencing of LOX expression affects the induction of the differentiation program and strongly impairs terminal and functional epidermal differentiation in reconstructed-epidermis. Therefore, LOX protein acts during the first steps of keratinocyte differentiation, independently of its enzymatic activity, and is implied for subsequent commitment into terminal differentiation. Taken together, these results suggest that a finely regulated expression of LOX is required for normal keratinocyte differentiation, and thus for maintenance of epidermal

Au sein d’une tumeur des régions hypoxiques se forment ce qui conduit à l’activation du facteur de transcription HIF1. HIF1, composé des deux protéines HIF1a et HIF1b, permet l’adaptation des cellules à des faibles concentrations d’oxygène en activant la transcription de gène cible. Un de ces gènes est celui codant pour la lysyl oxydase (LOX). Cette enzyme structure la matrice extracellulaire et est impliquée dans la tumorigénèse. Pour comprendre les liens entre LOX et HIF1a, nous avons modulé leurs expressions dans des lignées humaines de carcinome du côlon. En condition hypoxique, HIF1a contrôle l’expression de LOX et réciproquement, LOX régule la synthèse protéique d’HIF1a via l’activation de la voie de signalisation PI3K/AKT. Nous avons donc mis en évidence l’existence d’une boucle de régulation positive entre LOX et HIF1 en conditions hypoxique. Sachant que ces deux protéines sont des acteurs majeurs de la progression tumorale, nous avons cherché à comprendre le rôle de cette régulation mutuelle dans ce processus. Nos résultats démontrent que l’activité enzymatique de LOX promeut la croissance tumorale in vitro et in vivo et que son action est potentialisée par la présence de son partenaire HIF1a. De plus, LOX et HIF1a agissent en synergie afin d’augmenter la potentiel métastatiques des cellules tumorale de côlon in vitro. Ainsi, ce travail de thèse a permis de mettre en évidence l’existence d’une boucle de régulation entre HIF1a et LOX qui est critique dans la progression tumorale et semble également être impliquée dans le processus métastatiques / The microenvironment of solid tumors is exposed to hypoxic conditions which lead to the activation of Hypoxia‐Inducible Factor 1 (HIF1). HIF1, composed by a heterodimer of HIF1a and HIF1b protein, is a key transcription factor involved in cellular adaptation to changes in oxygen level, inducing the expression of several transcriptional targets such as Lysyl Oxidase (LOX). LOX is an amine oxidase that catalyzes crosslinking of fibrillar collagens and elastin in the extracellular matrix. Furthermore, LOX is implied in tumor progression. To clarify, the link between LOX and HIF1a, their expression were modulated in human colorectal carcinoma cell lines. We pointed out that besides HIF1‐dependant regulation of LOX, LOX can also act on the HIF1 pathway under hypoxic conditions. Indeed, LOX enzymatic activity upregulates HIF1a protein synthesis, and this action is mediated by the PI3K/AKT pathway. Thus, these results emphasize the existence of a regulation loop between HIF‐1a and LOX, which represent two main actors of tumoral progression. Thus, we wanted to determine the implication of this amplification loop in tumor progression. Our results show that LOX enzymatic activity increase tumor growth in vitro and in vivo, and this role is partially dependant of its partner HIF1a. Furthermore, we established that that LOX and HIF1a act in synergy to foster metastatic potential in colorectal carcinoma cell lines. Taken together, our results demonstrate a regulation loop between LOX and HIF1a with is critical for tumor progression and metastasis formation

L'importation de ARNtLys CUU (tRK1) de levure dans les mitochondries humaines indique que la cellule humaine possède la machinerie pour importation d'ARNt. Dans la présente étude, nous montrons que le précurseur de la lysyl-ARNt synthétase mitochondriale peut interagir avec tRK1 et ses dérivés contenant les déterminants d'import mitochondrial, et facilite leur internalisation par les mitochondries humaines. L'efficacité de l'importation augmentait à l'addition de l'énolase, d'enzyme glycolytique fonctionnant comme ARN chaperon. La translocation de tRK1 et de ses dérivés dans la matrice mitochondriale dépend également d'une autre protéine, la polynucléotide phosphorylase (PNPase). Mutation ponctuelle pathogénique qui prévient la trimérisation de PNPase diminue l'importation des ARNr 5S et ARN MRP dans les mitochondries ceci affectant la traduction mitochondriale. La surexpression de PNPase induit une augmentation des ARN importé et complémente le déficit de traduction mitochondriale. / The import of yeast tRNALys (tRK1) into human mitochondria in the presence of cytosolic extract suggests that human cell possesses machinery for tRK1 import. Here, we show that precursor of mitochondrial lysyl-tRNA synthetase (preKARS2) interact with tRK1 and its derivatives containing tRK1 import determinants, and facilitates their import into isolated mitochondria and in vivo, when preKARS2 was overexpressed or downregulated. tRK1 import efficiency increased upon addition of glycolytic enzyme enolase, previously found as an actor of RNA import in yeast. We found that tRK1 and its derivatives translocate into mitochondrial matrix in polynucleotide phosphorylase (PNPase) dependent manner. Furthermore, a point mutation preventing trimerization of PNPase affect import of 5S rRNA and MRP RNA into mitochondria and subsequently mitochondrial translation. Overexpression of the wild-type PNPase induced an increase of 5S rRNA import into mitochondria and rescued translation.

La matrice extracellulaire est un réseau tridimensionnel complexe qui joue le rôle de support aux cellules ainsi que de réservoir de molécules bioactives régulant le comportement cellulaire. Elle est composée de 1027 protéines chez l’Homme (Naba et al., Matrix Biol. 2016), 274 protéines constituant le matrisome et 753 associées (facteurs de croissance et protéines régulatrices de la matrice extracellulaire) et de 6 glycosaminoglycanes dont 5 sulfatés. La matrice extracellulaire est impliquée dans de nombreuses pathologies (Bonnans et al., Nat. Rev. Mol. Cell Biol. 2014). La lysyl oxydase, responsable de la réticulation des collagènes et de l’élastine est impliquée dans de nombreux cancers. La matrice extracellulaire est un réservoir de fragments bioactifs, nommés matricryptines, qui sont libérés par protéolyse des biomolécules de la matrice et régulent de nombreux processus biologiques tels que l’angiogenèse et l’adipogenèse (Ricard-Blum et Vallet Matrix Biol. 2017). Nous avons exprimé en cellules humaines plusieurs matricryptines dont les ectodomaines des collagènes membranaires XIII, XVII, XXIII et XXV et identifié leurs partenaires extracellulaires. Nous avons caractérisé le propeptide de la lysyl oxydase par SEC-MALS, diffusion dynamique de la lumière et par SAXS et avons modélisé à partir des données de SAXS sa structure tridimensionnelle. Nous avons identifié 17 nouveaux partenaires de ce fragment et analysé le mutant Arg158Gln dépourvu d’activité biologique. Cette mutation identifiée chez l’Homme inhibe les activités anti-prolifératives du propeptide et est associée à un risque accru de cancer du sein (Min et al., Cancer Res. 2009). Nous avons exprimé la lysyl oxydase mature et modélisé sa structure tridimensionnelle en utilisant toutes les données disponibles. Les interactions identifiées au cours de ce travail ont été associées à celles obtenues par curation manuelle de la littérature pour construire la première version de l’interactome extracellulaire humain / The extracellular matrix is an intricate tridimensional network supporting cells and a bioactive molecule reservoir involved in the regulation of cell behavior. It is composed of 1027 proteins in humans (Naba et al., Matrix Biol. 2016), including 274 of the core matrisome and 753 associated proteins (growth factors and extracellular matrix regulators) and 6 glycosaminoglycans including 5 sulfated. The extracellular matrix is altered in numerous pathologies (Bonnans et al., Nat. Rev. Mol. Cell Biol. 2014). The lysyl oxidase is responsible for the cross-linking of collagens and elastin and is involved in many cancers. The extracellular matrix is a reservoir of bioactive fragments named matricryptins which are released by proteolysis of extracellular matrix proteins and regulate numerous biological processes like angiogenesis and adipogenesis (Ricard-Blum et Vallet, Matrix Biol. 2017). We have expressed under a recombinant form in human cells some matricryptins including the ectodomains of the membrane collagens XIII, XVII, XXIII and XXV and have identified their extracellular partners. We have characterized the propeptide of lysyl oxidase by SEC-MALS, dynamic light scattering, and SAXS and have built a coarse-grained 3D model by SAXS-derived constraints. We have identified 17 new partners of this fragment and analyzed the mutant Arg158Gln which has no biological activity. This mutation has been identified in humans and inhibits the propeptide anti-proliferative properties. It is associated to an increased risk of breast cancer (Min et al., Cancer Res. 2009). We have expressed the mature lysyl oxidase and modelled its tridimensional structure using available data. All the interactions identified in this study were associated to manually curated interactions described in the literature to build the first version of the human extracellular interactions network

A better understanding of these structural changes that occur before Hypertension (HTN) could ultimately result in a treatment that can prevent or reverse this disease state before its onset. T cells have been shown essential for the development of HTN. The aim of these murine studies was to investigate the role of the T-helper CD4⁺ lymphocytes in initiating vascular remodeling and HTN in the absence of an increased mechanical load and to investigate the role of T-helper 17 (Th17) CD4⁺ lymphocyte initiating vascular remodeling and HTN by stimulating Lysyl Oxidase (LOX). LOX is known to cross-link collagen and elastin and. Excess synthesis of collagen and elastin results in a stiffer artery and hypertension. We established L-NAME-induce HTN in wild type (WT) mice. CD4⁺ splenic lymphocytes were isolated from these mice and adoptively transferred into naïve syngeneic severe combined immunodeficient (SCID) mice. The SCID mice receiving these cells became hypertensive. Cytokine analysis demonstrated an increase in both Th1 and Th17 cytokine in HTN donor mice and of lymphocytes in the aortic infiltrates of the HTN recipient mice. The increased collagen and LOX expression in recipient mice suggest that the adoptively transfer CD4⁺ lymphocytes are associated with vascular extracellular matrix remodeling. Furthermore we examined the role of Th17 lymphocyte in aortic LOX regulation in Angiotensin II-induced hypertension. The Increase in blood pressure and Velocity Time Integral (VTI) was measured in WT Angiotensin II treated mice whereas no change was detected in the Th17 deficient (RORT KO) Angiotensin II treated group. When compared to the control group the WT group infused with Angiotensin II had higher LOX protein expression, LOX fluorescent Immunohistochemical stain and LOX activity. This group also had increased hydroxyproline levels, collagen stain, hyperplasia and aortic thickening. In contrast, the Th17 deficient mice Angiotensin II treated group had no changes in these parameters. The results provide evidence that IL-17 mediates Angiotensin II-induced hypertension and vascular dysfunction by the overstimulation of LOX. Potentially targeting T17 cells will allow for a drug-specific therapeutic approach and delay the progression of hypertension pathology.

Several members of the lysyl oxidase family of copper-dependent amine oxidases have been implicated in tumor development. The Iysyl oxidase (LOX) and LOX-like 2 (LOXL2) genes have been mapped to chromosomal regions affected by loss of heterozygosity (LOH) in several cancers, including those of the colon and esophagus. Indeed, there have been numerous reports of reduced LOX and a few reports of reduced LOXL2 expression in various cancers. Identification of microsatellite markers within the LOX locus and the LOXL2 gene allowed for evaluation ofthe status of these gene alleles in colon and esophageal tumors. There was significant LOH of the LOX locus in colon tumors that was accompanied by reduced mRNA expression and a spectrum of alterations and mutations affecting the LOX gene. This study demonstrated, for the first time, that genetic events, namely LOH, deletions and mutations ofthe LOX gene, were responsible, at least partly, for the reduction of LOX gene expression. There was also significant LOH of the LOXL2 gene in both colon and esophageal tumors. However, instead of a reduction of LOXL2 expression, there was increased expression that correlated with less differentiated tumors and absent elastosis, both indicators of poor prognosis. Further studies indicated that both LOX and LOXL2 are absent in non-invasive tumor cell lines but re-expressed in invasive cell lines, likely as part of the thelial-mesenchymal transition that occurs in the last steps of tumorigenesis to facilitate metastasis. The results presented and research strategy outlined in this dissertation will define the importance of LOXL2 amine oxidase activity and protein interactions in the critical but poorly understood process oftumor cell migration and invasion.

Abstract Lysyl hydroxylase (E.C. 1.14.11.4) catalyzes the formation of hydroxylysine in collagens and other proteins with collagenous domains. The resulting hydroxylysine residues participate in the formation of collagen crosslinks, and serve as attachment sites for carbohydrate units. They have been regarded as non-essential, since the absence of lysyl hydroxylase 1 activity is not lethal, although it leads to the kyphoscoliotic type of Ehlers-Danlos syndrome, and since recombinant collagens I and III lacking any hydroxylysine form native-type fibrils in vitro. A novel human lysyl hydroxylase isoenzyme, lysyl hydroxylase 3, was identified, cloned and characterized here. The novel isoenzyme was expressed as a recombinant protein in insect cells, and the protein was shown to catalyze hydroxylation of lysine residues in vitro. No differences were found in the catalytic properties between the recombinant lysyl hydroxylases 3 and 1. The human lysyl hydroxylase 3 gene was shown to be 11.6 kb in size and to contain 19 exons. The introns contain 15 full-length or partial Alu retroposons, which are known to be involved in most human gene rearrangements that occur by homologous recombination. The three recombinant human lysyl hydroxylase isoenzymes were isolated here for the first time as homogenous proteins. Limited proteolysis data suggested that the lysyl hydroxylase polypeptides might consist of at least three distinct domains, A-C. The N-terminal domain A was found to play no role in lysyl hydroxylase activity as a recombinant B-C polypeptide was a fully active hydroxylase. This work also confirmed that lysyl hydroxylase 3 has collagen glucosyltransferase activity as well as trace amounts of collagen galactosyltransferase activity. However, the levels of these activities were so low that their biological significance remains to be determined. In the last part of this work, lysyl hydroxylase 3 knock-out mice were produced and analyzed. The homozygous null embryos were found to die at a very early stage of development due to lack of type IV collagen in the basement membranes. The data demonstrated that hydroxylysine formed by lysyl hydroxylase 3 is essential for early mouse development and that lysyl hydroxylase 1 or 2 cannot compensate for the lack of its function.

Abstract Lysyl hydroxylase (LH) catalyzes the post-translational formation of hydroxylysines in collagens and collagenous proteins. Three lysyl hydroxylase isoforms, LH1, LH2 and LH3, have been identified from different species. In addition, LH2 has two alternatively spliced forms, LH2a and LH2b. The hydroxylysines have an important role in the formation of the intermolecular collagen crosslinks that stabilize the collagen fibrils. Some of the hydroxylysine residues are further glycosylated. In this thesis the substrate amino acid sequence specificities of the LH isoforms were analyzed using synthetic peptide substrates. The data did not indicate strict amino acid sequence specificity for the LH isoforms. However, there seemed to be a preference for some sequences to be bound and hydroxylated by a certain isoform. Galactosylhydroxylysyl glucosyltransferase (GGT) catalyzes the formation of glucosylgalactosylhydroxylysine. In this study, LH3 was shown to be a multifunctional enzyme, possessing LH and GGT activities. The DXD-like motif, characteristic of many glycosyltransferase families, and the conserved cysteine and leucine residues in the N-terminal part of the LH3 molecule were critical for the GGT activity, but not for the LH activity of the molecule. The GGT/LH3 protein level was found to be decreased in skin fibroblasts and in the culture media of cells collected from members of a Finnish epidermolysis bullosa simplex (EBS) family, which was earlier reported to have a deficiency of GGT activity. In this study, we showed that the reduction of enzyme activity is not due to a mutation or lower expression of the LH3 gene. Our data indicate that the decreased GGT/LH3 activity in cells has an effect on the deposition and organization of the key extracellular matrix components, collagen types VI and I and fibronectin, and these changes are transmitted to the cytoskeletal network. These findings underline LH3 as an important extracellular regulator.

L’angiogenèse est un processus majeur intervenant au cours du remodelage du microenvironnement tumoral, induit par l’hypoxie et le VEGF. La lysyl oxydase like-2 (LOXL2) appartient à la famille des lysyl oxydases, impliquée dans le pontage de constituants matriciels. Notre équipe a montré que l’induction de LOXL2 par l’hypoxie conduit à sa sécrétion par les cellules endothéliales et son accumulation dans la matrice extracellulaire endothéliale. Nous avons montré que LOXL2 joue un rôle dans l’angiogenèse au cours du développement. Des études ont montré que LOXL2 est surexprimée dans de nombreux cancers et que l’inhibition de LOXL2 extracellulaire empêche la formation d’un microenvironnement tumoral. Mon travail de thèse a porté sur l’étude du rôle de LOXL2, exprimée par les cellules endothéliales et tumorales, au cours de l’angiogenèse dans le carcinome du rein à cellules claires (ccRCC) humain. Nous avons montré que LOXL2 est exprimée à la fois par les cellules stromales et tumorales dans le ccRCC humain, mais aussi que LOXL2 pourrait jouer un rôle spécifique en fonction de son origine cellulaire dans ces tumeurs. L’étude de la contribution de LOXL2 endothéliale nous a permis de démontrer que LOXL2 promeut l’angiogenèse in vitro et in vivo dans le ccRCC, avec une implication partielle de son activité catalytique dans ce processus. Nous avons montré que LOXL2 sécrétée par les cellules tumorales stimule l’angiogenèse in vitro et in vivo, avec la participation de son activité catalytique, notamment en modulant la prolifération des cellules endothéliales. LOXL2 endothéliale et tumorale promeuvent l’angiogenèse dans le ccRCC, dépendamment ou non de son activité catalytique. / Angiogenesis is a major process in microenvironment remodeling which is mainly induced by hypoxia and VEGF. Lysyl oxidase like-2 (LOXL2) belongs to lysyl oxidase family involved in extracellular matrix crosslinking. Our team previously described that LOXL2 is a hypoxia-target, which is secreted by endothelial cells and accumulated into endothelial extracellular matrix. We also demonstrated that LOXL2 stimulates developmental angiogenesis. Moreover, several studies showed that LOXL2 is overexpressed in many cancers and inhibition of extracellular LOXL2 impedes the formation of a tumor microenvironment. My PhD work focused on the contribution of LOXL2 secreted by stromal cells (endothelial cells and cancer associated fibroblasts) and tumor cells in clear cell renal cell carcinoma (ccRCC) angiogenesis. ccRCC is a highly vascularized and metastatic tumor. We showed that LOXL2 is expressed both by stromal and tumor cells in ccRCC and might play a specific role depending on its cellular origin in these tumors. Then we demonstrated that LOXL2 secreted by endothelial cells promotes angiogenesis in vitro and in vivo with a partial contribution of its catalytic activity. We also demonstrated that LOXL2 secreted by tumor cells stimulates angiogenesis in vitro and in vivo and that LOXL2 catalytic activity is involved in this process, notably modulating endothelial cells proliferation. Moreover, we showed that endothelial and tumor LOXL2 regulate several signaling pathways implicated in different steps of the angiogenic process.Both tumor and endothelial LOXL2 are involved in angiogenesis of ccRCC, in a dependent or independent catalytic activity manner.