Nous nous sommes intéressés à l’étude génétique de la PR, maladie auto-immune, chronique et inflammatoire affectant principalement les articulations et entraînant leur destruction. La PR est une pathologie multifactorielle où le système HLA semble être le principal, mais non unique, facteur de prédisposition génétique.Pour la première partie de notre étude, nous nous sommes intéressés à la recherche d’association avec la PR, dans la population Algérienne, pour des polymorphismes de gènes déjà confirmés dans d’autres populations. Cette approche a permis d’établir une preuve solide d’association pour les deux SNPs les plus importants PTPN22rs2476601 et STAT4rs7574865. De plus amples études avec des échantillons élargis et l’inclusion de nouveaux polymorphismes de gènes candidats permettraient d’établir de nouvelles preuves d’association génétique avec la PR dans la population Algérienne.Dans un second temps, nous nous sommes intéressés à l’analyse familiale d’association génétique de polymorphismes de gènes présentant un différentiel d’expression dans la PR. Cette partie de l’étude représente un complément d’information pour la compréhension du fonctionnement de ces gènes et de leur implication dans la PR. Ce travail d’analyse d’association génétique a été complété par l’étude de la relation entre les génotypes des SNPs étudiés et le taux d’expression des gènes considérés.Les polymorphismes d’intérêts mis en évidence au cours de cette thèse représentent des cibles de choix pour l’analyse conjointe de la PR dans les deux populations algérienne et française en vu d’une comparaison ethnique des différents facteurs de prédisposition génétique à la PR. / We are interested in genetic study of rheumatoid arthritis “ra”, an autoimmune and chronic inflammatory disease affecting mainly joints and involving their destruction.“ra” is a multi-factor pathology in which the hla region seems to be the main but not unique genetic factor predisposition.for the first part of our study, we are interested in search of association with “ra” in the algerian population for genes polymorphisms already confirmed in other populations. this approach has allowed us establishing an association with solid evidence for the two most important snps ptpn22rs2476601 and stat4rs7574865. further studies with expanded samples and the inclusion of new genes polymorphisms candidates could establish new evidence of genetic association with pr population in algeria.in a second time, we are interested to family association analysis of genetic polymorphism gene having differential expression in pr. this part of the study represents supplementary information for understanding genes these operating and their involvement in pr. this work analysis genetics association was supplemented by the study of relationship between genotypes of snps studied and the rate of gene expression considered.polymorphisms of interest shown during this study represent good targets for a combined analysis of “ra” in both french and algerian populations to establish an ethnic comparison of various factors for genetic predisposition to “ra”.

Signals via the T cell receptor (TCR) are critical for the development of T cells in the thymus, maintenance of a self-tolerant peripheral T cell repertoire and the activation of T cells in secondary lymphoid organs. A dynamic balance between tyrosine phosphorylation and dephosphorylation is essential for the maintenance of homeostasis and proper regulation of the immune system. The cytoplasmic phosphatase, PTPN22 (protein tyrosine phosphatase non-receptor type 22) is involved in negative modulation of signal transduction through the TCR and plays a central role in regulating lymphocyte homeostasis. Genome wide association studies reveal that point mutations in PTPN22 confer an increased risk of developing multiple autoimmune diseases in humans. The precise function of PTPN22 and how mutations contribute to autoimmunity is controversial. Loss-of-function mutations in PTPN22 are associated with elevated T effector cell expansion and autoreactive B cells in both humans and mice. A thorough dissection of the molecular involvement of PTPN22 and its allelic variant R619W is important to delineate its role in autoimmunity, to this end we utilised the Ptpn22-/- mice generated in our laboratory. In order to address whether R619W allelic variant is a gain- or loss-of-function mutation, we expressed both PTPN22WT and PTPN22R619W constructs in primary activated Ptpn22-/- T lymphocytes using lentiviral transduction. Surprisingly expression of either wild type or variant phosphatase showed no affect on cytokine production. Preliminary results from bone marrow chimeras generated by retroviral expression of PTPN22WT and PTPN22R619W in Ptpn22 deficient mice showed reduced T cell activation compared to Ptpn22-/- T cells. PTPN22WT appeared to be more suppressive of T cell responses than variant PTPN22R619W. Consistent with studies conducted in comparable knock-in mouse models, our data point to the variant PTPN22R619W as being a partial loss of function allele. To elucidate the mechanism of PTPN22 action in context of an autoimmune disease, we investigated the effect of Ptpn22 deficiency on the phenotype of SKG mice. The SKG mouse harbours a point mutation (W163C) within the carboxyl terminal SH2- domain of ZAP-70, which results in decreased TCR signalling and impaired thymocyte development with defective positive and negative selection. These mice are prone to developing CD4+ T cell mediated autoimmune arthritis that closely resembles rheumatoid arthritis in humans. We found that thymus differentiation was partially restored in SKG Ptpn22-/- thymocytes and Ptpn22 deficiency enhanced TCR mediated signalling in SKG Ptpn22-/- thymocytes relative to SKG thymocytes. Consistent with increased signalling observed in the thymocytes, there was improved in vitro proliferation and IL-2 production of CD4+ T lymphocytes from SKG Ptpn22-/- mice compared to SKG mice. By contrast to SKG mice, SKG Ptpn22-/- mice developed less severe mannan-induced arthritis and showed decreased proportions of Th17 and higher numbers of regulatory T cells. These results show that removal of PTPN22 can compensate, at least partially, for the deficient ZAP-70 activity in the SKG mouse, thus linking PTPN22 and ZAP-70 to the same signalling pathway. This study advances our understanding of how manipulating TCR signals impacts on downstream T cell functions, suggesting PTPN22 may be a valuable target for the treatment of autoimmune diseases. Further studies to determine physiological role of the phosphatase and its disease-associated variants could provide insight into mechanism of immune activation, tolerance and autoimmunity.

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation eventually leading to the destruction of cartilage and bone. The aetiopathogenesis is not completely understood, but previous studies have shown that the disease is multifactorial with genetic, environmental and hormonal factors involved. Immune cells, e.g., T- and B-cells, and macrophages, migrate into the joints, with increased expression of numerous soluble factors such as cytokines, chemokines and adhesion molecules functionally active both locally and systemically. Analyses of blood samples from the Medical Biobank in Umeå from individuals before the onset of symptoms of joint disease showed that anti-citrullinated protein/peptide antibodies (ACPA) preceded the development of disease by years and this finding has been confirmed by other studies.                                         The aim of this thesis was to identify signs of activation of the immune system analysed as up-regulation of pro- and anti-inflammatory cytokines, sero-positivity for autoantibodies, and genetic factors identified as relevant for the development and disease progression of RA. The concentrations of 30 cytokines and chemokines were measured in blood samples from individuals before the onset of symptoms, and when diagnosed with RA, together with population-based matched controls using a multiplex system. The predictive value of different isotypes (IgG, IgA, and IgM) of ACPA and rheumatoid factor (RF) before onset of symptoms and different types of ACPA (e.g., mutated citrullinated vimentin, MCV) were analysed for disease development and progression in patients with early RA and controls from Northern Sweden. These factors were related to the genetic markers, HLA- shared epitope (SE) alleles and the 1858C/T polymorphism of the protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene.                            In paper I, it was shown that in individuals who later developed RA (i.e., pre-patients) the levels of several cytokines and related factors that represent the adaptive immune system (Th1, Th2, and T regulatory cell related factors) were significantly elevated compared with controls, whereas, after the onset of disease the involvement of the immune system was more general and widespread. In paper II, the presence of different isotypes (IgM, IgA and IgG) of ACPA in pre-patients, patients and controls was evaluated showing that both the IgG and IgA isotype predicted the onset of RA by years with the IgG isotype having the highest predictive value. In paper III, the association of the 1858T variant of PTPN22 with RA was confirmed. Furthermore, the association was restricted to autoantibody positive disease and this variant was correlated with an earlier age for disease onset. In paper IV, anti-MCV antibodies were identified as being associated with a more severe disease course of RA, measured by disease activity score, erythrocyte sedimentation rate, and swollen joint count over time compared with anti-CCP2, anti-CCP3, and anti-CCP3.1 antibodies.                                                                                                In conclusion, individuals who later developed RA had increased concentrations of inflammatory markers reflecting an activation of the immune system years before the clinical symptoms of the disease developed. Also, the presence of ACPA of IgG and IgA isotype prior to disease onset predicted the development of RA. The PTPN22 1858T variant was associated with sero-positive RA and anti-MCV antibodies were associated with a higher inflammatory activity compared with anti-CCP2, -CCP3 and -CCP3.1 antibodies. These findings together present a possibility to better predict the development and progression of RA.

The haematopoietic phosphatase PTPN22 is a key regulator in balancing immune responses between self-reactivity and tolerance. PTPN22 downregulates T cell signaling and harbors the non-HLA genetic variation most strongly associated with autoimmune disease in humans, the single nucleotide polymorphism R620W. The effect of this mutation is currently controversial due to confounding results in mouse and human models. The polymorphism is linked to increased susceptibility to autoimmunity in both human and mouse models, although the latter does depend on genetic background. However, mouse data clearly shows that the polymorphism has a loss-of-function effect on T cell signalling, whereas studies in human models largely demonstrate a gain-of-function effect for R620W. A confounding issue in human studies is that they depend on comparison of T cells from distinct individuals, on protein over-expression, or on RNA interference, techniques for which it is difficult to control for genetic and environmental variables, changes in stoichiometry, and off-target effects or incomplete knockdown, respectively. We aimed to create isogenic human cell lines with mutations in PTPN22 at the genomic level to alleviate the complications inherent in analysing human data. In addition to autoimmune pathogenesis, we are interested in the role of PTPN22 in a cancer setting. Because PTPN22 has a strong suppressive effect on T cell responses to weak affinity antigen, which encompass most tumour antigens, we postulated that knocking out PTPN22 may better enable T cells to kill tumour cells. Furthermore, we have shown that PTPN22 knockout (KO) leads to increased IL-2 expression in mouse T cells, and that this effect is protective against TGF-β mediated suppression, a common driver of T cell inhibition in the tumour microenvironment. T cell transfer experiments in mice showed that PTPN22 KO T cells are indeed more effective at reducing tumour size. Based on these findings, we aim to determine whether PTPN22 KO in human cells confers a similar effect on signaling. To investigate the effects of PTPN22 KO on human T cell signaling, we used CRISPR gene-editing to target PTPN22 in a Jurkat cell line. By combining this technique with lentiviral transduction of a specific T cell receptor, we generated human cell lines which are genetically identical, save for specific alterations to PTPN22, and which can be stimulated with strong or weak cognate antigen. We found that PTPN22 KO Jurkat cells develop an enhanced activation phenotype upon stimulation, including increased IL-2 expression. Additionally, PTPN22 KO Jurkat cells show enhanced Erk signalling following stimulation with weak affinity antigen, but this difference is lost as stimulus strength increases. CRISPR technology has presented the opportunity to create novel models of PTPN22 signalling in the context of human T cell lines. The data from these lines suggests that, unlike the R620W mutation, complete loss of PTPN22 has a comparable effect in human and mouse T cells. In conjunction with our previous findings, these results suggest that knocking out PTPN22 may lead to signalling alterations that improve adoptive T cell cancer therapy.

Tumor-necrosis factor (TNF)-receptor (R) associated factor 3 (TRAF3) is an important adaptor protein that plays a variety of context-dependent regulatory roles in all types of immune cells. In B cells, TRAF3 mediates signaling downstream of CD40, B cell activating factor (BAFF)-R, and toll-like receptors (TLR)s to restrain B cell survival and function. Downstream of CD40 and BAFF-R, TRAF3 negatively regulates NF-κB2 activation through NF-κB inducing kinase (NIK) stabilization. NF-κB2 activation is important for B cell-homeostatic survival. However, the constitutively active NF-κB2 in other TRAF3 deficient immune cell types does not lead to increased cell survival. More importantly, loss-of-function mutations of the TRAF3 gene are found at relatively high frequencies in B cell malignancies such as multiple myeloma and B cell lymphoma. Therefore, TRAF3 plays a critical and unique role in B cells to restrain cell survival and differentiation that contributes to B cell malignancies. In this study, we aim to identify TRAF3 modulated survival pathways that contribute to homeostatic B-cell survival and B-cell differentiation. We found that TRAF3 degradation was not sufficient or necessary to induce NF-κB2 activation. We also showed that TRAF3 degradation is dependent on association with TRAF2 and cytoplasmic tail of CD40 or BAFF-R. TRAF3 regulation of NIK is important for mature B cell development; however, NIK only partially contributes to TRAF3-mediated B cell survival. TRAF3 also regulates the protein level of proviral integrations of Moloney virus (Pim2), a pro-survival serine/threonine protein kinase encoded by the Pim2 gene, to restrain B cell survival; this regulation can operate independently of the NF-κB2 pathway. Furthermore, we showed that TRAF3 negatively regulates IL-6R signaling, a pathway that contributes to expansion of the plasma cell compartment and to the pathogenesis of multiple myeloma, a plasma cell malignancy. We found that TRAF3 facilitates recruitment of PTPN22, a tyrosine phosphatase, to associate with Jak1 following IL-6 binding to the IL-6R complex. This regulation by TRAF3 restrains plasma cell differentiation, and also provides the first demonstration that PTPN22 regulates cytokine receptor signaling. Collectively, these findings highlight the importance of TRAF3 in the regulation of B cell-specific survival and differentiation pathways. This information could be exploited for more precise and effective therapeutic choices in treatment of B cell malignancies with TRAF3 deficiencies.

Systemic lupus erythematosus (SLE) is an autoimmune rheumatic disease with systemic manifestations characterized by auto-antibodies directed against different parts of the cell nucleus including DNA, histones and ribosomes. The systemic inflammation can cause damage to multiple organs, e.g., kidneys, skin, heart, lungs and the nervous system. Rheumatoid arthritis (RA) is another autoimmune rheumatic disease characterized by auto-antibodies, mainly directed against the Fc-part of immunoglobulin G (rheumatoid factor (RF)) but also against citrullinated peptides/proteins (ACPAs). The inflammation in RA primarily involves the joints resulting in inflamed synovial tissue and destruction of cartilage. The aetiology of both SLE and RA is unclear but there is a genetic contribution predominantly of genes involved in inflammation. The diseases are believed to be multifactorial, or complex, meaning that multiple genes interact with environmental, infectious and hormonal factors, thus increasing the risk of developing disease. The aim of this study was to investigate different candidate genes involved in functions of the immune system and their relationship with SLE and RA susceptibility and severity. The patients and controls were from the four northernmost counties of Sweden, which is a fairly homogenous population well suited for genetic studies. Two single nucleotide polymorphisms (SNPs) in the oestrogen receptor α (ESR1) gene were analysed in SLE. No association was found between the SNPs and SLE per se however the minor alleles (PvuII C and XbaI G) were associated with skin manifestations and later disease onset, thus representing a milder form of the disease. A SNP in the programmed cell-death 1 (PDCD1) gene, which codes for PD-1, an inhibitory molecule involved in T-cell activation, was studied. No association was seen between the risk allele (PD-1.3A) and SLE susceptibility but a strong association was found with renal disease. A risk allele of the protein tyrosine phosphatase non-receptor type 22 (PTPN22) gene that codes for a protein called Lyp which acts as a negative regulator of T-cell receptor (TCR) signalling was significantly associated with SLE in three different case-control sets across Sweden. Both PDCD1 and PTPN22 were independently associated with renal disease. The PTPN22 gene has been associated with numerous autoimmune diseases and was evaluated in another auto-antibody producing disease, RA. From the Medical Biobank of northern Sweden samples donated before the development of symptoms of RA were identified. In these individuals, who subsequently developed RA, the 1858T risk allele in combination with ACPAs gave a high relative risk (>132) for developing RA. The association between PTPN22 and RA was confirmed in a larger material of patients with early RA. The 1858T allele, of the three SNPs investigated, was shown to be the true risk allele associated with auto-antibody positive RA. A functional role of PTPN22 in TCR-mediated activation of T cells from patients with SLE and RA was not demonstrated. In conclusion, minor alleles of two SNPs in the ESR1 gene were associated with a milder form of SLE. The risk allele in the PDCD1 gene was associated with renal disorder in SLE. The risk allele 1858T of the PTPN22 gene was associated with SLE, particularly with renal disease. The 1858T allele in combination with auto-antibodies was a risk factor for developing RA. In early diagnosed RA, the 1858T allele was highly associated with RA and in particular with auto-antibody positive RA.

Rheumatoid arthritis is a chronic inflammatory autoimmune disease. Measurement of the level of serum markers (sRAGE, S100A9, S100A8 and S100A12) and genetic testing for the presence of the PTPN22 genetic polymorphism could help elucidate the underlying cause of inflammation and complications in RA, such as atherosclerosis. Therefore, serum levels of sRAGE, S100A9, S100A8 and S100A12 were measured by ELISA in patients with established RA (n=138). The associations between the serum levels of these molecules; and inflammatory markers and RA complications were analysed by multiple linear regression modelling. Established RA patients (n=192) were investigated for the PTPN22 C1858T genetic polymorphism by PCR-RFLP. Multiple logistic regression modelling was used to examine the association between PTPN22 C1858T genetic polymorphism and inflammatory markers and RA complications. In RA patients, we found that serum levels of S100A9 were associated with the body mass index (BMI); and the presence of S100A8 and S100A12. The serum levels of S100A8 in RA patients were associated with the presence of anti-citrullinated peptide antibodies, rheumatoid factor and S100A9. The serum levels of S100A12 in RA patients were associated with the presence of anti-citrullinated peptide antibodies and S100A9; and a history of diabetes. Inflammatory markers and RA complications were not associated with the PTPN22 genetic polymorphism in established RA patients; serum level of triglyceride was the only variable associated with PTPN22 C1858T in multiple logistic regression analysis. Taken together, these data suggest that serum levels of sRAGE, S100A9 and S100A12 protein may be useful correlates of inflammation and autoantibody production in RA patients. Further studies are recommended to determine whether these markers predict clinical outcomes when measured at the onset of RA.

<p dir="ltr">Within the last decade, cancer immunotherapy, the therapeutic strategy of enhancing the body’s immune system to curb tumor growth, has reached the front lines in the war on cancer. Although common strategies such as adoptive cell transfer and immune checkpoint blockade have enjoyed success against some cancers, they regrettably lack durable efficacy across a broad patient population inflicted by heterogeneous and diverse cancer types. Moreover, application of these biological therapeutics is likewise limited due to various toxicities frequently encountered in the clinic. Taking these into account, the next generation of immunotherapies must exploit novel immunomodulatory targets and therapeutic strategies that can possess both enhanced efficacy compared to current options and more acceptable toxicity profiles in patients. Compared to biologics, small molecule inhibitors are desirable as they may circumvent concerns involving efficacy and toxicity, while allowing access to a broader arsenal of macromolecular targets. Recently, protein tyrosine phosphatase nonreceptor 22 (PTPN22), a key desensitization node in T cell signaling, has emerged as a systemic and translatable cancer immunotherapy target. Nonetheless, many of its precise functions in various immune cells is not fully resolved, thus there is a critical need for both novel chemical probes for biological interrogation and inhibitors with improved <i>in vivo </i>efficacy for further therapeutic development.</p><p dir="ltr">Built upon an overview of PTPN22’s structure, function, and value as an immunotherapy target, as well as a comprehensive assessment of reported inhibitors, this dissertation documents two separate medicinal chemistry campaigns on existing PTPN22 scaffolds. Herein, the structure activity relationships, design, and biological evaluation of a novel, superiorly selective and cell-active probe/ lead compound is disclosed. This dissertation also reports the design of a novel PTPN22 inhibitor with enhanced potency, selectivity, cellular efficacy, <i>in vivo </i>pharmacokinetics, and <i>in vivo </i>antitumor efficacy in mice. Our research efforts and the overall status and future directions of the field are also succinctly discussed.</p>

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No. of bitstreams: 1 Tese - Antonio Luiz Ribeiro Boechat Lopes.pdf: 13031715 bytes, checksum: d88fbd133c649844648684a05e01cc76 (MD5) Previous issue date: 2010-12-15 / Não Informada / Rheumatoid Arthritis (RA) is a autoimmune disease that affects 1% of worldwide population and promotes polyarthritis and joint destruction with work disability. About 60% of the risk factors of RA are related to genetic characteristics of individuals. The functional polymorphisms of the TNF gene -308 G/A andPTPN22 1858 C/T were associated with RA in several studies.The aim of this study was to investigate the influence of the TNF 308 G/A polymorphism in the promoter region of the tumor necrosis factor- gene and PTPN22 1858 C/T on rheumatoid arthritisand tuberculosis patients from the Brazilian Amazon. A total of 545 individuals 205 healthy controls without arthritis and 132 individuals suffering from rheumatoid arthritis and 208 tuberculosis patients  were genotyped for these polymorphisms using a methodology based on PCR-RFLP. Rheumatoid factor, age more than 60 years old and more than 10 disease years, was found to be risk factors for systemic disease (p=0,0001). The frequency of the A allele (TNF2) in rheumatoid arthritis sufferers was not found to be significantly higher than in the controls (p=0.671; OR=1.16; confidence interval=0.59 – 2.25). However, using a logistic regression model when the patients were stratified according to whether the manifestations were preponderantly articular or systemic, there was a strong association between the TNF2 allele and the systemic disease (p=0.001; OR=4.75; confidence interval=1.82 – 12.40) as well as the use of anti-TNF immunotherapy (p=0.021; OR 2.93; confidence interval=1.15 –7.46). On the other hand, PTPN22 1858T allele was not associated with systemicdisease (p=0,071; OR=3,17; confidence interval=0.83 – 11.73), but we found association between this allele and biologic anti-TNF immunotherapy (p=0,021; OR=4.39; confidence interval=1.08 – 17.86). Moreover, there was found no association between PTPN22 15858 C/T and rheumatoid arthritis nor tuberculosis. These results suggest that the TNF2 allele is associated with the more serious forms of the disease in individuals from the Brazilian Amazon but not with a risk for developing RA. / A Artrite Reumatoide (AR) é uma doença autoimune que afeta 1% da população geral, promovendo poliartrite e destruição articular com variados graus de incapacidade. Cerca de 60% dos fatores de risco da AR são relacionados a caracteres genéticos do indivíduo. Os polimorfismos funcionais dos genes TNF -308 G/A e PTPN22 1858 C/T foram associados à AR e à Tuberculose em diversos estudos. O objetivo deste estudo foi analisar a influência do polimorfismo da região promotora do gene do Fator de Necrose Tumoral-α, TNF -308 G/A e do gene PTPN22 1858 C/T na Artrite Reumatoide (AR) e na Tuberculose pulmonar em indivíduos procedentes do Amazonas. Para isso, foram genotipados, pela técnica baseada em PCR-RFLP para o polimorfismo TNF 308 G/A (TNF2) e PTPN22 1858T, 545 indivíduos sendo 205 controles sem Artrite, 208 pacientes com Tuberculose e 132 portadores de AR. Não foi observado aumento da frequência dos alelosTNF2ouPTPN22 1858T em portadores de Artrite Reumatoide e Tuberculose em comparação aos controles (p=0,218; p=0,376, respectivamente). Foram identificados como fatores preditivos para manifestações sistêmicas da Artrite Reumatoide: o Fator Reumatoide positivo, a idade maior que 60 anos e o tempo de doença (p=0001).Quando os dados foram estratificados segundo as formas predominantemente articulares ou sistêmicas, o alelo TNF2 esteve fortemente associado às formas sistêmicas (p=0,001; OR=4,75; Intervalo de confiança = 1,82 – 12,40), além de estar associado ao uso de imunobiológicos Anti-TNF (p=0,021; OR=2,93; Intervalo de confiança=1,15 – 7,49). O alelo PTPN22 1858T também está associado ao uso de imunobiológicos (p=0,021; OR= 4,39; Intervalo de Confiança=1,08 – 17,86), mas não está relacionado às formas sistêmicas (p=0,071; OR = 3,17; Intervalo de Confiança = 0,83 – 11,73). Entretanto, o polimorfismo de PTPN22 1858 C/T não foi associado à Artrite Reumatoide ou à Tuberculose Pulmonar. Estes resultados sugerem que o alelo TNF2 está associado às formas mais graves da AR em indivíduos do Amazonas, mas não ao risco de desenvolver Artrite Reumatoide.

Diss. (sammanfattning) Umeå : Umeå universitet, 2010. / Härtill 5 uppsatser.