Base teórica: A introdução de agentes biológicos, especialmente os bloqueadores do fator de necrose tumoral (anti-TNF), para o tratamento de doenças reumáticas aumentou o risco de desenvolver tuberculose (TB). O rastreio para infecção tuberculosa latente (ILTB) é fortemente recomendado antes de iniciar a terapia com agentes anti-TNF. Os objetivos deste estudo foram identificar a prevalência de ILTB e TB entre pacientes com doenças reumáticas em uso dos medicamentos anti-TNF. Métodos: Estudo transversal. Foram revisados os registros médicos eletrónicos de todos os doentes adultos (≥ 18 anos) em uso da terapia anti-TNF. Todos os pacientes foram submetidos ao teste tuberculínico (TT) antes de iniciar o tratamento com os medicamentos anti-TNF. Resultados: No total, 176 pacientes foram incluídos no estudo. A idade média de todos os pacientes foi de 51,9 ± 12,4 anos, 34,7% eram do sexo masculino e 90,9% eram brancos. As doenças subjacentes mais comuns foram: Artite Reumatóide (AR) em 89 pacientes (50,6%), Espondilite Anquilosante (EA) em 49 (27,8%) e Artrite Psoriática (AP) em 31 (17,6%). A prevalência de TT positivo foi de 29,5%. O contato domiciliar com TB foi significativamente associado com TT positivo (p = 0,020). Os pacientes com AR apresentaram reações TT menores do que os pacientes com EA (p = 0,022). Houve seis casos de TB (3,4%) diagnosticados durante a terapia anti-TNF. Conclusões: Demonstrou-se alta prevalência de TT positivo (29,5%) em pacientes com doenças reumáticas em uma região com alta prevalência de TB. Nossos dados corroboram a recomendação do Colégio Americano de Reumatologia (ACR) de que os pacientes que vivem em configurações de alta incidência de TB devem ser testados anualmente para ILTB. / Background: The introduction of biological agents, especially the blockers of tumor necrosis factor (anti-TNF), for the treatment of rheumatic diseases increased the risk of developing tuberculosis (TB). Screening for latent TB infection (LTBI|) is strongly recommended before starting therapy with anti-TNF agents. The objectives of this study were to identify the prevalence of LTBI and TB among patients with rheumatic diseases on anti-TNF drugs. Methods: Cross-sectional study. The electronic medical records of all adult patients (≥ 18 years old) undergoing anti-TNF treatment were reviewed. Every patient underwent TST test before starting anti-TNF treatment. Results: In total, 176 patients were included in the study. The mean age of all patients was 51.9 ± 12.4 years, 34.7% were males, and 90.9% were white. The most common underlying diseases were: RA in 89 patients (50.6%), AS in 49 (27.8%), and PA in 31 (17.6%). The prevalence of positive TST was 29.5%. Household contact with TB was significantly associated with a positive TST (p=0.020). RA patients had lower TST reactions than AS patients (p=0.022). There were six cases of TB (3.4%) diagnosed during anti-TNF therapy. Conclusions: We demonstrated a high prevalence of positive TST (29.5%) among patients with rheumatic diseases in a region with high TB prevalence. Our data corroborates the ACR’s recommendation that patients who live in high TB incidence settings should be tested annually for LTBI.

Base teórica: A introdução de agentes biológicos, especialmente os bloqueadores do fator de necrose tumoral (anti-TNF), para o tratamento de doenças reumáticas aumentou o risco de desenvolver tuberculose (TB). O rastreio para infecção tuberculosa latente (ILTB) é fortemente recomendado antes de iniciar a terapia com agentes anti-TNF. Os objetivos deste estudo foram identificar a prevalência de ILTB e TB entre pacientes com doenças reumáticas em uso dos medicamentos anti-TNF. Métodos: Estudo transversal. Foram revisados os registros médicos eletrónicos de todos os doentes adultos (≥ 18 anos) em uso da terapia anti-TNF. Todos os pacientes foram submetidos ao teste tuberculínico (TT) antes de iniciar o tratamento com os medicamentos anti-TNF. Resultados: No total, 176 pacientes foram incluídos no estudo. A idade média de todos os pacientes foi de 51,9 ± 12,4 anos, 34,7% eram do sexo masculino e 90,9% eram brancos. As doenças subjacentes mais comuns foram: Artite Reumatóide (AR) em 89 pacientes (50,6%), Espondilite Anquilosante (EA) em 49 (27,8%) e Artrite Psoriática (AP) em 31 (17,6%). A prevalência de TT positivo foi de 29,5%. O contato domiciliar com TB foi significativamente associado com TT positivo (p = 0,020). Os pacientes com AR apresentaram reações TT menores do que os pacientes com EA (p = 0,022). Houve seis casos de TB (3,4%) diagnosticados durante a terapia anti-TNF. Conclusões: Demonstrou-se alta prevalência de TT positivo (29,5%) em pacientes com doenças reumáticas em uma região com alta prevalência de TB. Nossos dados corroboram a recomendação do Colégio Americano de Reumatologia (ACR) de que os pacientes que vivem em configurações de alta incidência de TB devem ser testados anualmente para ILTB. / Background: The introduction of biological agents, especially the blockers of tumor necrosis factor (anti-TNF), for the treatment of rheumatic diseases increased the risk of developing tuberculosis (TB). Screening for latent TB infection (LTBI|) is strongly recommended before starting therapy with anti-TNF agents. The objectives of this study were to identify the prevalence of LTBI and TB among patients with rheumatic diseases on anti-TNF drugs. Methods: Cross-sectional study. The electronic medical records of all adult patients (≥ 18 years old) undergoing anti-TNF treatment were reviewed. Every patient underwent TST test before starting anti-TNF treatment. Results: In total, 176 patients were included in the study. The mean age of all patients was 51.9 ± 12.4 years, 34.7% were males, and 90.9% were white. The most common underlying diseases were: RA in 89 patients (50.6%), AS in 49 (27.8%), and PA in 31 (17.6%). The prevalence of positive TST was 29.5%. Household contact with TB was significantly associated with a positive TST (p=0.020). RA patients had lower TST reactions than AS patients (p=0.022). There were six cases of TB (3.4%) diagnosed during anti-TNF therapy. Conclusions: We demonstrated a high prevalence of positive TST (29.5%) among patients with rheumatic diseases in a region with high TB prevalence. Our data corroborates the ACR’s recommendation that patients who live in high TB incidence settings should be tested annually for LTBI.

La maladie de Crohn (MC) a une incidence élevée dans la population pédiatrique en Amérique du Nord et cette incidence est en augmentation. L’évolution naturelle de la MC est mal comprise. L'évolution du délai à la rémission au fil des ans et les causes influençant le délai à la rémission sont très limitées dans la littérature. Peu de facteurs de risque sont identifiés dans la littérature pour prédire les rechutes de la maladie chez les enfants. Le premier objectif de cette étude était de décrire les variations du phénotype clinique, des caractéristiques endoscopiques, histologiques et de laboratoire de la MC pédiatrique au cours de la dernière décennie et de décrire les variations saisonnières de la présentation de la maladie au moment du diagnostic. Le deuxième objectif était de décrire le délai à la rémission chez les enfants atteints de MC ainsi que son évolution au cours de la dernière décennie et de déterminer les facteurs associés au délai à la rémission. Le troisième objectif de l’étude était de décrire le taux de rechutes chez les enfants atteints de la MC, son évolution au cours de la dernière décennie et de déterminer les facteurs de risque associés à la rechute de la maladie. Les patients éligibles étaient âgés de 4 à 18 ans et diagnostiqués entre 2009 et 2019. Toutes les caractéristiques cliniques, endoscopiques, histologiques et de laboratoire des patients, ainsi que leurs traitements, ont été recueillis à partir de leurs dossiers médicaux. Des analyses de survie et des modèles de régression linéaire ont été utilisés pour évaluer l'impact de ces facteurs sur le délai à la rémission et des analyses de survie et des modèles de régression de Cox ont été utilisés pour évaluer l'impact de ces facteurs sur le risque de rechute. 654 patients ont été inclus dans cette étude de cohorte rétrospective. Le nombre de nouveaux diagnostics annuels de MC a augmenté au fil des ans et les patients diagnostiqués entre 2015 et 2019 avaient un âge au diagnostic plus bas (OR 2.53, IC à 95% [1.29; 4.98]), plus de maladies périanales (OR: 2.30, IC à 95% [ 1.52; 3.48]), plus de granulomes (OR: 1.61, IC à 95% [1.17; 2.22]), mais moins d’éosinophiles (OR: 0.35, IC à 95% [0.25; 0.48]) et moins d’infiltrat lympho-plasmocytaire chronique (OR: 0.56, IC à 95% [0.36; 0.86]) comparé aux patients diagnostiqués entre 2009 et 2014. Il y avait moins de diagnostics de MC chez les enfants en hiver. Les patients diagnostiqués à l'automne avaient une activité de la maladie plus faible (score PCDAI), moins de retard de croissance et des maladies digestives moins diffuses. Les MC diagnostiquées au printemps et à l’été avaient des taux d'hémoglobine plus faibles et des taux de vitesse de sédimentation plus élevés associées à plus d’atteintes articulaires et plus d'érythème noueux. La localisation colique était significativement plus fréquente l’été et l’automne. Il n'y a pas eu de changement dans le délai à la rémission au cours de la dernière décennie. Le sexe féminin chez les adolescents (coefficient de regression bêta ajusté (aβ) = 31.8 jours, p=0.02), l'atteinte du tube digestif supérieur (aβ= 46.4 jours, p=0.04), la maladie périanale (aβ= 32.2 jours, p=0.04), les signes d'inflammation active sur les biopsies (aβ= 46.7 jours, p=0.01) et l’exposition aux 5-ASA oraux lors de la phase d'induction (aβ= 56.6 jours, p=0.002) étaient associés à un délai à la rémission plus long. À l’inverse, l'utilisation d'antibiotiques (aβ= -29.3 jours, p=0.04), l’augmentation des éosinophiles sur les biopsies (aβ= -29.6 jours, p=0.008) et l'utilisation de la nutrition entérale exclusive comme traitement d'induction avec les anti TNF-alpha (aβ= -36.8 jours, p=0.04) étaient associés à un délai à la rémission plus court. Il y a eu une diminution du taux de rechute au cours de la dernière décennie : 69.59% chez les patients diagnostiqués entre 2009 et 2014 et 47.76% chez les patients diagnostiqués entre 2015 et 2019 (p<0.0001). Le sexe féminin (hazard ratio ajusté (aHR) = 1.51, p=0.0009), les scores PCDAI (aHR= 1.02, p=0.04) et SES-CD élevés (aHR= 1.03, p=0.03) au diagnostic, l'atteinte du tube digestif supérieur (aHR= 1.59, p=0.0003), l’utilisation des 5-ASA oraux (aHR= 1.91, p=0.0003), l’usage d'agents immunomodulateurs par rapport aux biologiques (methotrexate aHR= 1.91, p=0.0006; thiopurines aHR= 2.06, p<0.0001), la présence de granulomes (aHR= 1.27, p=0.04) et l’augmentation des éosinophiles sur les biopsies (aHR= 1.34, p=0.02), des niveaux élevés de protéine C-réactive (aHR= 1.01, p<0.0001) et de calprotectine fécale (aHR=1.09, p<0.0001) pendant la rémission clinique et de faibles taux sériques d'infliximab en post-induction (aHR pour les niveau moyen d’infliximab inférieur à 7ug/mL = 2.48, p=0.005) étaient indépendamment associés à la rechute. Le phénotype de la maladie a changé au fil des ans et des tendances saisonnières dans la fréquence et la gravité des diagnostics existent, suggérant des hypothèses étiologiques telles que la carence en vitamine D en hiver, les colites bactériennes saisonnières, les processus de réactivation virale et les changements dans la composition du microbiote. Plusieurs résultats de l'étude sont originaux et ceux-ci ont apporté de nouvelles connaissances et certains pourraient être intégrés dans les lignes directrices de prise en charge de la MC pédiatrique afin d’améliorer la qualité de vie des patients, soit obtenir une rémission rapide et durable. / Crohn's disease (CD) has a high incidence in the pediatric population in North America. The etiology of CD remains unknown and the disease incidence has been increasing. The natural evolution of CD is misunderstood, especially in the pediatric population. The trends of time-to-remission over the years and the influencing factors are very limited in the literature. Few risk factors are identified in the literature to predict relapses of the disease in children. The first part of this study was to describe the trends in the clinical phenotype, endoscopic, histological, and laboratory characteristics of pediatric CD during the last decade and to describe the seasonal variation of disease presentation at diagnosis. The secondary part of this study was to describe the time to remission in children with CD as well as its evolution over the past decade and to determine factors associated with time to remission. The third part of the study was to describe the rate of relapses in children with CD, its evolution over the past decade and to determine risk factors associated with relapse of the disease. Eligible patients were aged from 4 to 18 years and diagnosed between 2009 and 2019. All clinical, endoscopic, histological, laboratory and treatment data were collected from their medical records. Survival analyses and linear regression models were used to assess the impact of those factors on time to remission. Likewise, survival analyses and Cox regression models were applied to assess the impact of those risk factors on relapse. A total of 654 patients were included in this retrospective cohort study. The number of new diagnoses per year increased over the decade. Patients diagnosed between 2015 and 2019 had a lower age at diagnosis (OR 2.53, 95% CI [1.29; 4.98]), more perianal diseases (OR: 2.30, 95% CI [1.52; 3.48]), more granulomas (OR: 1.61, 95% CI [1.17; 2.22]), but less eosinophils (OR: 0.35, 95% CI [0.25; 0.48]) and less chronic lympho-plasma cells infiltrate (OR: 0.56, 95% CI [0.36; 0.86]) on ileo-colonic biopsies compared to patients diagnosed in 2015-2019. There were fewer diagnoses of CD in children in winter. Patients diagnosed in fall had lower PCDAIs and less failure to thrive. CD diagnosed in spring and summer had lower hemoglobin levels and higher erythrocyte sedimentation rate levels. In addition, arthritis and erythema nodosum were more frequent in spring and summer. Colonic location was significantly more frequent in summer and fall. There was no change in the time to clinical remission over the past decade. Female sex in adolescents (adjusted bêta regression coefficient (aβ)= 31.8 days, p=0.02), upper digestive tract involvement (aβ= 46.4 days, p=0.04) perianal disease (aβ= 32.2 days, p=0.04), presence of active inflammation on biopsies (aβ= 46.7 days, p=0.01) and oral 5-ASA exposure (aβ= 56.6 days, p=0.002) were all associated with longer time to clinical remission. However, antibiotic exposure (aβ= -29.3 days, p=0.04), increased eosinophils on biopsies (aβ= -29.6 days, p=0.008) and combination of exclusive enteral nutrition and TNF-alpha inhibitors as induction therapy (aβ= -36.8 days, p=0.04) were associated with shorter time to clinical remission. There has been a decrease in the relapse rate over the past decade : 69.6% in patients diagnosed between 2009 and 2014 and 47.8% in patients diagnosed between 2015 and 2019 (p<0.0001). Female sex (adjusted hazard ratio (aHR) = 1.51, p=0.0009), high PCDAI (aHR= 1.02, p=0.04) and SES-CD (aHR= 1.03, p=0.03) scores at diagnosis, upper digestive tract involvement (aHR= 1.59, p=0.0003), exposure to oral 5-ASA (aHR= 1.91, p=0.0003), use of immunomodulatory agents compared to TNF-alpha inhibitors (methotrexate aHR= 1.91, p=0.0006; thiopurines aHR= 2.06, p<0.0001), presence of granulomas (aHR= 1.27, p=0.04) and increased eosinophils on biopsies (aHR= 1.34, p=0.02), high levels of C-reactive protein (aHR= 1.01, p<0.0001) and fecal calprotectin (aHR=1.09, p<0.0001) during clinical remission and low serum infliximab levels during maintenance (aHR for mean serum infliximab level under 7ug/mL = 2.48, p=0.005) were all significantly associated with relapse in patients. The disease phenotype has changed over the years and important trends in the frequency and severity of diagnoses exist according to the diagnosis period within a year, suggesting etiological hypotheses such as vitamin D deficiency in winter, seasonal bacterial and viral colitis and academic stress. Many of the results of the study are original and brought new knowledge while confirming certain statements which had not obtained consensus in recent studies of expert opinions and some could be incorporated into management guidelines of pediatric CD to short time to remission and avoid relapse in patients.

Ankylosing spondylitis (AS) is a common inflammatory arthritis of the spine and other affected joints, which is highly heritable, being strongly influenced by the HLA-B27 status, as well as hundreds of mostly unknown genetic variants of smaller effect. The aim of my research was to confirm some of the previously observed genetic associations and to identify new associations, many of which are in biological pathways relevant to AS pathogenesis, most notably the IL-23/T_H17 axis (IL23R) and antigen presentation (ERAP1 and ERAP2). Studies presented in this thesis include replication and refinement of several potential associations initially identified by earlier GWAS (WTCCC-TASC, 2007 and TASC, 2010). I conducted an extended study of IL23R association with AS and undertook a meta-analysis, confirming the association between AS and IL23R (non-synonymous SNP rs11209026, p=1.5 x 10-9, OR=0.61). An extensive re-sequencing and fine mapping project, including a meta-analysis, to replicate and refine the association of TNFRSF1A with AS was also undertaken; a novel variant in intron 6 was identified and a weak association with a low frequency variant, rs4149584 (p=0.01, OR=1.58), was detected. Somewhat stronger associations were seen with rs4149577 (p=0.002, OR=0.91) and rs4149578 (p=0.015, OR=1.14) in the meta-analysis. Associations at several additional loci had been identified by a more recent GWAS (WTCCC2-TASC, 2011). I used in silico techniques, including imputation using a denser panel of variants from the 1000 Genomes Project, conditional analysis and rare/low frequency variant analysis, to refine these associations. Imputation analysis (1782 cases/5167 controls) revealed novel associations with ERAP2 (rs4869313, p=7.3 x 10-8, OR=0.79) and several additional candidate loci including IL6R, UBE2L3 and 2p16.3. Ten SNPs were then directly typed in an independent sample (1804 cases/1848 controls) to replicate selected associations and to determine the imputation accuracy. I established that imputation using the 1000 Genomes Project pilot data was largely reliable, specifically for common variants (genotype concordence~97%). However, more accurate imputation of low frequency variants may require larger reference populations, like the most recent 1000 Genomes reference panels. The results of my research provide a better understanding of the complex genetics of AS, and help identify future targets for genetic and functional studies.