L’enzyme Activation-induced cytidine deaminase (AID) initie la diversification des immunoglobulines (Ig) par l’induction de dommages à l’ADN. Alors que les lésions induites aux gènes des Ig sont cruciales pour l’établissement de réponses immunes hautement spécifiques et adaptées, ce même type de lésions provoquées ailleurs dans le génome contribue à la transformation cellulaire et à l’apparition de cancer. Les mécanismes impliqués dans la protection de l’intégrité génomique des cellules B restent à définir. D’une part, nous avons développé une approche de protéomique locus-unique en couplant une technique d’identification de protéine par biotinylation de proximité avec l’outil d’édition du génome CRISPR/Cas9. Cette technique innovante, dont nous avons fait la preuve de principe pour des loci abondants, pourra être utilisée pour identifier le protéome des différentes cibles génomiques d’AID. D’autre part, nous avons caractérisé le rôle de Parp3, Parp9 et Med1, identifiées comme partenaires d’AID, éclairant ainsi les mécanismes qui contrôlent l’activité d’AID et la réparation des lésions induites par AID lors de la diversification des Ig. / Activation-induced cytidine deaminase (AID) initiates immunoglobulin (Ig) diversification by inducing DNA damage. While on-target lesions are crucial for mounting highly specific and adaptive immune responses, off-target lesions contribute to malignant cell transformation. Despite its implications, the events following AID recruitment that enforce genome integrity in B cells remain poorly defined. It is not understood why multiple non-Ig loci bound by AID are not mutated or why AID-induced DNA lesions may lead to mutations or DNA breaks. To address this question, we developed a single-locus proteomic approach coupling proximity-dependent protein identification and genome editing (CRISPR/Cas9) to identify and compare the proteins recruited at individual genomic loci bound by AID. We performed the proof of principle of this innovative tool by identifying the proteome of abundant genomic loci. On the other hand, we functionally characterized Parp3, Parp9 and Med1, identified as AID partners, revealing novel mechanisms that tightly control AID activity and DNA repair during Ig diversification.

The mammalian epigenome is globally reprogrammed at two stages of development; this involves the erasure and re-establishment of DNA methylation by both passive and active mechanisms, including DNA repair pathways, and occurs concurrently with an increase in developmental potency. In addition to Uhrf1 and the Tet enzymes, the interplay between activation induced cytidine deaminase (AID) and the DNA repair machinery has been implicated in epigenetic reprogramming of various in vivo and in vitro systems including mouse primordial germ cells, zygotes and induced pluripotent stem cells. AID deaminates cytosine to uracil and can also deaminate methylcytosine, whereas the primary role of UNG is to maintain the integrity of the genome through erasure of uracil. In this thesis, I have aimed to investigate the role of DNA repair in demethylation. To do this I have focused on the specific role of AID and UNG in the demethylation of a static system – primed serum ESCs and a dynamic system – serum to 2i (naïve) to epiblast-like ES cells. As the role of both AID and UNG involves genomic uracil, the central theme of my thesis is the impact of accumulation of uracil on DNA methylation levels in the genome. Therefore, my first aim was to develop a quantitative method to detect low levels of genomic uracil in DNA firstly, by mass spectrometry and secondly, by whole genome sequencing. In Chapter Three, I show that the impact of deamination during DNA preparation can be minimised, such that the level of genomic ESC uracil can be accurately determined as around 12,000 uracil per genome and that, as anticipated, Ung null ESCs have almost twice the genomic uracil content of wildtype ESCs. Secondly, I address the main question which is the impact of uracil accumulation on methylation levels. In order to do this, I generate two cell lines: Ung knockout and Aid over expressing, both of which should result in an increase in genomic uracil. I demonstrate that while over expression of Aid stimulates demethylation in static system and in a dynamic demethylating system, the impact of Ung knockout is less clear. In (static) serum ESCs, loss of Ung results in hypomethylation however, in order to transition to 2i (naïve) ESCs, a process which involves demethylation of the genome, it appears the Ung is required as loss of this gene inhibits proper demethylation. As such, I conclude that UNG-mediated DNA repair functions alongside passive demethylation, by reduction of UHRF1 levels, to demethylate 2i ESCs. To probe the mechanism by which accumulation of uracil in the genome alters methylation levels, I investigate the impact of Ung KO and Aid OE on global levels of DNA damage. I show that both cell lines have a greater incidence of double strand breaks compared to a wild type cell line, and accordingly, upregulate their DNA damage response pathway and the expression of certain repair genes. I suggest that increasing genomic levels of uracil causes genomic instability and that DNA demethylation occurs as a consequence of the repair of extensive DNA damage. More broadly, I suggest that ESCs are uniquely poised, due to their heightened DNA damage response, to use uracil as an intermediate of DNA demethylation. Interestingly, I also note that the biological impact on serum ESCs of loss of Ung appears to be an increase in pluripotency.

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During my PhD, I have participated to the characterization of Pleurodeles waltl (urodele amphibian) antibody heavy chains and to the discovery of a new isotype that we named IgP. I have also demonstrated that each antibody heavy chain has its human counterpart. P. waltl IgM are the counterpart of human IgM. IgY are expressed in mucosa and are therefore the physiological counterpart of human IgA. Finally, IgP are predominantly expressed in larvae and are less diverse than IgM. These two characteristics are shared with antibodies produced by mammalian B1 cells. These studies allowed me to approach the effects of a long term spaceflight on the humoral immune response, i.e. the antibody mediated response, which up to now has been poorly studied. The Development and Immunogenetics team, JE 2537, has immunized adult P. waltl during their five month stay onboard the Mir space station and showed that heavy chain variable domains of specific IgM are encoded by genes belonging to the VHII and VHVI families. However, these families are used in different proportions in animals immunized onboard Mir by comparison to animals immunized on Earth. To better understand this difference, I have determined how these animals use their individual VHII and VHVI genes. My work revealed that only one VHII gene and four VHVI genes (A, B, C and D) are used by immunized animals. I observed an increase in the expression of IgM heavy chain mRNAs encoded by the VHII, VHVI.C and VHVI.D genes and a strong decrease in the expression of IgM heavy chain mRNAs encoded by the VHVI.A and VHVI.B genes in spaceflight animals, demonstrating that this environment affects the humoral response. These observations may be due to a change in B-cell selection under spaceflight conditions. Furthermore, I described for the first time the effects of spaceflight on somatic hypermutations. I isolated and characterized the P. waltl mRNA coding for the main effector of these mutations: the activation-induced cytidine deaminase (AID). I demonstrated that this protein is present and conserved in P. waltl. Then, I described somatic hypermutations in P. waltl. I mapped somatic hypermutations, studied their distribution and calculated their frequency in animals immunized on Earth and in animals immunized onboard the Mir space station. This work revealed a strong depression of somatic hypermutations in animals immunized onboard Mir. This observation does not result from a change in AID transcription. We believe that this may be the consequence of a lower B lymphocyte survival under spaceflight conditions. / Durant ma thèse, j'ai participé à la caractérisation des isotypes de chaînes lourdes d'anticorps chez le pleurodèle (Pleurodeles waltl, amphibien urodèle) et à la mise en évidence d'un nouvel isotype d'anticorps : les IgP. J'ai également montré que chaque chaîne lourde a son équivalent humain. Les IgM du pleurodèle sont l'équivalent des IgM humaines. Les IgY sont exprimées principalement au niveau des muqueuses tout comme les IgA humaines. Enfin, les IgP sont observées majoritairement chez les larves et ont une diversité plus faible que les IgM. Ces deux caractéristiques sont partagées avec les anticorps produits par les cellules B1. Ces travaux m'ont ensuite permis d'aborder l'impact d'un séjour de longue durée dans l'espace sur la réponse immunitaire humorale, c'est-à-dire la réponse médiée par les anticorps qui, jusqu'à présent, a été très peu étudiée. L'équipe Développement et Immunogénétique, JE 2537, a immunisé des pleurodèles lors d'un séjour de 5 mois à bord de la station spatiale Mir et a montré que les chaînes lourdes d'IgM produites en réponse à la stimulation antigénique sont fabriquées à partir de gènes des familles VHII et VHVI. Cependant ces familles sont utilisées dans des proportions différentes chez les animaux immunisés dans Mir. Mes travaux ont permis d'approfondir ces résultats par une étude des gènes VHII et VHVI utilisés dans ces chaînes lourdes. J'ai ainsi montré qu'un seul gène VHII et quatre gènes VHVI (A, B, C et D) sont utilisés par les animaux immunisés. Les gènes VHII, VHVI.C et VHVI.D sont plus exprimés chez les animaux immunisés dans Mir alors que l'expression des gènes VHVI.A et VHVI.B est fortement diminuée chez ces mêmes animaux. Ces résultats démontrent clairement que le séjour dans Mir a affecté la réponse immunitaire humorale de ces animaux. Ces observations pourraient résulter d'un changement de la distribution et de sélection des lymphocytes B dans l'espace. Par ailleurs, j'ai décrit pour la première fois les effets d'un séjour dans l'espace sur les hypermutations somatiques. Avant d'étudier ce phénomène, j'ai isolé et caractérisé chez le pleurodèle l'ARNm codant l'effecteur indispensable pour ces mutations : la protéine AID (activation-induced cytidine deaminase). J'ai ainsi montré que cette protéine est bien présente et conservée dans cette espèce. J'ai ensuite mis en évidence et caractérisé pour la première fois le phénomène des hypermutations somatiques chez le pleurodèle. Pour cela, j'ai étudié les profils des mutations observées, cartographié ces dernières et calculé leur fréquence. Ces différents critères ont été comparés entre les animaux immunisés sur Terre et les animaux immunisés à bord de la station Mir. Ainsi, j'ai pu montrer que la fréquence des hypermutations somatiques est diminuée chez les pleurodèles immunisés dans Mir. Cette diminution n'est pas due à un changement de la transcription d'AID mais pourrait être due à une diminution de la survie des lymphocytes B dans l'espace.

La prise en charge du cancer reste dépendante de l’utilisation des agents cytotoxiques, avec les analogues nucléosidiques. Au-delà de leur similarité structurelle, certains de ces composés partagent une voie métabolique commune, où la cytidine déaminase apparaît comme enzyme majeure. L’existence d’une variabilité génétique et/ou phénotypique de la CDA nous a mené à nous intéresser aux relations entre le statut CDA et l’issue clinique des patients afin de déterminer si la CDA pouvait être considérée comme biomarqueur d’issue clinique chez les patients.Nos travaux personnels ont consisté à évaluer deux techniques permettant de mesurer l’activité de la CDA. Nous avons publié le premier cas mondial de toxicités mortelles sous azacytidine chez un patient CDA-déficient, ainsi que le premier cas de déficience en CDA et de toxicités sous cytarabine causées par la présence d’une variation génétique du gène CDA chez une patiente transplantée hépatique. L’influence du statut CDA a également été étudiée chez deux patients traités par azacytidine. Concernant la gemcitabine, nous avons démontré l’impact délétère en terme d’efficacité de l’augmentation de l’activité CDA chez les patients, ainsi que les résultats d’une étude multicentrique prospective dont le but était de déterminer si la CDA pouvait être un marqueur prédictif de l’apparition des toxicités sous gemcitabine, avec une étude pharmacocinétique en support. Les travaux préliminaires du pyroséquençage partiel de la CDA sur technologie Roche® sont présentés. L’ensemble de ces travaux de thèse confirme l’intérêt d’évaluer le statut CDA chez les patients susceptibles de recevoir une thérapie à base d’analogues nucléosidiques. / Nowadays, the management of cancer pathology remains largely dependent on the use of cytotoxic agents, including nucleoside analogs, used in a variety of settings. Beyond their structural similarity, some of these compounds also share a common metabolic pathway, wherein the cytidine deaminase (CDA) plays a pivotal role. The existence of constitutional genetic and / or phenotypic variability in CDA prompted us to study the relationships between the CDA status and clinical outcome in patients, and to determine if the constitutional CDA could be considered as a biomarker of efficacy and toxicity in patients treated with this class of drugs.Our personal work first consisted in evaluating two methods to measure the CDA enzymatic activity, in terms of robustness and cost. Then we published the first case-report of life-threatening toxicities in a CDA-deficient patient treated with azacytidine, and the first case of CDA deficiency and cytarabine-caused toxicities correlated with presence of a genetic variation in CDA gene in a liver-transplant patient. The influence of CDA status was also assessed in two patients treated with azacytidine. Regarding gemcitabine, we present the impact of an increase in CDA activity on loss of efficacy in patients, and the results of a prospective multicenter study whose purpose was to determine whether the CDA could be a predictive marker of the occurrence of gemcitabine-toxicities, with a pharmacokinetic study support. Finally, preliminary data on partial Roche®-pyrosequencing of CDA, also presented.All these thesis work confirms the interest to evaluate the CDA status in patients likely to receive a nucleosidic analogues-based therapy.

APOBEC3s (A3s) are a family of human cytidine deaminases that play important roles in both innate immunity and cancer. A3s protect host cells against retroviruses and retrotransposons by deaminating cytosine to uracil on foreign pathogenic genomes. However, when mis-regulated, A3s can cause heterogeneities in host genome and thus promote cancer and the development of therapeutic resistance. The family consists of seven members with either one (A3A, A3C and A3H) or two zinc-binding domains (A3B, A3D, A3D and A3G). Despite overall similarity, A3 proteins have distinct deamination activity and substrate specificity. Over the past years, several crystal and NMR structures of apo A3s and DNA/RNA-bound A3s have been determined. These structures have suggested the importance of the loops around the active site for nucleotide specificity and binding. However, the structural mechanism underlying A3 activity and substrate specificity requires further examination. Using a combination of computational molecular modeling and parallel molecular dynamics (pMD) simulations followed by experimental verifications, I investigated the roles of active site residues and surrounding loops in determining the substrate specificity and RNA versus DNA binding among A3s. Starting with A3B, I revealed the structural basis and gatekeeper residue for DNA binding. I also identified a unique auto-inhibited conformation in A3B that restricts access to the active site and may underlie lower catalytic activity compared to the highly similar A3A. Besides, I investigated the structural mechanism of substrate specificity and ssDNA binding conformation in A3s. I found an interdependence between substrate conformation and specificity. Specifically, the linear DNA conformation helps accommodate CC dinucleotide motif while the U-shaped conformation prefers TC. I also identified the molecular mechanisms of substrate sequence specificity at -1’ and -2’ positions. Characterization of substrate binding to A3A revealed that intra-DNA interactions may be responsible for the specificity in A3A. Finally, I investigated the structural mechanism for exclusion of RNA from A3G catalytic activity using similar methods. Overall, the comprehensive analysis of A3s in this thesis shed light into the structural mechanism of substrate specificity and broaden the understanding of molecular interactions underlying the biological function of these enzymes. These results have implications for designing specific A3 inhibitors as well as base editing systems for gene therapy.

Human Immunodeficiency Virus Type 1 (HIV-1), the virus that causes Acquired Immunodeficiency Syndrome (AIDS), attacks the immune system leaving patients susceptible to opportunistic infections that eventually cause death. Highly Active Antiretroviral Therapy, HAART, is the current drug strategy used to combat HIV. It is a combination therapy that includes HIV-1 Reverse Transcriptase and HIV-1 Protease inhibitors. Drug resistant strains arise that evade current HAART treatments; therefore novel drugs are needed. HIV-1 regulatory proteins such as Tat, Rev, Nef, Vpr, Vpu, and Vif are attractive new drug targets. Of particular interest is the HIV-1 Vif protein and its cellular binding partner APOBEC3G. In the absence of HIV-1 Vif, APOBEC3G, a cytidine deaminase, is able to mutate the viral cDNA and render the virus noninfectious. HIV-1 Vif binds to APOBEC3G and targets it for proteosomal degradation through an interaction with a Cullin-RING ligase complex. Blocking the HIV-1 Vif APOBEC3G interaction would allow APOBEC3G to perform its antiviral function. An attractive strategy to target the HIV-1 Vif APOBEC3G interaction would be a structure-based one. To apply structure-based drug design approaches to HIV-1 Vif and APOBEC3G, I attempted to collect high resolution structural data on HIV-1 Vif and APOBEC3G. My attempts were unsuccessful because the milligram quantities of soluble protein required were not obtained. Therefore, in Chapter III I used chemical cross-linking and mass spectrometry to probe the structural topology of HIV-1 Vif obtaining low resolution structural data. Chemical cross-linking formed HIV-1 Vif multimers including dimers, trimers, and tetramers. Analysis of the cross-linked monomer revealed that HIV-1 Vif’s N-terminal domain is a well-folded, compact, globular domain, where as the C-teriminal domain is predicted to be disordered. In addition, disorder prediction programs predicted the C-terminal domain of HIV-1 Vif to be disordered. Upon oligomerization the C-terminal domain undergoes a disorder-to-order transition that not only facilitates oligomerization but may facilitate other protein-protein interactions. In addition, HIV-1 Vif oligomerization bring Lys34 and Glu134 in close proximity to each other likely creating one molecular surface forming a “hot spot” of biological activity. In Chapter IV I confirmed my low resolution structural data via peptide competition experiments where I identified peptides that can be used as scaffolds for future drug design. HIV-1 Vif oligomerization is concentration dependent. The HIV-1 Vif peptides Vif(29-43) and Vif(125-139) were able to disrupt HIV-1 Vif oligomerization, which confirms the low resolution structural data. HIV-1 Vif peptides Vif(25-39) and Vif(29-43) reduced the amount of APOBEC3G immobilized on the Protein A beads, reduced the amount of HIV-1 Vif interacting with APOBEC3G, or degraded APOBEC3G itself. These peptides could be used as scaffolds to design novel drugs that disrupt the function of HIV-1 Vif and or APOBEC3G. Therefore, low resolution structural data and peptide competition experiments were successful in identifying structurally important domains in HIV-1 Vif. They also provided insight into a possible mechanism for HIV-1 Vif function where a disorder-to-order transition facilitates HIV-1 Vif’s ability to interact with a diverse set of macromolecules. These data advance our structural understanding of HIV-1 Vif and they will facilitate future highresolution studies and novel drug designs.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第19177号 / 医博第4019号 / 新制||医||1010(附属図書館) / 32169 / 京都大学大学院医学研究科医学専攻 / (主査)教授 武藤 学, 教授 武田 俊一, 教授 小川 誠司 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

B cells play crucial roles in the development of the two human autoimmune diseases, type 1 diabetes (T1D) and systemic lupus erythematosus (SLE). In the past decade, numerous studies showed positive responses of B cell depletion therapies in these two diseases. However, the beneficial effects are temporary and accompanied with adverse events. In this dissertation, we aimed to identify novel targets for a better modulation of disease development using mouse models. These diseases have circulating autoantibodies that are mostly mutated with an IgG isotype, indicating B cells that are producing them have been through the process of affinity maturation. Activation-induced cytidine deaminase (AID) is a core enzyme that regulates somatic hypermutation (SHM) and class switch recombination (CSR), the two key mechanisms in affinity maturation. We showed that genetic ablation of AID significantly inhibited the development of TID in NOD mice. Homologous recombination (HR) pathway is important for the repair of AID-induced DNA double strand breaks during CSR. 4,4'-Diisothiocyano-2,2'-stilbenedisulfonic acid, also known as DIDS, is a small molecule that inhibits HR pathway and subsequently leads to apoptosis of class switching cells. DIDS treatment remarkably retarded the progression of TID, even when started at a relatively late stage, indicating the potential of this treatment for disease reversal. In both approaches, we observed a notable expansion of CD73+ B cells, which exerted an immunosuppressive role and could be responsible for T1D resistance. Next we examined the effect of targeting affinity maturation through these two approaches in lupus-prone mice. The genetic abrogation of AID in BXSB mice significantly ameliorated lupus nephritis and prolonged their lifespan. AID-deficient mice also exhibited improvement on disease hallmarks with increased marginal zone B cells and more normal splenic architecture. DIDS treatment notably reduced class switching when B cells were stimulated in vitro. However, the administration of DIDS did not strikingly alter the course of SLE in either BXSB mice or MRL/lpr mice. These findings demonstrated that affinity maturation could be a potential target for T1D and SLE, while further explorations into targeting other components in the repair pathway are warranted for SLE. Lastly, we assessed the effect of maternal AID modulation on the SLE development in the offspring using BXSB mouse model. Interestingly, the absence of maternal AID resulted in offspring that developed significantly more severe lupus nephritis compared to control. The offspring born to AID-deficient dams also exhibited elevated levels of pathogenic autoantibodies and exacerbated disease features. Therefore, the modulation of maternal AID could influence the SLE development in the offspring, and future investigations are needed to determine the underlying mechanisms responsible for the disease acceleration. / Doctor of Philosophy / The failure of the immune system to differentiate self from non-self leads to the development of autoimmune diseases. Type 1 diabetes (T1D) and systemic lupus erythematosus (SLE) are complex autoimmune diseases affecting millions of people in the world. Despite intensive research regarding these two diseases, no known cure is available indicating an imperative need for the development of novel therapies. With the importance of B cells in the pathogenesis of these two diseases, intensive research focused on whole B cell depletion therapies. However, these therapies exhibited high risks of infections as a result of depleting all the B cells. In this dissertation, we sought to selectively target specific B lymphocyte subsets that are crucial contributing factors in the development of T1D and SLE. While the effect of therapeutic treatment varied among different mouse models, the genetic manipulation of specific B cells successfully retarded the progression of both T1D and SLE and extended the lifespan of the mice. Further studies shed light on the possible mechanisms that are responsible for the disease inhibition. These data proved that targeting specific B cell compartment could be a potential disease management in T1D and SLE patients. In addition, using the established mouse model, we demonstrated the modulation of maternal factors significantly impact the SLE development in the offspring. Future experiments to identify the underlying mechanisms could provide more targets for the therapeutic development.

The binding of HIV-1 Vif to the cellular cytidine deaminase Apobec3G and subsequent prevention of Apobec3G virion incorporation have recently been identified as critical steps for the successful completion of the HIV-1 viral life cycle. This interaction occurs in the cytoplasm where Vif complexes with Apobec3G and directs its degradation via the proteasome pathway or sequesters it away from the assembling virion, thereby preventing viral packaging of Apobec3G. While many recent studies have focused on several aspects of Vif interaction with Apobec3G, the subcellular localization of Vif and Apobec3G during the viral life cycle have not been fully considered. Inhibition of Apobec3G requires direct interaction of Vif with Apobec3G, which can only be achieved when both proteins are present in the same subcellular compartment. In this thesis, a unique approach was utilized to study the impact of Vif subcellular localization on Vif function. The question of whether localization could influence function was brought about during the course of studying a severely attenuated viral isolate from a long-term non-progressor who displayed a remarkable disease course. Initial observations indicated that this highly attenuated virus contained a mutant Vif protein that inhibited growth and replication. Upon further investigation, it was found that the Vif defect was atypical in that the mutant was fully functional in in vitro assays, but that it was aberrantly localized to the nucleus in the cell. This provided the basis for the study of Vif localization and its contribution to Vif function. In addition to the unique Vif mutant that was employed, while determining the localization and replication phenotypes of the differentially localized Vif proteins, a novel pathway for Vif function was defined. Copious publications have recently defined the mechanism for Vif inhibition of Apobec3G. Vif is able to recruit Apobec3G into a complex that is targeted for degradation by the proteasome. However, this directed degradation model did not fully explain the complete neutralization of Apobec3G observed in cell culture. Other recent works have proposed the existence of a second, complementary pathway for Vif function. This pathway is defined here as formation of an aggresome that prevents Apobec3G packaging by binding and sequestering Apobec3G in a perinuclear aggregate. This second mechanism is believed to work in parallel with the already defined directed degradation pathway to promote complete exclusion of Apobec3G from the virion. The data presented here provide insight into two areas of HIV research. First, the work on the naturally occurring Vif mutant isolated from a long-term non-progress or confirms the importance of Vif in in vivo pathogenesis and points to Vif as a potentially useful gene for manipulation in vaccine or therapy design due to its critical contributions to in vivo virus replication. Additionally, the work done to address the subcellular localization of Vif led to the proposal of a second pathway for Vif function. This could have implications in the field of basic Vif research in terms of completely understanding and defining the functions of Vif. Again, a more complete knowledge about Vif can help in the development of novel therapies aimed at disrupting Vif function and abrogating HIV-1 replication.