O objetivo desse estudo foi avaliar o comprometimento de pequenas vias aéreas na Fibrose Pulmonar Idiopática (FPI) analisando curvas Pressão- Volume (PV) do sistema respiratório. Coletamos curvas PV de doze pacientes antes da biopsia pulmonar, que confirmou FPI em sete pacientes e Pneumonite de Hipersensibilidade em cinco. Todas as curvas foram ajustadas com modelo sigmóide, V = a + b / (1 + e -(P-c/d)), e exponencial V = A - B . e -k.P (aplicado apenas à parte superior). O modelo exponencial, apesar do bom ajuste à parte superior, não representou a parte inicial da curva, gerando parâmetros sem significado. O modelo sigmóide ajustou bem toda a curva e gerou parâmetros com significado fisiológico, que sugerem a presença de colapso de pequenas vias aéreas na FPI. / The objective of this study was to evaluate small airways compromise in Idiopathic Pulmonary Fibrosis (IPF) using pressure-volume (PV) curves of the respiratory system. We collected PV curves from twelve patients before lung biopsy, which confirmed IPF in seven patients and Hipersensitivity Pneumonia in five. All curves were fitted with a sigmoid model, V = a + b / (1 + e -(P-c/d)), and an exponential model, V = A - B . e -k.P (applied only to the superior part of the curve). The exponential model, despite having a good fit to the superior part of the curve, did not represent the initial part, and yielded parameters with no physiological meaning. The sigmoid model had a good fit to the entire curve and yielded parameters with physiological meaning, suggesting the presence of small airways collapse in IPF.

Orientador: Luiz Roberto Lopes / Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-19T19:36:32Z (GMT). No. of bitstreams: 1 Bianchi_RenataCristianeGennari_D.pdf: 1264896 bytes, checksum: e7f0d2b827693233f95ddfd5a5e1ab93 (MD5) Previous issue date: 2012 / Resumo: As neoplasias esofágicas passíveis de tratamento por radioterapia podem induzir seqüelas clínicas importantes como a pneumonite radioinduzida e a fibrose pulmonar. É sabido que os exercícios físicos promovem uma seqüência de liberação de citocinas pró-inflamatórias, com diminuição dos efeitos deletérios das desordens cardiovasculares e promoção de efeito protetor contra as doenças associadas à inflamação sistêmica. Diante deste fato, o presente estudo teve o objetivo de verificar se a atividade física pré-radioterapia possui elementos radioprotetores, medindo-se a ativação de citocinas pró-inflamatórias como a interleucina-6 (IL-6), fator transformador de crescimento-bete (TGF-'beta'), fator de necrose tumoral-alfa (TNF-'alfa') e quinase de proteína beta (IKK'beta'), por meio da análise de Western Blotting (WB). Para isto, foi realizado um estudo randomizado empregando 28 ratos Wistar Hannover, machos, com idade média de 90 dias e e peso aproximado de 200 gramas. Os animais foram divididos em 3 grupos. Gl (grupo controle), Gll (grupo que foi submetido à radioterapia e sacrificado no 1o dia pós-radioterapia - Glla ou sacrificado no 7o dia pós-radioterapia - Gllb) e Glll (grupo que realizou atividade física e radioterapia e foi sacrificado no 1°dia pós-radioterapia- Gllla ou sacrificado no 7°dia pós-radioterapia- Glllb). A atividade física do grupo Glll consistiu em natação, durante 8 semanas (carga zero, 3 vezes por semana, cerca de 30 minutos). Após tal atividade física, Gll e Glll foram submetidos à irradiação por cobaltoterapia, dose única de 3,5 grays em corpo inteiro. Todos os animais foram sacrificados por overdose de pentobarbital, de acordo com o tempo de análise de citocinas, e em seguida, um fragmento do lobo inferior do pulmão direito foi foi analisado por WB. Como resultado, a expressão das citocinas IKK'beta', TNF-'alfa' e IL-6 induzidas por radiação no pulmão foi menor nos animais que se exercitaram e que foram sacrificados no 7°dia pós-radioterapia (Glllb), com significância estatística através do teste de ANOVA (p<0,05). No entanto, o exercício não alterou o aumento induzido pela radiação em relação à TGF-'beta'. Concluiu-se que a atividade física possui elementos radioprotetores, pois houve menor aumento de IKK'beta', TNF-'alfa' e IL-6 nos grupos pós-atividade física (Glllb), com sugestão de menor inflamação e lesão tecidual pós-radioterapia. Possivelmente não houve significância estatística em relação à TGF-'beta', pois tal citocina tem papel preponderante numa fase mais tardia de injúria tecidual, ou seja, na fibrose pulmonar. Além disso, as citocinas analisadas mostraram-se bons marcadores para mensurar a resposta inflamatória tecidual pulmonar / Abstract: Esophageal neoplasms amenable to treatment by radiation therapy may induce important clinical radioinduced sequelae as pneumonitis and pulmonary fibrosis. It is known that exercise promotes a sequence of release of proinflammatory cytokines, decreasing the deleterious effects of cardiovascular disorders and promotion of protective effect against diseases associated with systemic inflammation. Given this fact, this study aimed to determine whether physical activity pre-radiotherapy has radioprotective elements by measuring the activation of proinflammatory cytokines such as interleukin-6 (IL-6), transforming growth factor-beta (TGF-'beta'), tumor necrosis factor-alpha (TNF-'alpha') and beta protein kinase (IKK'beta') by means of Western Blotting (WB) analysis. For this, we performed a randomized study using 28 male Wistar Hannover rats, males with a mean age of 90 days and and weighing approximately 200 grams. The animals were divided into 3 groups. Gl (control group), Gil (group underwent radiotherapy and sacrificed on day 1 after radiation therapy - Gila or sacrificed on day 7 post-radiotherapy -Glib) and GIN (the group that performed physical activity and radiotherapy and was sacrificed on day 1 post-radiotherapy-Gllla or sacrificed on day 7 post-radiotherapy-Glllb). The physical activity of the group GIN consisted of swimming for 8 weeks (zero load, three times per week, about 30 minutes). After this activity, Gil and GIN were subjected to irradiation by cobalt, a single dose of 3.5 Gy of whole body. All animals were sacrificed by an overdose of pentobarbital, according to the analysis time of cytokines, and then a fragment of the lower lobe of right lung was analyzed by WB. As a result, the expression of cytokines IKK 'beta', TNF-'alpha' and IL-6 induced by radiation in the lungs was lower in the exercised animals and that were sacrificed on day 7 post-radiotherapy (Glllb), with statistical significance by ANOVA test (p<0,05) . However, the exercise did not affect the increase induced by radiation in relation to TGF-'beta'. It was concluded that physical activity has radioprotective elements because there was a lower increase of IKK 'beta', TNF-'alpha' and IL-6 in post-exercise groups (Glllb), with suggestion of less inflammation and tissue injury after radiation therapy. Possibly there was no statistical significance in relation to TGF-'beta', as this cytokine plays an important role in a later phase of tissue injury, namely pulmonary fibrosis. Furthermore, the cytokines analyzed proved to be good markers to measure the pulmonary inflammatory response / Doutorado / Fisiopatologia Cirúrgica / Doutor em Ciências

Orientador: Manoel Barros Bertolo / Dissertação (mestrado) - Universidade Estadual de Campinas, Faculdade de Ciências Médicas / Made available in DSpace on 2018-08-21T17:57:00Z (GMT). No. of bitstreams: 1 DelRio_AnaPaulaToledo_M.pdf: 1151549 bytes, checksum: 2407595c8d19b5531c6d084bba4d3238 (MD5) Previous issue date: 2012 / Resumo: Introdução: A esclerose sistêmica (ES) é uma doença autoimune caracterizada por disfunção endotelial, vasculopatia obliterativa, fibrose cutânea e visceral. Trata-se de doença poligênica complexa que se manifesta em indivíduos geneticamente predispostos com exposição a fator ambiental ou outro precipitante e seu desenvolvimento depende da interação entre processos imunológicos, vasculares e fibróticos. Estudos genéticos prévios procuram correlacionar os alelos HLA classe I e II e as manifestações clínicas da doença. A fibrose pulmonar (FP) e a hipertensão arterial pulmonar (HAP) são, atualmente, os acometimentos com maior impacto prognóstico e as principais causas de óbito nos pacientes com ES. A expressão do autoanticorpo antitopoisomerase I (anti-Scl70) é um forte preditor de FP, associada à forma difusa e a HAP está relacionada ao anticorpo anticentrômero e à forma limitada da doença. Objetivos: O objetivo deste estudo foi avaliar a participação do HLA na expressão da doença e suas manifestações clínicas de pior prognóstico (FP e HAP) em pacientes com ES em uma população miscigenada. Métodos: Foram incluídos os pacientes com ES seguidos no ambulatório de Reumatologia da Universidade Estadual de Campinas (UNICAMP) de 2008 a 2011. Os dados clínicos foram obtidos através da análise dos prontuários. A genotipagem dos alelos Classe I e II foi realizada através da técnica de amplificação pela reação em cadeia da polimerase, utilizando seqüências específicas de primers. A análise estatística incluiu o teste exato de Fisher e o teste do qui-quadrado de Pearson. Foram considerados significativos valores de p ? 0,05. A razão de prevalência foi estimada pelo método delta. Resultados Cento e quarenta e um pacientes (120 mulheres e 21 homens) foram estudados, sendo 33,3% ES difusa, 62,4% ES limitada e 4,3% ES sine scleroderma. A FP foi considerada em 61 pacientes (43,3%), os alelos HLA-A*30 e DQB1*04 foram relacionados à suscetibilidade. No entanto, os alelos HLA-DRB1*01 e DQB1*05 foram relacionados à ausência desta manifestação. A HAP foi diagnosticada em 19 pacientes (13,5%) e teve associação com HLA-B*35 e C*04, enquanto o alelo C*03 pareceu ser protetor. Conclusões: Este estudo aponta para associação de alguns alelos do HLA classe I e II às manifestações clínicas de maior morbimortalidade na ES nesta série de casos. Estes achados não foram semelhantes aos encontrados previamente em outras populações, o que evidencia múltiplos padrões genéticos na ES / Abstract: Introduction: Systemic sclerosis (SSc) is an autoimmune disease characterized by endothelial dysfunction, occlusive vasculopathy, cutaneous and visceral fibrosis. This is a complex polygenic disease that manifests in genetically predisposed individuals with environmental or other precipitating factor exposure and its development depends on the interaction between immunological, vascular and fibrotic processes. Previous genetic studies aimed to correlate class I and II HLA and the clinical manifestations of the disease. Pulmonary fibrosis (PF) and pulmonary arterial hypertension (PAH) are currently the worse prognostic features and the main causes of death in patients with SSc. The presence of anti-topoisomerase I antibody (anti-Scl70) is a strong predictor of FP, associated with diffuse SSc and PAH is related to anticentromere and the limited form of the disease. Objectives: The aim of this study was to evaluate the HLA involvement in disease expression and poor prognostic clinical features, pulmonary fibrosis (PF) and pulmonary arterial hypertension (PAH), in patients diagnosed with systemic sclerosis (SSc) in a multiethnic population. Methods: SSc patients followed 2008-2011 were included and clinical data were obtained through records review. Molecular HLA typing was performed (PCR amplification technique using sequence of specific primers). Statistical analysis included Fisher's exact test and Pearson's corrected chi-square test. P values ? 0.05 were considered significant. The prevalence ratio was estimated by delta method. Results: One hundred forty-one patients (120 women and 21 men) were studied, 33,3% dcSSc, 62,4% lcSSc and 4,3% sine scleroderma. PF was present in 61 patients (43,3%), HLA-A*30 and DQB1*04 were related to susceptibility. However, HLA-DRB1*01 and DQB1*05 alleles were protective. PAH was diagnosed in 19 (13,5%) and had association with HLA-B*35 and C*04, whereas C*03 seemed to be protective. Conclusions: Our current study documents the association of some class I and II HLA alleles with the most severe clinical manifestations in a multiethnic case series. Our findings were not absolutely similar to the previous data in other populations / Mestrado / Clinica Medica / Mestra em Clínica Médica

La voie RhoA/Rho-kinases (ROCK) joue un rôle important dans la physiopathologie de l’hypertension pulmonaire (HTP) par son implication dans le dysfonctionnement endothélial, la constriction et le remodelage des vaisseaux pulmonaires. Selon les classifications internationales, la bronchopneumopathie chronique obstructive (BPCO) et la pneumopathie infiltrante diffuse (PID) sont deux causes fréquentes d’HTP ayant en commun plusieurs mécanismes physiopathologiques dont le dysfonctionnement endothélial, le remodelage vasculaire et la fibrose parenchymateuse. Les objectifs de ce travail étaient d’étudier le rôle de la voie RhoA/ROCK dans la physiopathologie de la BPCO et de la PID avec ou sans HTP et de préciser les anomalies moléculaires liées à la perturbation de la signalisation de cette voie dans chacune de ces situations.Le dysfonctionnement endothélial est un événement essentiel dans l’initiation et la progression de la BPCO. L’activation de la voie RhoA/ROCK dans le dysfonctionnement endothélial systémique et pulmonaire a été mise en évidence chez les tabagiques avec ou sans BPCO. Les résultats de notre première étude montrent l’existence d’une activation de la voie RhoA/ROCK au niveau des artères pulmonaires chez les patients BPCO ayant un dysfonctionnement endothélial, et une corrélation entre l’activité de la RhoA et l’expression génique et l’activité de la NO synthase endothéliale (NOS-3).L’HTP est une complication grave des PID. Nous avons montré dans notre deuxième étude l’implication de la voie RhoA/ROCK dans la réponse inflammatoire et la fibrose pulmonaire (FP) dans un modèle murin de PID induite par injection intratrachéale de bléomycine (BLM). Nous avons ensuite testé l’effet préventif du fasudil, un inhibiteur des ROCK, sur l’apparition de la FP et l’HTP expérimentales induites par la BLM. Les résultats de cette deuxième étude montrent que la FP et l’HTP sont associées à une activation de la voie RhoA/ROCK dans ce modèle murin et que le fasudil inhibe la réponse inflammatoire, la FP et l’HTP, via l’inhibition de la phosphorylation de Smad2/3 de la voie de signalisation par le TGF-β1.La FP et l’HTP représentent deux causes principales de mortalité liée à la sclérodermie systémique (ScS). Nous avons étudié le rôle de la voie RhoA/ROCK dans la physiopathologie de la fibrose cutanée et l’atteinte pulmonaire dans un modèle murin de ScS induite par injection intradermique d’acide hypochloreux (HOCl). Les résultats de cette troisième étude montrent l’association entre la fibrose cutanée induite par l’HOCl et l’activation de la voie RhoA/ROCK au niveau de la peau, et l’effet préventif du fasudil sur la fibrose cutanée et pulmonaire, en partie via l’inhibition de la phosphorylation de Smad2/3 et de l’activation des protéines ERK1/2. Ces résultats suggèrent l’implication de la voie RhoA/ROCK dans la physiopathologie de la BPCO et de la PID avec ou sans HTP. La voie RhoA/ROCK pourrait de ce fait représenter une nouvelle cible thérapeutique dans la BPCO et la PID avec ou sans HTP.Mots-clés : RhoA, Rho-kinases, fasudil, BPCO, fibrose pulmonaire, hypertension pulmonaire. / The RhoA/Rho-kinases (ROCK) pathway plays a pivotal role in the pathophysiology of pulmonary hypertension (PH) as its abnormal activation leads to endothelial dysfunction, sustained vasoconstriction and pulmonary vascular remodeling. According to the international classification of PH, chronic obstructive pulmonary disease (COPD) and interstitial lung disease (ILD) represent two main causes of PH associated with chronic respiratory diseases. These two causes have in common major pathophysiological mechanisms such as endothelial dysfunction, vascular remodeling and interstitial fibrosis. The aims of the present study were to investigate the role of the RhoA/ROCK pathway in the pathophysiology of lung vascular and interstitial injuries in COPD and ILD with or without development of PH, and to study the molecular mechanisms associated with regulation of the RhoA/ROCK pathway in each of these situations.The pulmonary endothelial dysfunction is an essential event in the initiation and progression of COPD. Although the role of the RhoA/Rho-kinase pathway in pulmonary endothelial dysfunction has been demonstrated in smokers with normal lung function, little is known about its role in patients with COPD. The results of our first study demonstrated an increase in RhoA and ROCK activity in pulmonary arteries of patients with COPD, simultaneously with an altered pulmonary endothelial-dependent vasodilation. The increased RhoA activity in patients with COPD was correlated with an impairment of the gene expression and activity of endothelial NO synthase (eNOS).PH associated with pulmonary fibrosis (PF) considerably worsens prognosis of ILD. The results of our second study showed an activation of the RhoA/ROCK pathway in lung tissues of mice intoxicated by intratracheal instillation of bleomycin (BLM). BLM induced severe PF and PH in mice, associated with an increased RhoA and ROCK activity in the lung. We further demonstrated that long-term treatment with fasudil, a selective ROCK inhibitor, reduced BLM-induced lung inflammation, lung fibrosis and PH in mice, at least in part, via inhibition of Smad2/3 phosphorylation in TGF-β1 signaling.PF and PH represent two leading causes of death in patients with systemic sclerosis (SSc). In our third study, we investigated the role of the RhoA/ROCK pathway in the pathophysiology of skin fibrosis and lung injuries in a murine model of SSc induced by intradermal injection of hypochlorous acid (HOCl). We demonstrated that HOCl-induced skin fibrosis was associated with an activation of the RhoA/ROCK pathway in the fibrotic skin, and that long-term treatment with fasudil reduced both skin and lung fibrosis through inhibition of the phosphorylation of Smad2/3 and ERK1/2 in the fibrotic skin.These results suggest the implications of the RhoA/ROCK pathway in the pathophysiology of lung vascular and interstitial injuries in COPD and ILD with and without development of PH. The RhoA/ROCK pathway might be a promising therapeutic target for patients with COPD or ILD with and without PH.

Nous nous intéressons aux mécanismes moléculaires impliqués dans la physiopathologie de la fibrose pulmonaire idiopathique. La fibrose pulmonaire estcaractérisée par l’accumulation de protéines de la matrice extracellulaire et de fibroblastes dans les espaces aériens distaux. La désorganisation et la destructionalvéolaires qui résultent de la fibrose aboutissent à une altération des propriétés mécaniques du poumon et à une incapacité à réaliser les échanges gazeux responsables d’une insuffisance respiratoire parfois mortelle. Le pronostic de la fibrose pulmonaire idiopathique (FPI) est particulièrement mauvais puisque la médiane de survie est de 3 à 5 ans. Il n’existe actuellement aucune thérapeutique efficace dans la fibrose pulmonaire. Ainsi, il est crucial d’explorer de nouvelles hypothèses physiopathologiques dans cette maladie afin d’ouvrir de nouvelles voies thérapeutiques. L'apoptose joue un rôle clé dans le développement de nombreux organes et dans l'homéostasie tissulaire chez l'adulte. Les protéines de la famille BCL-2 sont des éléments essentiels de la machinerie apoptotique. Ces protéines agissent comme des régulateurs anti- ou pro-apoptotiques. Parmi les membres de la famille BCL-2, le facteur pro-apoptotique BAX contrôle la voie mitochondriale de l’apoptose. Des perturbations de l’apoptose ont été mises en cause dans des maladies pulmonaires comme la fibrose pulmonaire idiopathique. Des études récentes suggèrent fortement que les protéines de la famille BCL-2 sont également impliquées dans d’autres fonctions cellulaires que le contrôle de l'apoptose. De plus, la protéine BAX est aussi localisée dans le noyau de nombreux types cellulaires. Même si le rôle de la fraction cytoplasmique de BAX au cours de l’apoptose est assez bien caractérisé, les fonctions nucléaires de BAX ne sont pas connues. Ce travail de thèse a pour but de mieux comprendre le rôle de la forme nucléaire de BAX dans différents processus cellulaires fondamentaux impliqués dans la fibrogenèse. Notre étude montre que la protéine BAX est présente dans le noyau à proximité de l’euchromatine dans différentes lignées d’origine pulmonaire in vitro. Ensuite, nous montrons que la forme nucléaire de BAX est impliquée dans la progression du cycle cellulaire et dans le contrôle de l’état de différenciation myofibroblastique en condition basale. Enfin, nous avons détecté la forme nucléaire de BAX dans l’épithélium hyperplasique et les foyers de fibrose dans le poumon de FPI. / Summary not transmitted

Idiopathic Pulmonary Fibrosis (IPF) is a deadly disease of unknown origin, which causes 80,000 deaths every year in the US and Europe combined. Unknown etiology and late diagnosis, combined with limited treatment options, contribute to a dismal survival rate of 3-5 years post diagnosis. Although molecular mechanisms underlying IPF pathogenesis and progression have been studied for over two decades, lack of in vivo models that recapitulate chronic, progressive, and irreversible nature of IPF have contributed to limited therapeutic success in clinical trials. Currently, only two drugs, Pirfenidone and Nintedanib, are approved for IPF treatment in the US, with their efficacy yet to be completely determined. Patients with IPF often observe lung infections, alveolar collapse, and respiratory failure, which are associated with focal edema and local hypoxia and contribute to development of hypoxemia associated with acute exacerbation of IPF (AE-IPF). In my thesis, I posit that hypoxic injury to the lung epithelium can initiate profibrotic signaling that can contribute to pathogenesis and progression of pulmonary fibrosis in vitro and in vivo. In my in silico studies, I analyzed human protein kinases to identify structural peculiarities that diversify their functions and highlight central hub kinases governing cell signaling. Using this approach, I identified Focal Adhesion Kinase 1 (FAK1) as a central hub kinase contributing to cytoskeletal remodeling. My proteomics and transcriptional studies defined in vitro effect of hypoxia in activation of lung epithelial cells. Using systems biology approaches, I identified interplay between transforming growth factor – β (TGF–β) signaling, hypoxia signaling, and FAK1 signaling. Further, my studies identified Galectin-1 as a novel mediator of hypoxia-induced pulmonary fibrosis. To mimic exacerbation of PF in patients, I developed a novel mouse model of exacerbated pulmonary fibrosis using subclinical bleomycin injury with chronic hypoxia. Further, to fill the existing requirement of an in vivo model of chronic PF, I characterized a triple transgenic mouse model that conditionally activates hypoxia signaling in the lung epithelial cells and causes progressive PF over a span of 12 weeks. Lastly, I performed RNA-Seq experiments on primary AEC2s isolated from our transgenic mouse model to identify a hypoxia-mediated profibrotic role of microRNA-96 in down-regulation of PTEN, a tumor suppressor and anti-fibrotic protein. In conclusion, my studies established in vitro and in vivo roles of hypoxia in profibrotic activation of lung epithelium and identifies FAK1 and Gal-1 as key drivers of hypoxia-mediated fibrosis, which should be further evaluated in animal and human studies to determine their therapeutic potential.

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22003号 / 医博第4517号 / 新制||医||1038(附属図書館) / 京都大学大学院医学研究科医学専攻 / (主査)教授 長船 健二, 教授 川口 義弥, 教授 柳田 素子 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Preclinical models of lupus indicate that T cell-B cell collaboration drives antinuclear antibody (ANA) production and sustains T cell activation. Autoreactive B lymphocytes are present in the normal repertoire but persist as ignorant or anergic cells. Mechanisms that normally limit T cell activation of autoreactive B cells remain incompletely resolved, but potentially include the absence of autoreactive effector T cell subsets and/or the presence of autoAgspecific regulatory T cells (Tregs). Several studies have addressed this issue by using experimental systems dependent on transgenic autoreactive B cells, but much less is known about the activation of autoreactive B cells present in a polyclonal repertoire. In the second chapter of this thesis, I have explored the role of effector T cells and Tregs using mice that express an inducible pseudoautoAg expressed on B cells and other antigen presenting cells (APCs). In this system, activated Th2 cells, but not naïve T cells, elicit the production of ANAs, but ANA production is severely limited by autoAg-specific Tregs. Bone marrow chimera experiments further demonstrated that this B cell activation is constrained by radioresistant autoantigen-expressing APCs (rAPC) present in the thymus as well as by non-hematopoietic stromal cells located in peripheral lymphoid tissue. Importantly, peripheral rAPC expression of autoAg induced the expansion of a highly effective subset of CD62L+CD69+ Tregs. The third chapter of this thesis focuses on the contribution of CD8+ T cells to fibrosis resulting from sterile lung injury. Type 2 effector production of IL-13 is v a demonstrated requirement in several models of fibrosis, and is routinely ascribed to CD4+ Th2 cells. However, we now demonstrate a major role for pulmonary CD8+ T cells, which mediate an exaggerated wound healing response and fibrosis through robust differentiation into IL-13-producing pro-fibrotic type 2 effectors (Tc2). Remarkably, differentiation of these Tc2 cells in the lung requires IL-21. We further show that the combination of IL-4 and IL-21 skews naïve CD8+ T cells to produce IL-21, which in turn acts in an autocrine manner to support robust IL-13 production. TGF-β negatively regulates production of IL-13 by suppressing CD8+ T cell responsiveness to IL-21. Our data illuminate a novel pathway involved in the onset and regulation of pulmonary fibrosis, and identify Tc2 cells as key mediators of fibrogenesis.

Chronic Obstructive Pulmonary Disease (COPD) is the 3rd leading cause of death in the US, and idiopathic pulmonary fibrosis (IPF), a type of Interstitial Lung Disease (ILD), is a fast acting, irreversible disease that leads to mortality within 3-5 years. RNA-sequencing provides the opportunity to quantitatively examine the sequences of millions mRNAs, and offers the potential to gain unprecedented insights into the structure of chronic non-malignant lung disease transcriptome. By identifying changes in splicing and novel loci expression associated with disease, we may be able to gain a better understanding of their pathogenesis, identify novel disease-specific biomarkers, and find better targets for therapy. Using RNA-seq data that our group generated on 281 human lung tissue samples (47=Control, 131=COPD, 103=ILD), I initially defined the transcriptomic landscape of lung tissue by identifying which genes were expressed in each tissue sample. I used a mixture model to separate genes into reliable and not reliable expression. Next, I employed reads that overlapped splice junctions in a linear model interaction term to identify disease-specific differential splicing. I identified alternatively spliced genes between control and disease tissues and validated three (PDGFA, NUMB, SCEL) of these genes with qPCR and nanostring (a hybridization-based barcoding technique used to quantify transcripts). Finally, I implemented and improved a pipeline to perform transcriptome assembly using Cufflinks that led to the identification of 1,855 novel loci that did not overlap with UCSC, Vega, and Ensembl annotations. The loci were classified into potential coding and non-coding loci (191 and 1,664, respectively). Expression analysis revealed that there were 120 IPF-associated and 10 emphysema-associated differentially expressed (q < 0.01) novel loci. RNA-seq provides a high-resolution transcript-level view of the pulmonary transcriptome and its modification in lung disease. It has enabled a new understanding of the lung transcriptome structure because it measures not only the transcripts we know but also the ones we do not know. The approaches and improvements I have employed have identified these novel targets and make possible further downstream functional analysis that could identify better targets for therapy and lead to an even better understanding of chronic lung disease pathogenesis. / 2031-01-01T00:00:00Z

京都大学 / マギル大学 / 新制・課程博士 / 博士(ゲノム医学) / 甲第24203号 / 医博JD第1号 / 新制||医||JD1(附属図書館) / 京都大学大学院医学研究科京都大学マギル大学ゲノム医学国際連携専攻 / (主査)教授 稲垣 暢也, 教授 YOUSSEFIAN Shohab, 准教授 Majewski Jacek (マギル大学), 准教授 Gravel Simon (マギル大学), 教授 Gagneur Julien (ミュンヘン工科大学) / 学位規則第4条第1項該当 / Doctor of Philosophy in Human Genetics / Kyoto University / McGill University / DFAM