Made available in DSpace on 2015-12-06T23:47:21Z (GMT). No. of bitstreams: 0 / Objetivo: Analisar as diferenças histopatológicas entre os lobos pulmonares submetidos a biópsia cirúrgica de pacientes com fibrose pulmonar idiopática. Métodos: Foram incluídos 16 pacientes com resultados de biópsias concordantes de dois sítios pulmonares, o lobo médio ou o segmento lingular. Técnicas semiquantitativas foram utilizadas na avaliação histológica pulmonar, aplicando-se um escore com base nas alterações encontradas no padrão histológico de pneumonia intersticial usual (PIU). Resultados: Encontrou-se maior incidência de foco fibroblástico em lobo inferior esquerdo e maior volume médio dos fragmentos pulmonares originários do lobo médio. Nenhuma diferença significante, que viesse a mudar o estadiamento da doença, e independentemente do local de origem da biópsia, foi encontrada. Conclusão: Não há dados que fundamentem a rejeição ao uso dos lobos médios e segmentos lingulares na investigação histológica de doenças intersticiais, em especial a fibrose pulmonar idiopática.. / Objective: To analyze the histopathology differences between the pulmonary lobes submitted to surgical biopsy in patients with idiopathic pulmonary fibrosis. Methods: Sixteen patients with usual interstitial pneumonia and concordant biopsies of two distinct lobes (the middle lobe or the lingula) were included in this study. Semiquantitative techniques were used in the histological evaluation of fragments of different lobes of the lung. A score was applied for the evaluation of usual interstitial pneumonia. Results: A greater incidence of fibroblastic foci was found in the left inferior lobe, and a greater mean volume of pulmonary fragments was obtained from the middle lobe. No significant difference was found in variables related to disease staging, no matter what was the pulmonary lobe. Conclusion: There is no reason to despise the middle lobe and the lingula in the histopathological investigation of interstitial diseases of the lung, especially the idiopathic pulmonary fibrosis. / BV UNIFESP: Teses e dissertações

京都大学 / 0048 / 新制・課程博士 / 博士(医学) / 甲第22883号 / 医博第4677号 / 新制||医||1048(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 平井 豊博, 教授 川上 浩司, 教授 椛島 健治 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Idiopathic pulmonary fibrosis (IPF) is one of the most aggressive and severe interstitial lung diseases (ILDs) for which there is no cure. IPF is characterized by an excessive accumulation of fibroblasts which secrete an abundance of extracellular proteins such as collagen. These processes lead to repetitive tissue scarring and fibrosis in the lung parenchyma. As a result, lungs become rigid limiting oxygen intake and gas exchange. Once diagnosed, IPF is fatal within 2-3 years. There is no known cause or proven treatment that significantly improves outcomes. Although the cause is unknown, the current model of IPF suggests that an overactive epithelial repair mechanism caused by genetic and epigenetic factors as well as environmental exposures is responsible for the chronic fibrosis and scarring characteristic of IPF. The transforming growth factor beta (TGF-B) signaling pathway has been implicated as a major contributor in activating this chronic fibrosis. An upstream activator of the TGF-B pathway, avB6, has been identified as a potential therapeutic target. My collaborators in Dr. David Baker's lab at the University of Washington have created a novel avB6 integrin inhibitor (BP2_disulf) whose efficacy in improving IPF outcomes has yet to be tested. In my study, I test the ability of BP2_disulf to combat IPF through the use of the standard IPF murine model and translatable end points like non-invasive uCT scans, pulmonary function tests, bronchoalveolar lavage fluid (BALF) profiles, and histology. With these methods, I demonstrate that intraperitoneal injection of BP2_disulf in bleomycin-injured mice has the ability to decrease rate of fibrotic progression and pulmonary function decline compared to mice treated with bleomycin alone. These results prove that BP2_disulf is a promising therapeutic not only for IPF but other ILDs as well. Further efficacy validation and investigation into an aerosolized delivery method will advance this drug to clinical trials and make it accessible to those in need.

Les mutations du gène codant pour la protéine C (SP-C) du surfactant pulmonaire (SFTPC) sont à l’origine de pathologies interstitielles chroniques du nourrisson, de l’enfant mais également de l’adulte. Une importante hétérogénéité phénotypique est cependant observée, y compris au sein d’une même famille. Par un épissage alternatif, le gène SFTPC permet la synthèse de deux isoformes du précurseur protéique de SP-C (proSP-C) pour aboutir à la protéine mature après plusieurs modifications post-traductionnelles. Les conséquences des mutations de SFTPC sur l'homéostasie du surfactant ne sont pas clairement élucidées, mais il semble que le mauvais repliement de la protéine soit une caractéristique commune. A l’issue de nos travaux antérieurs, nous avons mis en évidence un effet de certaines mutations et de polymorphismes sur l’épissage de SFTPC faisant ainsi varier significativement l’expression de chacune des deux isoformes protéiques, sans qu’à l’heure actuelle nous ne connaissions le rôle de chacune dans la synthèse de la protéine SP-C mature. Notre projet, s’inscrivant dans la continuité de mon master 2, a pour but de mieux comprendre les mécanismes physiopathologiques pré et post-transcriptionnels associés aux variations de SFTPC et leurs conséquences sur le développement des pneumopathies interstitielles. Le premier axe de notre projet repose sur l’étude in vitro (lignées cellulaires) et in vivo (modèle murin, ARN des patients) des variations de chacun des isoformes. Dans un second axe, nous souhaitons poursuivre l'étude de facteurs pouvant influencer le phénotype des patients porteurs de mutations du gène SFTPC, qu'ils soient d'origine externes (infections virales et bactériennes ou environnementaux comme le tabac) ou génétique. Collectivement, ces études nous permettrons de fournir une signature moléculaire pour cette maladie et d’identifier de nouvelles cibles thérapeutiques afin d’en améliorer le pronostic mais également la prise en charge et la qualité de vie des patients. / Surfactant pathologies linked to mutations in the SFTPC gene, via autosomal dominant transmission, are most commonly associated with diffuse interstitial diseases in infants, children and adults, and may also be responsible for acute respiratory distress syndrome in newborns. They are most often accompanied by a high morbidity and mortality rate, thus rendering early diagnosis essential for ideal intervention and support. Mutations in the SFTPC gene lead to alveolar and intracellular accumulation of an abnormal form of the precursor protein SP-C (ProSP-C), which is responsible for the resulting tissue damage. However, the pathophysiological mechanisms are not yet completely deciphered. The gene encodes two isoforms of ProSP-C from three alternative transcripts. The expression level of each is currently unknown and the vast majority of studies evaluating the effect of mutations are performed on only one isoform. Incidentally, our preliminary results on the analysis of RNA extracted from bronchoalveolar washing, both from control subjects and patients harboring a mutation, show that the all three SFTPC transcripts are expressed and that the presence of a mutation is associated with a variation in the expression levels of the transcripts. The aim of my project is to study the expression level of SFTPC transcripts and ProSP-C isoforms from the heterologous expression of the SFTPC gene (exons and introns) in cell lines. I will beanalyzing the post-translational maturation profile of these pro-proteins and evaluating the effect of the mutations on their expression and maturation in both our cellular models and in vivo with two Knock-in mice models.A better understanding of the pathophysiology of genetic abnormalities associated with mutations in the SFTPC gene will not only greatly contribute to earlier management of patients, but also it will help in modifying the progression of lung injury and its prognosis.

京都大学 / 新制・課程博士 / 博士(医学) / 甲第23782号 / 医博第4828号 / 新制||医||1057(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 羽賀 博典, 教授 波多野 悦朗, 教授 溝脇 尚志 / 学位規則第4条第1項該当 / Doctor of Medical Science / Kyoto University / DFAM

Idiopathic pulmonary fibrosis (IPF) is a disease of unknown pathogenesis characterized by scarring of the lung and declining respiratory function. Originating from bone marrow, circulating monocytes can be recruited into the lung tissue and polarized toward the alternatively activated (M2) profibrotic macrophage phenotype. Recent literature has shown that cluster of differentiation 14 positive (CD14+) monocytes are more abundant in IPF patient blood and are associated with disease outcome and acute exacerbation. Additionally, a 52-gene risk profile from peripheral blood mononuclear cells for outcome prediction in IPF was recently published. Here, we began by characterizing macrophages in human IPF lung tissue. We then assembled a biobank and examined transcriptomic characteristics of blood-derived circulating monocytes from IPF patients. Various histological assessments were completed on a tissue microarray including lung biopsies from 24 IPF patients and 17 controls, to characterize M2 macrophage expression in human tissue. Whole blood samples were collected from 50 IPF patients and 12 control subjects. CD14+ monocytes were isolated and mRNA was extracted for bulk RNA sequencing. Data were analyzed for differential expression (DE), and Gene Set Enrichment Analysis (GSEA) was performed to examine enrichment of the previously published 52-gene risk profile in our dataset. We found that M2 macrophage expression was increased in IPF lung tissue compared to controls. CD14+ monocyte levels were significantly elevated in IPF patients in our cohort compared to control participants, and was negatively correlated with forced vital capacity (FVC). DE analysis comparing IPF and control monocytes yielded a 35-gene signature, with 16 up-regulated genes and 19 down-regulated genes. When comparing the signature related to long transplant-free survival from the published dataset to our data, GSEA demonstrated that this signature is enriched in donors from our dataset, supporting concurrence between the meanings of the two datasets. Overall, these results provide insight to identify targets to modulate monocyte/macrophage function in IPF and potentially affect progressive disease. / Thesis / Master of Science (MSc) / Idiopathic pulmonary fibrosis (IPF) is a disease of unknown cause that results in excessive scarring of the lungs and progressive impairment in lung function. We believe that white blood cells called monocytes and macrophages play a key role in the development and progression of this disease. Overall, it is thought that monocytes, which circulate in the blood, enter the lung tissue and become macrophages. These macrophages then lead to the formation of scar tissue, which is characteristic to IPF. In order to better understand how these cells contribute to IPF, we studied their properties in blood and lung biopsies from IPF patients. We found significant differences between monocytes/macrophages in IPF than those in healthy controls, that may help explain disease progression. We hope that these findings will provide insight into causes of the IPF, and potential avenues for therapeutic intervention.

Introdução: A doença intersticial pulmonar (DIP) é uma forma de acometimento visceral grave pela esclerose sistêmica (ES), correspondendo na atualidade à principal causa de mortalidade pela doença. Atualmente, a tomografia computadorizada de alta resolução pulmonar (TCAR) é considerada o padrão-ouro no seu diagnóstico. Estudos recentes têm proposto diversos algoritmos clínicos para a predição diagnóstica e prognóstica da DIP-ES, objetivando ampliar sua detecção precoce e auxiliar na determinação de sua evolução e prognóstico. Objetivo: Testar os algoritmos clínicos propostos na literatura na predição diagnóstica e prognóstica na DIP-ES, estimar sua prevalência e avaliar a associação da extensão do acometimento pulmonar na TCAR com mortalidade em uma coorte de pacientes com ES. Métodos: Estudo de coorte prospectivo, incluindo 177 pacientes com ES recrutados no período de abril de 2000 a abril de 2009, avaliados através de entrevista, exame físico, exames laboratoriais, provas de função pulmonar e TCAR. Algoritmos clínicos (A, B e C), combinando dados da ausculta pulmonar, radiografia de tórax e capacidade vital forçada (CVF), foram aplicados para o diagnóstico de diferentes extensões da pneumopatia intersticial na TCAR. Curvas de Kaplan-Meier e Regressão de Cox uni e multivariada foram utilizadas para analisar a associação dos algoritmos e da extensão de DIP na TCAR com a mortalidade. Resultados: A prevalência estimada de DIP na TCAR do baseline foi de 57,1% e 79 pacientes (44,6%) morreram em uma mediana de 11,1 anos de seguimento. Para identificação de DIP com extensão ≥10 e ≥20% na TCAR, todos os algoritmos apresentaram uma alta sensibilidade (>89%) e um likelihoodratio negativo muito baixo (<0,16). Para fins prognósticos, sobrevida foi reduzida para todos os algoritmos, com destaque para o algoritmo C, o qual identifica DIP considerando a presença de crepitantes na ausculta pulmonar, alterações na radiografia de tórax ou CVF <80% (HR 3,47; IC 95% 1,62-7,42). Pacientes com doença extensa como proposto por Goh e Wells (extensão >20% na TCAR ou, em casos indeterminados, CVF <70%) apresentam uma significativa redução na sobrevida (HR 3,42; IC 95% 2,12-5,52). Sobrevida não foi diferente entre pacientes com extensão ≥10 ou ≥20% na TCAR e análise de mortalidade em 10 anos sugere que extensão >10% na TCAR apresenta uma boa capacidade preditiva para mortalidade, embora não haja um ponto de corte claro a partir do qual ocorra um maior incremento na mortalidade. Conclusão: Algoritmos clínicos apresentam uma alta sensibilidade e um likelihood ratio negativo muito baixo para o diagnóstico de extensões de DIP com relevância clínica e prognóstica (≥10 e ≥20%) e foram fortemente associados com mortalidade. Assim sendo, a utilização desses algoritmos pode evitar a necessidade de realização de TCAR em alguns casos. / Introduction: Interstitial lung disease (ILD) is a form of severe visceral involvement by systemic sclerosis (SSc) and currently is the primary cause of death by disease. Thoracic high-resolution computed tomography (HRCT) is considered the gold standard for diagnosis. Recent studies have proposed several clinical algorithms to predict the diagnosis of SSc-ILD, aiming to expand its early detection and estimate prognosis. Objective: To test the clinical algorithms to predict the presence and prognosis of SSc-ILD, to estimate the prevalence of SSc-ILD, and to evaluate the association of extent of ILD with mortality in a cohort of SSc patients. Methods: Prospective cohort study, including 177 SSc patients assessed by clinical evaluation, laboratory tests, pulmonary function tests, and HRCT. Clinical algorithms, combining lung auscultation, chest radiography and % predicted forced vital capacity (FVC), were applied for the diagnosis of different extents of ILD on HRCT. Univariate and multivariate Cox proportional models were used to analyze the association of algorithms and the extent of ILD on HRCT with the risk of death using hazard ratios (HR). Results: The prevalence of ILD was 57.1% on baseline HRCT and 79 patients died (44.6%) in a median follow-up of 11.1 years. For identification of ILD with extent ≥10 and ≥20% on HRCT, all algorithms presented a high sensitivity (>89%) and a very low negative likelihood ratio (<0.16). For prognosis, survival was decreased for all algorithms, especially the algorithm C (HR 3.47, 95% CI 1.62-7.42), which identified the presence of ILD based on crackles on lung auscultation, findings on chest X-ray or FVC <80%. Extensive disease as proposed by Goh and Wells (extent of ILD >20% on HRCT or, in indeterminate cases, FVC <70%) had a significantly higher risk of death (HR 3.42, 95% CI 2.12 to 5.52). Survival was not different between patients with extent of 10 or 20% of ILD on HRCT, and analysis of 10-year mortality suggested that a threshold of 10% may also have a good predictive value for mortality. However, there is no clear cutoff above which mortality is sharply increased. Conclusion: Clinical algorithms had a good diagnostic performance for extent of SSc-ILD on HRCT with clinical and prognostic relevance (≥10 and ≥20%), and were also strongly related to mortality. Therefore, they probably could be used to obviate the requirement of HRCT in some cases.

Introdução: A doença intersticial pulmonar (DIP) é uma forma de acometimento visceral grave pela esclerose sistêmica (ES), correspondendo na atualidade à principal causa de mortalidade pela doença. Atualmente, a tomografia computadorizada de alta resolução pulmonar (TCAR) é considerada o padrão-ouro no seu diagnóstico. Estudos recentes têm proposto diversos algoritmos clínicos para a predição diagnóstica e prognóstica da DIP-ES, objetivando ampliar sua detecção precoce e auxiliar na determinação de sua evolução e prognóstico. Objetivo: Testar os algoritmos clínicos propostos na literatura na predição diagnóstica e prognóstica na DIP-ES, estimar sua prevalência e avaliar a associação da extensão do acometimento pulmonar na TCAR com mortalidade em uma coorte de pacientes com ES. Métodos: Estudo de coorte prospectivo, incluindo 177 pacientes com ES recrutados no período de abril de 2000 a abril de 2009, avaliados através de entrevista, exame físico, exames laboratoriais, provas de função pulmonar e TCAR. Algoritmos clínicos (A, B e C), combinando dados da ausculta pulmonar, radiografia de tórax e capacidade vital forçada (CVF), foram aplicados para o diagnóstico de diferentes extensões da pneumopatia intersticial na TCAR. Curvas de Kaplan-Meier e Regressão de Cox uni e multivariada foram utilizadas para analisar a associação dos algoritmos e da extensão de DIP na TCAR com a mortalidade. Resultados: A prevalência estimada de DIP na TCAR do baseline foi de 57,1% e 79 pacientes (44,6%) morreram em uma mediana de 11,1 anos de seguimento. Para identificação de DIP com extensão ≥10 e ≥20% na TCAR, todos os algoritmos apresentaram uma alta sensibilidade (>89%) e um likelihoodratio negativo muito baixo (<0,16). Para fins prognósticos, sobrevida foi reduzida para todos os algoritmos, com destaque para o algoritmo C, o qual identifica DIP considerando a presença de crepitantes na ausculta pulmonar, alterações na radiografia de tórax ou CVF <80% (HR 3,47; IC 95% 1,62-7,42). Pacientes com doença extensa como proposto por Goh e Wells (extensão >20% na TCAR ou, em casos indeterminados, CVF <70%) apresentam uma significativa redução na sobrevida (HR 3,42; IC 95% 2,12-5,52). Sobrevida não foi diferente entre pacientes com extensão ≥10 ou ≥20% na TCAR e análise de mortalidade em 10 anos sugere que extensão >10% na TCAR apresenta uma boa capacidade preditiva para mortalidade, embora não haja um ponto de corte claro a partir do qual ocorra um maior incremento na mortalidade. Conclusão: Algoritmos clínicos apresentam uma alta sensibilidade e um likelihood ratio negativo muito baixo para o diagnóstico de extensões de DIP com relevância clínica e prognóstica (≥10 e ≥20%) e foram fortemente associados com mortalidade. Assim sendo, a utilização desses algoritmos pode evitar a necessidade de realização de TCAR em alguns casos. / Introduction: Interstitial lung disease (ILD) is a form of severe visceral involvement by systemic sclerosis (SSc) and currently is the primary cause of death by disease. Thoracic high-resolution computed tomography (HRCT) is considered the gold standard for diagnosis. Recent studies have proposed several clinical algorithms to predict the diagnosis of SSc-ILD, aiming to expand its early detection and estimate prognosis. Objective: To test the clinical algorithms to predict the presence and prognosis of SSc-ILD, to estimate the prevalence of SSc-ILD, and to evaluate the association of extent of ILD with mortality in a cohort of SSc patients. Methods: Prospective cohort study, including 177 SSc patients assessed by clinical evaluation, laboratory tests, pulmonary function tests, and HRCT. Clinical algorithms, combining lung auscultation, chest radiography and % predicted forced vital capacity (FVC), were applied for the diagnosis of different extents of ILD on HRCT. Univariate and multivariate Cox proportional models were used to analyze the association of algorithms and the extent of ILD on HRCT with the risk of death using hazard ratios (HR). Results: The prevalence of ILD was 57.1% on baseline HRCT and 79 patients died (44.6%) in a median follow-up of 11.1 years. For identification of ILD with extent ≥10 and ≥20% on HRCT, all algorithms presented a high sensitivity (>89%) and a very low negative likelihood ratio (<0.16). For prognosis, survival was decreased for all algorithms, especially the algorithm C (HR 3.47, 95% CI 1.62-7.42), which identified the presence of ILD based on crackles on lung auscultation, findings on chest X-ray or FVC <80%. Extensive disease as proposed by Goh and Wells (extent of ILD >20% on HRCT or, in indeterminate cases, FVC <70%) had a significantly higher risk of death (HR 3.42, 95% CI 2.12 to 5.52). Survival was not different between patients with extent of 10 or 20% of ILD on HRCT, and analysis of 10-year mortality suggested that a threshold of 10% may also have a good predictive value for mortality. However, there is no clear cutoff above which mortality is sharply increased. Conclusion: Clinical algorithms had a good diagnostic performance for extent of SSc-ILD on HRCT with clinical and prognostic relevance (≥10 and ≥20%), and were also strongly related to mortality. Therefore, they probably could be used to obviate the requirement of HRCT in some cases.

Introdução: A doença intersticial pulmonar (DIP) é uma forma de acometimento visceral grave pela esclerose sistêmica (ES), correspondendo na atualidade à principal causa de mortalidade pela doença. Atualmente, a tomografia computadorizada de alta resolução pulmonar (TCAR) é considerada o padrão-ouro no seu diagnóstico. Estudos recentes têm proposto diversos algoritmos clínicos para a predição diagnóstica e prognóstica da DIP-ES, objetivando ampliar sua detecção precoce e auxiliar na determinação de sua evolução e prognóstico. Objetivo: Testar os algoritmos clínicos propostos na literatura na predição diagnóstica e prognóstica na DIP-ES, estimar sua prevalência e avaliar a associação da extensão do acometimento pulmonar na TCAR com mortalidade em uma coorte de pacientes com ES. Métodos: Estudo de coorte prospectivo, incluindo 177 pacientes com ES recrutados no período de abril de 2000 a abril de 2009, avaliados através de entrevista, exame físico, exames laboratoriais, provas de função pulmonar e TCAR. Algoritmos clínicos (A, B e C), combinando dados da ausculta pulmonar, radiografia de tórax e capacidade vital forçada (CVF), foram aplicados para o diagnóstico de diferentes extensões da pneumopatia intersticial na TCAR. Curvas de Kaplan-Meier e Regressão de Cox uni e multivariada foram utilizadas para analisar a associação dos algoritmos e da extensão de DIP na TCAR com a mortalidade. Resultados: A prevalência estimada de DIP na TCAR do baseline foi de 57,1% e 79 pacientes (44,6%) morreram em uma mediana de 11,1 anos de seguimento. Para identificação de DIP com extensão ≥10 e ≥20% na TCAR, todos os algoritmos apresentaram uma alta sensibilidade (>89%) e um likelihoodratio negativo muito baixo (<0,16). Para fins prognósticos, sobrevida foi reduzida para todos os algoritmos, com destaque para o algoritmo C, o qual identifica DIP considerando a presença de crepitantes na ausculta pulmonar, alterações na radiografia de tórax ou CVF <80% (HR 3,47; IC 95% 1,62-7,42). Pacientes com doença extensa como proposto por Goh e Wells (extensão >20% na TCAR ou, em casos indeterminados, CVF <70%) apresentam uma significativa redução na sobrevida (HR 3,42; IC 95% 2,12-5,52). Sobrevida não foi diferente entre pacientes com extensão ≥10 ou ≥20% na TCAR e análise de mortalidade em 10 anos sugere que extensão >10% na TCAR apresenta uma boa capacidade preditiva para mortalidade, embora não haja um ponto de corte claro a partir do qual ocorra um maior incremento na mortalidade. Conclusão: Algoritmos clínicos apresentam uma alta sensibilidade e um likelihood ratio negativo muito baixo para o diagnóstico de extensões de DIP com relevância clínica e prognóstica (≥10 e ≥20%) e foram fortemente associados com mortalidade. Assim sendo, a utilização desses algoritmos pode evitar a necessidade de realização de TCAR em alguns casos. / Introduction: Interstitial lung disease (ILD) is a form of severe visceral involvement by systemic sclerosis (SSc) and currently is the primary cause of death by disease. Thoracic high-resolution computed tomography (HRCT) is considered the gold standard for diagnosis. Recent studies have proposed several clinical algorithms to predict the diagnosis of SSc-ILD, aiming to expand its early detection and estimate prognosis. Objective: To test the clinical algorithms to predict the presence and prognosis of SSc-ILD, to estimate the prevalence of SSc-ILD, and to evaluate the association of extent of ILD with mortality in a cohort of SSc patients. Methods: Prospective cohort study, including 177 SSc patients assessed by clinical evaluation, laboratory tests, pulmonary function tests, and HRCT. Clinical algorithms, combining lung auscultation, chest radiography and % predicted forced vital capacity (FVC), were applied for the diagnosis of different extents of ILD on HRCT. Univariate and multivariate Cox proportional models were used to analyze the association of algorithms and the extent of ILD on HRCT with the risk of death using hazard ratios (HR). Results: The prevalence of ILD was 57.1% on baseline HRCT and 79 patients died (44.6%) in a median follow-up of 11.1 years. For identification of ILD with extent ≥10 and ≥20% on HRCT, all algorithms presented a high sensitivity (>89%) and a very low negative likelihood ratio (<0.16). For prognosis, survival was decreased for all algorithms, especially the algorithm C (HR 3.47, 95% CI 1.62-7.42), which identified the presence of ILD based on crackles on lung auscultation, findings on chest X-ray or FVC <80%. Extensive disease as proposed by Goh and Wells (extent of ILD >20% on HRCT or, in indeterminate cases, FVC <70%) had a significantly higher risk of death (HR 3.42, 95% CI 2.12 to 5.52). Survival was not different between patients with extent of 10 or 20% of ILD on HRCT, and analysis of 10-year mortality suggested that a threshold of 10% may also have a good predictive value for mortality. However, there is no clear cutoff above which mortality is sharply increased. Conclusion: Clinical algorithms had a good diagnostic performance for extent of SSc-ILD on HRCT with clinical and prognostic relevance (≥10 and ≥20%), and were also strongly related to mortality. Therefore, they probably could be used to obviate the requirement of HRCT in some cases.

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