Fusarium graminearum is responsible for causing Fusarium head blight in cereals and maize imposing a significant impact in Canadian agriculture. While a handful of secondary metabolites produced by F. graminearum are recognized as contributors to disease virulence, the functions of numerous molecular products arising from biosynthetic gene clusters expressed during infection remain undiscovered. Presented here are the results of CRISPR-Cas9 mediated gene-deletion experiments disrupting core biosynthetic genes from four biosynthetic gene clusters with reported in-planta transcription: C08, C16, C13 and C70. Both wheat head infection assays and coleoptile infection assays were used to evaluate the pathology phenotypes of transformant strains illustrating potential links between C16 and pathogenicity. Culture medium screening experiments using transformant strains were profiled by UHPLC-HRMS and targeted MS2 experiments to confirm the associated secondary metabolite products and attempt to identify unknown secondary metabolites of the biosynthetic gene clusters. While C08 secondary metabolite remained elusive, confirmation of C16 secondary metabolites led to hypotheses regarding their potential connections to the inhibition of plant immune response and untargeted secondary metabolite profiling of the C13/C70 transformant strains suggests that this BGC may have significant implications for global secondary metabolite production.

Poplar (Populus spp. and hybrids) are used for pulp, paper and solid wood products. Furthermore, poplar is being developed as a dedicated biomass crop for biofuels and biomaterials. Thus, methods to accelerate genetic improvement to improve woody biomass yield, quality and optimal growth on marginal lands are of considerable interest. One approach is to identify genes that could be manipulated through breeding or biotechnology to achieve these goals. I studied two sets of candidate genes for improving biomass, growth and manipulating flowering time. First, I studied the functions of PopNAC154 and PopNAC156, co-orthologs of Arabidopsis SECONDARY CELL WALL NAC DOMAIN2 (SND2), which are putative regulators of wood cell wall synthesis, the source of lignocellulosic biomass. Second, I studied PopCEN1, PopCEN2, and PopBFT, members of the TERMINAL FLOWER1 (TFL1)/CENTRORADIALIS (CEN) gene family that act as flowering repressors in Arabidopsis and many plants. I studied INRA 717-1B (P. tremula x P. alba) transgenics with an artificial microRNA (AmiRNA) downregulating PopNAC154 and PopNAC156 (AmiSND2 trees). In a field trial, AmiSND2 trees showed higher mean height and diameter than wild-type (WT). We also observed that AmiSND2 transgenics showed delayed leaf senescence and leaf drop. After conducting controlled environment studies with AmiSND2 trees, I was able to confirm that downregulation of PopNAC154 and PopNAC156 genes does not alter the short daylength-induced bud set and growth cessation but it delays the low temperature induced leaf senescence and leaf drop. Further I was able to show that down regulation of the PopNAC154 and PopNAC156 genes resulted in significantly higher mean plant heights and delayed bud set compared to the WT plants under low soil nutrient conditions. Wood chemistry data analysis of field grown AmiSND2 trees showed that they have a significantly higher cellulose content a lower lignin content compared to that of the WT. Thus, these results show that downregulating the PopNAC154 and PopNAC156 genes has the potential to increase biomass yield and quality. In a previous study, simultaneous downregulation of PopCEN1 and PopCEN2 genes using RNA interference (RNAi) method caused poplar trees to flower only after two years of growth in the field. I used CRISPR/CAS9 method to knock-out each paralog individually as well as the related gene, PopBFT. The popcen1 mutant trees developed flowers even under in vitro conditions, but popcen2 mutants did not show an obvious phenotype. popbft mutant trees also did not show an obvious phenotype under standard growing conditions. However, when soil nutrient availability was allowed to deplete, the popbft mutants showed lower mean plant height compared to the WT and also showed lower root length and root volume under low Nitrogen conditions in an in vitro assay compared to the WT. These results prove that PopCEN1 gene is directly involved in repressing flowering in poplar and allele-specific mutation should be tested as an approach to accelerate breeding. PopCEN2 and PopBFT might not have a role in regulation of flowering time, and though additional studies are needed, PopBFT appears to have a role in regulating growth in response to nutrient availability. / Master of Science / Poplar (Populus spp. and hybrids) are used for pulp, paper and solid wood products. Furthermore, poplar is being developed as a dedicated biomass crop for biofuels and biomaterials. Genes control the woody biomass yield, and quality among all the other characteristics, thus, methods to accelerate genetic improvement to improve these characteristics is paramount. One approach is to identify genes that could be manipulated through breeding or biotechnology to achieve these goals. I studied two sets of candidate genes for improving biomass, growth and manipulating flowering time. First, I studied the functions of PopNAC154 and PopNAC156, genes which are putative regulators of wood cell wall synthesis, the source of lignocellulosic biomass. Second, I studied PopCEN1, PopCEN2, and PopBFT, genes that act as flowering repressors in Arabidopsis and many plants. I studied a genetically modified poplar, where PopNAC154 and PopNAC156 genes’ function were reduced. After subjecting these plants to shorter daylength periods and cold temperatures in controlled conditions I was able to show that decreased activity of the PopNAC154 and PopNAC156 genes causes the trees to slowdown the leaf senescence and retain their leaves under low temperature conditions compared to the genetically unaltered wildtype (WT) poplar. I was also able to show that decreased activity of the PopNAC154 and PopNAC156 genes allow the poplar plants to grow better than the WT plants under low soil nutrient conditions. I used gene editing to switch off PopCEN1, PopCEN2, and PopBFT genes. When PopCEN1 gene was switched off individually the young mutant trees flowered whereas normally trees take six to eight years to flower. However, when the PopCEN2, and PopBFT genes were switched off individually the resulting mutant plants did not show any signs of flowering. Hence, I was able to show that PopCEN1 gene is directly involved in repressing the flowering in poplar plants. In conclusion, my work identified PopNAC154 and PopNAC156 as candidate genes for manipulation by breeding or biotechnology to increase wood yield, and suggested ways to induce flowering to accelerate breeding through manipulation of PopCEN1.

Macrophage migration inhibitory factor (MIF) has been implicated in mediating both innate and adaptive immune responses in inflammatory and infectious diseases. The sequence and structure of MIF is highly conserved across the avian phylogeny, which underlies high sequence homology and functional similarities between turkey and chicken MIFs. Turkey MIF (TkMIF) inhibited cell migration and promoted cell proliferation with production of inflammatory mediators, comparable to the biological properties of chicken MIF (ChMIF), thus indicating the biological cross-reactivity between turkey and chicken MIFs. This study identified the cell surface receptor(s) that could bind ChMIF and the biological roles triggered by such interactions. In addition to CD74, a previously identified receptor, CXCR4 also interacts with ChMIF. Moreover, the formation of receptor complexes was shown between CXCR4 and CD74. MIF signaling through CXCR4 and CD74 led to cell chemotaxis and proliferation activity as well as intracellular calcium influx. Intriguingly, Eimeria MIF (EMIF), a homologue secreted following parasitic infection, also interacted with CD74 leading to comparable biological functions to those of ChMIF. Given such observations, we hypothesized that CXCR4 and CD74 are receptors for ChMIF leading to the functional consequences similarly manifested by EMIF interaction with the corresponding receptors. EMIF, predominantly secreted from the invasive merozoite stage, may help the parasite exploit the host immune response by interacting with common ChMIF receptors. This may lead to functional mimicry thus provoking the question of whether EMIF would modulate the biological functions of ChMIF to manipulate the host defense that allows more efficient invasion of the host. To evaluate this concept, a transgenic E. tenella lacking MIF was generated by in vivo passage of E. tenella transfected with a CRISPR plasmid targeting EMIF. Although not fully disrupted, reduction of EMIF expression was observed in the transgenic E. tenella itself as well as in inoculated cells, which resulted in enhanced survival of host cells. Herein, we achieved a better characterization of the functional roles of both avian and parasite MIFs underlying the interaction with common host receptors, along with the essential role of parasite MIF promoting host cell death during parasitic infection. / PHD / When animals get infected or injured, their immune system senses invading pathogens or damaged tissues as danger signals, which often elicits the production of inflammatory mediators. These are chemical messengers secreted mostly by immune cells that initiate cellular communication and infiltration of immune cells to the infection/damaged site leading to inflammatory responses to eliminate the infectious agents and repair damaged tissues. Among many inflammatory mediators, macrophage migration inhibitory factor (MIF) is involved in inflammatory and immune response by regulating cell migration. Interestingly, MIF is secreted by Eimeria parasites (that cause the costly coccidiosis disease in poultry) as well as by chickens (host animal) after infection with this pathogen. Toward a better understanding of the impacts of both avian and parasite MIFs on the host immune response, three specific studies were completed. First, MIF displayed high degree of gene sequence identity and functional similarity between chicken and turkey, supporting the evolutionarily conservation of MIF across birds. The second study identified the MIF receptors and their complexes, which engage in the biological functions of chicken MIF. Through binding to these cell surface receptors, chicken MIF can regulate cell migration and proliferation with calcium release. Intriguingly, Eimeria MIF secreted after parasitic infection is able to bind the same receptors leading to comparable biological functions to those of chicken MIF. Lastly, the role of Eimeria MIF was further evaluated by disrupting its gene in the parasite. Although not fully disrupted in the transgenic parasites, its expression was decreased resulting in enhanced survival of host cells, thus suggesting a deleterious effect of Eimeria MIF on the host, as well as its potential as a therapeutic target to control coccidiosis in poultry.

As integrinas constituem uma família de receptores de membrana que tem como função primária a adesão de células a proteínas da matriz extracelular e alguns de seus membros estão envolvidos nos processos de diferenciação osteoblástica e formação óssea, eventos diretamente relacionados à osseointegração de implantes de titânio (Ti). Sabe-se que superfícies de Ti com nano e microtopografia podem favorecer a diferenciação osteoblástica e a mineralização da matriz extracelular. No entanto, os mecanismos celulares envolvidos nesses processos não são completamente entendidos. Neste contexto, os objetivos deste estudo foram: (1) caracterizar as superfícies de Ti com nano (Ti-Nano) e microtopografia (Ti-Micro), (2) investigar a participação da integrina V na diferenciação osteoblástica induzida pelo Ti-Nano e (3) investigar a participação da integrina β3 na diferenciação osteoblástica induzida por Ti-Nano e Ti-Micro. Para isso, discos de Ti-Nano e Ti-Micro foram preparados por ataque ácido com H2SO4/H2O2 ou com HNO3/H2SO4 / HCl, respectivamente, e caracterizados quanto à topografia, rugosidade e composição química de superfície. Discos de Ti usinados foram usados com controle (Ti-Controle) em alguns experimentos. Células-tronco mesenquimais derivadas de medula óssea de ratos foram cultivadas sobre as três superfícies de Ti e foi avaliada a expressão gênica de componentes envolvidos na via de sinalização das integrinas por PCR array. Com base nos resultados do PCR array, as integrinas αV e β3 foram selecionadas e silenciadas por RNA de interferência (shRNA) ou CRISPR/Cas9, respectivamente, em células pré-osteoblásticas da linhagem MC3T3-E1 para investigarmos a participação dessas integrinas na diferenciação osteoblástica induzida por superfícies de Ti com diferentes topografias. Os resultados deste estudo mostraram que os tratamentos empregados foram eficientes para a produção de superfícies de Ti com topografias nas escalas nano e micrométrica. Além disso, foi demonstrado que o maior potencial osteogênico do Ti-Nano se deve, ao menos em parte, à integrina αV, uma vez que seu silenciamento reduziu a diferenciação osteoblástica induzida pela nanotopografia. Por fim, também demonstramos que a via de sinalização ativada pela integrina β3 exerce um papel fundamental no potencial osteogênico do Ti-Nano, mas não do Ti-Micro. O silenciamento da integrina β3 reduziu a diferenciação osteoblástica, concomitantemente com a regulação negativa da expressão de vários componentes das vias de sinalização de Wnt e de BMP, apenas nas células crescidas sobre a nanotopografia. Em conjunto, nossos resultados revelam um novo mecanismo para explicar a maior diferenciação osteoblástica induzida pelo Ti-Nano, que envolve uma complexa rede regulatória ativada pela maior expressão das integrinas αV e β3, esta última gerando ativação da transdução de sinal das vias de Wnt e de BMP / Integrins are a family of membrane receptors that primarily mediate cell adhesion to extracellular matrix proteins and some members are involved in the process of osteoblast differentiation and bone formation, key events of titanium (Ti) implant osseointegration. It is well known that Ti surfaces with nano and microtopography may favor osteoblast differentiation and matrix mineralization. However, the cellular mechanisms involved in this process are not entirely understood. In this context, the aims of this study were: (1) to characterize the Ti surfaces with nano (Ti-Nano) and microtopography (Ti-Micro), (2) to investigate the participation of integrin V on osteoblast differentiation induced by Ti-Nano and (3) to investigate the participation of integrin β3 on osteoblast differentiation induced by Ti-Nano and Ti-Micro. Discs of Ti-Nano and Ti-Micro were prepared with acid etching with H2SO4/H2O2 or with HNO3/H2SO4 / HCl, respectively, and characterized in terms of surface topography, roughness and chemical composition. Machined Ti discs (untreated) were used as control (Ti-Control) in some experiments. Mesenchymal stem cells from rat bone marrow were cultured on Ti discs with the three different surfaces and the gene expression of members of the integrin signaling pathway was evaluated by PCR array. Based on PCR array results, the integrins αV and β3 were selected and silenced using RNA interference (shRNA) or CRISPR-Cas9, respectively, in pre-osteoblastic cell line MC3T3-E1 to investigate the participation of these integrins in osteoblast differentiation induced by Ti with different surface topographies. The results showed that the treatments used were efficient to generate Ti surfaces with topographies at the nano and micrometric scales. We showed that the higher osteogenic potential of Ti-Nano may be, at least in part, due to the integrin &alphaV, since its silencing reduced the osteoblast differentiation induced by nanotopography. We also demonstrated that the signaling pathway triggered by integrin β3 plays a key role in the osteogenic potential of Ti-Nano, but not of Ti-Micro. The silencing of integrin β3 reduced the osteoblast differentiation concomitantly with the negative regulation of the gene expression of several Wnt and BMP signaling components only in cells grown on Ti-Nano. Taken together, our results uncover a novel mechanism to explain the higher osteoblast differentiation induced by Ti-Nano that involves a complex regulatory network triggered by integrins αV and β3 upregulation, with the integrin β3 activating the Wnt and BMP signal transductions

A produção de proteínas terapêuticas recombinantes compreende moléculas complexas e de alto valor agregado, incluindo a enzima glucocerebrosidase (GCase). Sua deficiência resulta na Doença de Gaucher, passível de tratamento por meio da terapia de reposição enzimática. A forma ativa da GCase recombinante usada na terapia apresenta resíduos terminais de manose expostos no seu perfil de glicosilação. Perfil este que espera-se ser reproduzido por meio da construção de uma linhagem de Pichia pastoris com um padrão de glicosilação humanizado, por meio da deleção de dois genes envolvidos no sistema de glicosilação da levedura: alg3 e och1, responsáveis pela posterior hiper-manosilação característica desse organismo. Assim, a expressão da GCase será usada como modelo no desenvolvimento desta linhagem de Pichia pastoris que permita a expressão de glicoproteínas com um perfil humanizado específico de glicosilação. Além da produção da linhagem mutante pela técnica de CRISPR/Cas9, propomos a construção de duas linhagens controle: uma expressando a proteína GCase para análise do seu padrão selvagem de glicosilação em P. pastoris e outra expressando a proteína Cas9 de Streptoccocus pyogenes (SpCas9). A linhagem P. pastoris/GCase foi construída testando-se duas sequências sinal de secreção diferentes: fosfatase alcalina (PHO1) e albumina humana (Alb). Resultados de western blot mostraram a GCase no lisado celular e baixos níveis de proteína secretada no sobrenadante de cultura, sendo mais expresso na linhagem contendo a sequência PHO1. A linhagem P. pastoris/SpCas9 foi construída e a enzima SpCas9 foi detectada via western blot no lisado celular após indução com metanol. Para a produção da linhagem com padrão de glicosilação humanizado propôs-se a deleção dos genes alg3 e och1 e a inserção, pela via de reparo por recombinação homóloga (HDR), de marcas de resistência aos antibióticos higromicina ou canamicina. Para tal, propusemos a construção de dois vetores finais de expressão do sistema CRISPR/Cas9 em P. pastoris, cada um contendo a enzima SpCas9 e os RNAs guia (gRNAs) para deleção do gene alg3 ou och1, e também a construção de dois fragmentos para HDR contendo o gene de resistência ao antibiótico flanqueado por regiões de 1Kb de homologia com a região de deleção do gene alg3 ou och1. A construção dos vetores e fragmentos para HDR foram inicialmente feitas por meio de técnicas de clonagem clássica. No entanto, apesar de inúmeras tentativas, resultados de PCR e sequenciamento mostraram o insucesso das construções. Partiu-se então para a técnica de Gibson Assembly®, através da qual os dois fragmentos para HDR foram construídos. Porém, os vetores de expressão contendo SpCas9 e os gRNAs ainda apresentam dificuldades na sua construção. Esforços ainda estão sendo feitos para a construção dos vetores e consequente tentativa de estabelecimento das linhagens mutantes. O sucesso no estabelecimento de um sistema de expressão de proteínas heterólogas com este padrão de glicosilação humano específico permitirá a obtenção e possível comercialização da GCase em sua forma terapêutica. Além disso, permitirá possíveis edições genômicas futuras para um padrão de maior complexidade de glicosilação humanizado, criando uma plataforma nacional para produção de outras glicoproteínas terapêuticas de interesse biotecnológico. / The production of therapeutic recombinant protein comprises complex and high valued molecules, including the glucocerebrosidase enzyme (GCase). Its deficiency results in Gaucher Disease, susceptible of treatment by enzymatic replacement therapy. The active form of recombinant GCase employed in therapy presents exposed terminal mannose residues in its glycosylation pattern. We hope to reproduce such pattern by constructing a Pichia pastoris strain with a specific human glycosylation pattern through the deletion of two genes involved in yeast glycosylation system, alg3 and och1, responsible for the final hyper-mannosylation characteristic of this organism. Therefore, the expression of GCase will be a case model for the development of the recombinant Pichia pastoris strain that could allow the expression of glycoproteins with a specific humanized glycosylation profile. Despite the establishment of the mutant strain using the CRISPR/Cas9 technique, we propose the construction of two control strains: one expressing the GCase protein for analysis of its wild type glycosylation pattern and another one expressing the Cas9 protein from Streptoccocus pyogenes (SpCas9). The P. pastoris/GCase strain was constructed testing two different secretion signal sequences: alkaline fosfatase (PHO1) and human albumin (Alb). Western blot results have shown GCase in cell lysate and in low expression levels in culture supernatant, being more expressed in the strain containing the PHO1 signal sequence. P. pastoris/SpCas9 strain was constructed and SpCas9 enzyme was detected via western blot in cell lysate after the induction with methanol. To produce the strain with the humanized glycosylation pattern, the deletion of alg3 and och1 genes was proposed along with the insertion, by homology directed repair pathway (HDR), of hygromycin and kanamycin antibiotics resistance marks. In order to do so, we have proposed the construction of two final expression vectors of the CRISPR/Cas9 system in P. pastoris, each one containing SpCas9 enzyme and the guide RNAs (gRNAs) for deletion of alg3 or och1, and also the construction of two fragments for HDR containing the antibiotics resistance gene flanked by 1Kb regions of homology with the deleted regions of alg3 or och1. Vectors and HDR fragments constructions were initially performed using classic cloning techniques. However, despite numerous tries, PCR and sequencing results have shown the failure of the constructions. Then, we moved on to the Gibson Assembly® technique, through which the two HDR fragments were built. Still, the expression vectors containing SpCas9 and the gRNAs presented difficulties in its assembly. Efforts continue to be made to successfully construct the remaining vectors and to establish the mutant lineage. Success in the establishment of a heterologous protein expression system with specific human glycosylation pattern will allow the obtainment and possible commercialization of the therapeutic form of GCase. Furthermore, it will also allow possible future genomic editing to a high complexity human glycosylation pattern, creating a national platform for the production of other therapeutic glycoproteins of biotechnological interest.

L’adrénoleucodystrophie liée à l’X (X-ALD) est une maladie neurodégénérative sévère caractérisée par une accumulation d’acides gras à très longue chaîne (AGTLC), conséquence d’un défaut de β-oxydation peroxysomale. La maladie est associée à l’absence de la protéine ABCD1, transporteur ABC du peroxysome qui, tout comme son homologue le plus proche, ABCD2, participe à l’import des AGTLC-CoA au sein du peroxysome, l’unique site de leur dégradation par β-oxydation. La compréhension des mécanismes physiopathologiques est aujourd’hui limitée par le manque de modèles expérimentaux pertinents, cellulaires ou animaux. Puisque le défaut peroxysomal dans la microglie apparait comme un événement pathogénique majeur, nous avons généré des lignées de cellules microgliales incapable de transporter et/ou β-oxyder les AGTLC au sein du peroxysome. Quatre lignées cellulaires microgliales BV-2 déficientes en ABCD1, ABCD2, ABCD1 et ABCD2 ou ACOX1 (l’enzyme limitante de la β-oxydation peroxysomale) ont ainsi été générées par édition génique par CRISPR-Cas9. Ces cellules déficientes présentent d’importants défauts biochimiques, une accumulation d’AGTLC mais aussi des changements des contenus en acides gras et cholestérol. Les analyses ultrastructurales effectuées démontrent l’existence d’importantes inclusions lipidiques et indiquent également une augmentation du nombre de peroxysomes et mitochondries dans ces cellules. Les profils transcriptomiques signalent des altérations de la plasticité de ces cellules microgliales et de leur capacité de reprogrammation métabolique en réponse à un stimulus inflammatoire. Les fonctions de phagocytose ou de présentation antigénique des cellules microgliales semblent être affectées par le défaut peroxysomal. Enfin, les résultats obtenus à l’aide de ces modèles suggèrent que l’altération du métabolisme lipidique peroxysomal modifie l’organisation des membranes cellulaires. Ces lignées cellulaires apparaissent donc comme des modèles prometteurs, d’un grand intérêt pour la compréhension de la physiopathologie et l’identification de cibles thérapeutiques de cette maladie neurodégénérative complexe. / X-linked adrenoleukodystrophy (X-ALD) is a severe neurodegenerative disorder characterized by very-long-chain fatty acid (VLCFA) accumulation resulting from a peroxisomal β-oxidation defect. The disease is caused by mutations in the ABCD1 gene, which encodes for a peroxisomal half ABC transporter predicted, like its closest homologue ABCD2, to participate in the entry of VLCFA-CoA into the peroxisome, the unique site of their β-oxidation. Progress in understanding the physiopathogenesis of X-ALD suffers from the lack of appropriate cell and animal models. Since peroxisomal defects in microglia seem to be a key element of the onset of the disease, we generated four microglial cell lines unable to transport and/or β-oxidize VLCFA into the peroxisome. BV-2 microglial cells were engineered with CRISPR-Cas9 to generate four microglial cell lines deficient in ABCD1, ABCD2, both ABCD1 and ABCD2 or ACOX-1 (the first rate-limiting enzyme of the peroxisomal β-oxidation system). Biochemical defects and lipid content changes associated with VLCFA accumulation but also fatty acids and cholesterol changes were identified in deficient microglia. Ultrastructural investigations confirmed cytosolic lipid inclusions and an increased number of peroxisome and mitochondria. Transcriptomic profiles of deficient microglia are indicative of an impaired plasticity and an impaired capacity to operate the metabolic shift required upon an inflammatory stimulation. Peroxisomal defect is likely to affect phagocytosis and antigen presentation capacity of microglia. Peroxisomal lipid metabolism defect is also suggested to modify cell membranes organization. Altogether, these novel mutant cell lines represent a promising model that should permit identification of new therapeutic targets for this complex neurodegenerative disease.

Les β-hémoglobinopathies (β-thalassémies et drépanocytose) sont des anémies génétiques qui touchent des milliers de nouveaux nés chaque année dans le monde. Ces maladies sont causées par des mutations affectant l'expression de l'hémoglobine chez l'adulte. Le seul traitement disponible est la transfusion sanguine à vie, associée à une chélation du fer. Pour les patients les plus touchés, la greffe de cellule souche hématopoïétique (CSH) demeure le seul traitement curatif. Néanmoins, la transplantation autologue de cellules souches génétiquement corrigées représente une alternative thérapeutique pour les patients dépourvus de donneur compatible. Certaines délétions naturelles comprenant les gènes de la β- et δ- globine dans le locus de l'hémoglobine sont corrélées à une persistance de l'expression de l'hémoglobine fœtale (HPFH) à l'âge adulte. Ainsi il a été démontré que un taux élevé d'hémoglobine fœtale (HbF) améliore l'évolution clinique de ces deux pathologies. Afin d'identifier les régions régulatrices potentielles de la γ-globine, nous avons combiné les données issues d'analyses de mutations rencontrées chez des patients HPFH avec les sites d'hybridation de facteur de transcription. Sur la base de cette analyse, en ayant recours à la technologie CRISPR/CAS9, nous avons développé un protocole permettant de générer: (i) la délétion d'un potentiel suppresseur de l'HbF situé entre les gènes des globines δ et γ, ciblé par le répresseur de l’HbF BCL11A chez les érythroblastes adultes; (ii) la plus courte délétion associée à des taux élevés d’HbF (délétion Corfu) chez les patients β-thalassemiques; (iii) une délétion de 13.6-kb rencontrée fréquemment chez les patients HPFH et incluant les gènes des globines β et δ ainsi que le potentiel suppresseur de l'HbF. Notre travail a montré que la délétion de la région génomique de 13.6-kb entraîne une forte production de HbF et une réduction concomitante de l'expression de la β-globine soit dans des lignées cellulaires érythroïdes humaines soit dans des érythroblastes primaires dérivées des cellules souches et progéniteurs hématopoïétiques (CSPH). Par ailleurs, nous avons montré que la génération de cette délétion sur des CSPHs issus de patients drépanocytaires entraîne une augmentation de la transcription de la γ-globine dans une proportion significative d'érythroblastes, conduisant à une amélioration du phénotype drépanocytaire. Enfin, nous avons exploré le mécanisme menant à la réactivation de l'expression de la γ-globine. Nous avons évalué des changements dans la conformation de la chromatine et des modifications épigénétiques dans le locus de la β-globine lors de la délétion ou de l'inversion de la région de 13.6 kb. Dans l'ensemble, cette étude contribue à la connaissance des mécanismes favorisant l'échange de l'hémoglobine fœtale à l'adulte et fournit des indices pour une approche d'édition du génome dans le traitement de la β-thalassémies et de la drépanocytose. / Β-hemoglobinopathies (β-thalassemias and sickle cell disease) are genetic anemias affecting thousands of newborns annually worldwide. β-thalassemias and sickle cell disease (SCD) are caused by mutations affecting the adult hemoglobin expression and are currently treated by red blood cell transfusion and iron chelation regiments. For patients affected by severe β-hemoglobinopathies, allogenic hematopoietic stem cell (HSCs) transplantation is the only definitive therapy. However, transplantation of autologous, genetically corrected HSCs represents an alternative therapy for patients lacking a suitable HSC donor. Naturally occurring large deletions encompassing β- and δ-globin genes in the β-globin gene cluster, defined as Hereditary Persistence of Fetal Hemoglobin (HPFH) traits, lead to increased fetal hemoglobin (HbF) expression ameliorating both thalassemic and SCD clinical phenotypes. In this study, we integrated transcription factor binding site analysis and HPFH genetic data to identify potential HbF silencers in the β-globin locus. Based on this analysis, we designed a CRISPR/Cas9 strategy disrupting: (i) a putative δγ-intergenic HbF silencer targeted by the HbF repressor BCL11A in adult erythroblasts; (ii) the shortest deletion associated with elevated HbF levels (“Corfu” deletion) in β-thalassemic patients, encompassing the putative δγ-intergenic HbF silencer; (iii) a 13.6-kb genomic region including the δ- and β-globin genes and the putative intergenic HbF silencer. Targeting the 13.6-kb region, but not the Corfu and the putative δγ-intergenic regions, caused a robust HbF re-activation and a concomitant reduction in β-globin expression in an adult erythroid cell line and in healthy donor hematopoietic stem/progenitor cells (HSPC)-derived erythroblasts. We provided a proof of principle of this potential therapeutic strategy: disruption of the 13.6-kb region in HSPCs from SCD donors favored the β-to-γ globin switching in a significant proportion of HSPC-derived erythroblasts, leading to the amelioration of the SCD cell phenotype. Finally, we dissected the mechanisms leading to HbF de-repression demonstrating changes in the chromatin conformation and epigenetic modifications within the β-globin locus upon deletion or inversion of the 13.6-kb region. Overall, this study contributes to the knowledge of the mechanisms underlying fetal to adult hemoglobin switching, and provides clues for a genome editing approach to the treatment of SCD and β-thalassemia.

A produção de proteínas terapêuticas recombinantes compreende moléculas complexas e de alto valor agregado, incluindo a enzima glucocerebrosidase (GCase). Sua deficiência resulta na Doença de Gaucher, passível de tratamento por meio da terapia de reposição enzimática. A forma ativa da GCase recombinante usada na terapia apresenta resíduos terminais de manose expostos no seu perfil de glicosilação. Perfil este que espera-se ser reproduzido por meio da construção de uma linhagem de Pichia pastoris com um padrão de glicosilação humanizado, por meio da deleção de dois genes envolvidos no sistema de glicosilação da levedura: alg3 e och1, responsáveis pela posterior hiper-manosilação característica desse organismo. Assim, a expressão da GCase será usada como modelo no desenvolvimento desta linhagem de Pichia pastoris que permita a expressão de glicoproteínas com um perfil humanizado específico de glicosilação. Além da produção da linhagem mutante pela técnica de CRISPR/Cas9, propomos a construção de duas linhagens controle: uma expressando a proteína GCase para análise do seu padrão selvagem de glicosilação em P. pastoris e outra expressando a proteína Cas9 de Streptoccocus pyogenes (SpCas9). A linhagem P. pastoris/GCase foi construída testando-se duas sequências sinal de secreção diferentes: fosfatase alcalina (PHO1) e albumina humana (Alb). Resultados de western blot mostraram a GCase no lisado celular e baixos níveis de proteína secretada no sobrenadante de cultura, sendo mais expresso na linhagem contendo a sequência PHO1. A linhagem P. pastoris/SpCas9 foi construída e a enzima SpCas9 foi detectada via western blot no lisado celular após indução com metanol. Para a produção da linhagem com padrão de glicosilação humanizado propôs-se a deleção dos genes alg3 e och1 e a inserção, pela via de reparo por recombinação homóloga (HDR), de marcas de resistência aos antibióticos higromicina ou canamicina. Para tal, propusemos a construção de dois vetores finais de expressão do sistema CRISPR/Cas9 em P. pastoris, cada um contendo a enzima SpCas9 e os RNAs guia (gRNAs) para deleção do gene alg3 ou och1, e também a construção de dois fragmentos para HDR contendo o gene de resistência ao antibiótico flanqueado por regiões de 1Kb de homologia com a região de deleção do gene alg3 ou och1. A construção dos vetores e fragmentos para HDR foram inicialmente feitas por meio de técnicas de clonagem clássica. No entanto, apesar de inúmeras tentativas, resultados de PCR e sequenciamento mostraram o insucesso das construções. Partiu-se então para a técnica de Gibson Assembly®, através da qual os dois fragmentos para HDR foram construídos. Porém, os vetores de expressão contendo SpCas9 e os gRNAs ainda apresentam dificuldades na sua construção. Esforços ainda estão sendo feitos para a construção dos vetores e consequente tentativa de estabelecimento das linhagens mutantes. O sucesso no estabelecimento de um sistema de expressão de proteínas heterólogas com este padrão de glicosilação humano específico permitirá a obtenção e possível comercialização da GCase em sua forma terapêutica. Além disso, permitirá possíveis edições genômicas futuras para um padrão de maior complexidade de glicosilação humanizado, criando uma plataforma nacional para produção de outras glicoproteínas terapêuticas de interesse biotecnológico. / The production of therapeutic recombinant protein comprises complex and high valued molecules, including the glucocerebrosidase enzyme (GCase). Its deficiency results in Gaucher Disease, susceptible of treatment by enzymatic replacement therapy. The active form of recombinant GCase employed in therapy presents exposed terminal mannose residues in its glycosylation pattern. We hope to reproduce such pattern by constructing a Pichia pastoris strain with a specific human glycosylation pattern through the deletion of two genes involved in yeast glycosylation system, alg3 and och1, responsible for the final hyper-mannosylation characteristic of this organism. Therefore, the expression of GCase will be a case model for the development of the recombinant Pichia pastoris strain that could allow the expression of glycoproteins with a specific humanized glycosylation profile. Despite the establishment of the mutant strain using the CRISPR/Cas9 technique, we propose the construction of two control strains: one expressing the GCase protein for analysis of its wild type glycosylation pattern and another one expressing the Cas9 protein from Streptoccocus pyogenes (SpCas9). The P. pastoris/GCase strain was constructed testing two different secretion signal sequences: alkaline fosfatase (PHO1) and human albumin (Alb). Western blot results have shown GCase in cell lysate and in low expression levels in culture supernatant, being more expressed in the strain containing the PHO1 signal sequence. P. pastoris/SpCas9 strain was constructed and SpCas9 enzyme was detected via western blot in cell lysate after the induction with methanol. To produce the strain with the humanized glycosylation pattern, the deletion of alg3 and och1 genes was proposed along with the insertion, by homology directed repair pathway (HDR), of hygromycin and kanamycin antibiotics resistance marks. In order to do so, we have proposed the construction of two final expression vectors of the CRISPR/Cas9 system in P. pastoris, each one containing SpCas9 enzyme and the guide RNAs (gRNAs) for deletion of alg3 or och1, and also the construction of two fragments for HDR containing the antibiotics resistance gene flanked by 1Kb regions of homology with the deleted regions of alg3 or och1. Vectors and HDR fragments constructions were initially performed using classic cloning techniques. However, despite numerous tries, PCR and sequencing results have shown the failure of the constructions. Then, we moved on to the Gibson Assembly® technique, through which the two HDR fragments were built. Still, the expression vectors containing SpCas9 and the gRNAs presented difficulties in its assembly. Efforts continue to be made to successfully construct the remaining vectors and to establish the mutant lineage. Success in the establishment of a heterologous protein expression system with specific human glycosylation pattern will allow the obtainment and possible commercialization of the therapeutic form of GCase. Furthermore, it will also allow possible future genomic editing to a high complexity human glycosylation pattern, creating a national platform for the production of other therapeutic glycoproteins of biotechnological interest.

L'intérêt de l’utilisation des vecteurs viraux comme le Adeno-Associated Virus recombinant (rAAV) dans la recherche pour le traitement des maladies génétiques a conduit à une évolution rapide des méthodes de production d'AAV au cours des deux dernières décennies (Ayuso et al., 2010). Leur large biodisponibilité in vivo et leur efficacité à long terme dans les tissus postmitotiques en font de bons candidats pour de nombreuses applications de transfert de gènes. En plus, la spécificité du traitement peut être augmentée lorsque le sérotype correct est choisi pour cibler un tissu spécifique. Parmi les méthodes de production actuellement utilisées, la tri-transfection de cellules embryonnaires humaines rénales 293 (HEK293) reste la plus populaire pour l'échelle de recherche; Et la production de rAAV médiée par des baculovirus pour des échelles plus importantes. L'importance croissante des vecteurs viraux dans l'application pratique de la thérapie génique exige l'amélioration des processus de production, en particulier en ce qui concerne les rendements et la pureté du produit final. Mon travail au cours de ces quatre années a été axé sur deux points principaux: (1) améliorer les processus biotechnologiques employés dans la production de rAAV pour la recherche et les échelles d'étude préclinique et (2) tester in vitro et in vivo les applications pour le rAAV dans le l’édition de genome. L'édition de gènes médiée par des nucléases spécialement conçues offre de nouveaux espoirs pour le traitement de plusieurs maladies héréditaires monogéniques. Récemment découvert, le système CRISPR Cas9 (Clustered Regular Interspaced Short Palindromic Repeats) fournit des outils importants nécessaires pour corriger les mutations par homologie. Notre modèle canonique est la souris mdx, un modèle animal naturel de la dystrophie musculaire de Duchenne (DMD). Les mutations DMD, qui conduisent à l'absence de protéine dystrophine, entraînent une myopathie progressive et fatale. Plusieurs stratégies, allant des stratégies pharmacologiques aux stratégies de saut-d’éxon, ont tenté de renverser le phénotype et ralentisser la progression de la maladie, mais les résultats ne sont pas encore satisfaisants. Ce nouvel et puissant outil d'édition de génome peut être vectorisé par rAAV. Les résultats de la première partie ont été publiés en 2015 et 2016 et seront présentés sous la forme d'articles et pour la deuxième partie, je présenterai les résultats préliminaires et les perspectives du travail qui se poursuivra dans le laboratoire. / The interest of recombinant Adeno-Associated Virus (rAAV) vectors for research and clinical purposes in the treatment of genetic diseases have led to the rapid evolution of methods for AAV production in the last two decades (Ayuso et al., 2010). Their broad in vivo biodistribution and long-term efficacy in postmitotic tissues make them good candidates for numerous gene transfer applications. In addition, the specificity of the treatment can be increased when the right serotype is chosen to target a specific tissue. Among the production methods currently in use, tri-transfection of human embryonic kidney 293 (HEK293) cells remains the most popular for research scale; and rAAV production mediated by baculoviruses for larger scales. The increasing importance of viral vectors in the practical application of gene therapy demands the improvement of production processes, especially when it concerns the yields and purity of the final product. My work during these four years was focused in two main points: (1) improve biotechnological processes employed in rAAV production for research and pre-clinical study scales and (2) test in vitro and in vivo the applications for rAAV in the field of genome editing. Gene-editing mediated by engineered nucleases offers new hopes for the treatment of several monogenic inherited diseases. Recently discovered, the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) Cas9 system provides important tools needed to correct by homology-directed repair mutations. Our canonical model is the mdx mouse, a naturally occurring animal model of Duchenne Muscular Dystrophy (DMD). DMD mutations, which lead to the absence of the protein dystrophin, results in a progressive and fatal myopathy. Several strategies, from pharmacological to exon-skipping strategies, have attempt to revert the phenotype and slow down the disease progress, however results are not yet satisfactory. This new and powerful genome editing tool can be vectorized by rAAV. Results for the first part were published in 2015 and 2016 and will be presented in the form of articles and for the second part I will present preliminary results and perspectives for the work that will be continued in the lab.

<p>Gene regulation is a complex and tightly controlled process that defines cell function in physiological and abnormal states. Programmable gene repression technologies enable loss-of-function studies for dissecting gene regulation mechanisms and represent an exciting avenue for gene therapy. Established and recently developed methods now exist to modulate gene sequence, epigenetic marks, transcriptional activity, and post-transcriptional processes, providing unprecedented genetic control over cell phenotype. Our objective was to apply and develop targeted repression technologies for regenerative medicine, genomics, and gene therapy applications. We used RNA interference to control cell cycle regulation in myogenic differentiation and enhance the proliferative capacity of tissue engineered cartilage constructs. These studies demonstrate how modulation of a single gene can be used to guide cell differentiation for regenerative medicine strategies. RNA-guided gene regulation with the CRISPR/Cas9 system has rapidly expanded the targeted repression repertoire from silencing single protein-coding genes to modulation of genes, promoters, and other distal regulatory elements. In order to facilitate its adaptation for basic research and translational applications, we demonstrated the high degree of specificity for gene targeting, gene silencing, and chromatin modification possible with Cas9 repressors. The specificity and effectiveness of RNA-guided transcriptional repressors for silencing endogenous genes are promising characteristics for mechanistic studies of gene regulation and cell phenotype. Furthermore, our results support the use of Cas9-based repressors as a platform for novel gene therapy strategies. We developed an in vivo AAV-based gene repression system for silencing endogenous genes in a mouse model. Together, these studies demonstrate the utility of gene repression tools for guiding cell phenotype and the potential of the RNA-guided CRISPR/Cas9 platform for applications such as causal studies of gene regulatory mechanisms and gene therapy.</p> / Dissertation