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

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This thesis focuses on the characterization of rhythmic activity in the colon of healthy subjects and patients diagnosed with refractory constipation; this activity is mediated by pacemaker cells in the gastrointestinal system, the Interstitial cells of Cajal (ICC). The myogenic activity described are the cyclic motor patterns (CMP) and haustral activity; characterization of these motor patterns in healthy subjects provided control values for the subsequent comparison in patients. Frequency analysis of CMP revealed a novel high-frequency activity (7-15cpm) unrelated to the breathing artefact. Three categories of cyclic motor patterns were observed: (1) CMP following mass peristaltic events (HAPW); (2) those that occur in isolation of other colonic motor patterns (HAPW) in the colon; and (3) low-frequency (2-6cpm), prominently retrograde rhythmic activity in the rectum. CMP were scarcely present in majority of the patients; however, elevated retrograde CMP in the distal colon and rectum in some patients plays a role in retarding flow of colonic content. A detailed characterization of haustral activity (comprised of 2 boundaries and the activity within a haustrum) is reported for the first time using high-resolution colonic manometry. Furthermore, we find that over expression of haustral boundary activity in patients serves as a disproportionate hindrance in colonic transit. An in-depth methodology is developed for the identification and subsequent analysis of haustral activity and CMP; this provides transparency in the data acquisition and analysis. Lastly, a sphincter at the rectosigmoid junction, sphincter of O’Beirne is presented in a patient case report. The persistent presence and paradoxical contractions of this sphincter served to impede flow colonic content, an important factor contributing to the pathophysiology of severe refractory constipation. / Thesis / Master of Science (MSc) / Colonic manometry tests and measures strength and coordination of colonic muscles contractions. This tool was used to understand the rhythmic colonic motor patterns and their contribution to motility in healthy subjects and patients with constipation. Rhythmic activity in the gut is mediated by pacemaker cells, Interstitial cells of Cajal (ICC). We present a detailed characterization of ICC-mediated rhythmic activity that (1) occurs in the small pouches making up the colon (haustra) and (2) is greater than 5cm along the length of the colon (cyclic motor patterns-CMP).CMP possess high-frequency activity (7-15cpm), in addition to activity observed in the low-frequency range (2-6cpm). Activity in the haustra, or haustral activity, is comprised of 2 boundaries with activity within these bounds (intra-haustral activity); the overexpression in patients serves to retard flow of colonic content. Sphincter of O’Beirne is the last haustral boundary at the rectosigmoid junction; its persistent presence was characterized in a patient with refractory constipation.

No description available.

<p>An investigation of the influence of three alloying elements Chromium, Phosphorus, and Nitrogen with the solute types of oversized substitutional, undersized substitutional, and interstitial on the irradiation induced microstructural evolution and hardening</p>

High interstitial fluid pressure (IFP) in tumours is recognized as a barrier to drug delivery resulting in reduced efficacy. High IFP impedes the normal process of convective fluid flow (CFF) from blood vessels into the interstitium. The aim of this study was to develop an in vitro model that could be used to measure CFF and to study its effects on drug delivery. The model consists of a transwell cell culture insert which supports the growth of multicell layers (MCL) on collagen coated membranes. A graduated tube is inserted into the transwell and a pressure gradient is applied across the membrane by raising the volume of medium in the tube above that of the bottom chamber. CFF is determined by measuring the weight of medium in the bottom chamber as a function of time. CFF was inversely proportional to MCL thickness and 41.1±3.6µm thick MCL has completely stopped CFF. Using a physiologically relevant hydrostatic pressure of 28mmHg, a CFF of 21µL/min was recorded using a DLD-1 MCL that was 12.21±3.2µm thick. Under these conditions, the rates of penetration of doxorubicin, imatinib and gefitinib were respectively 42, 26 and 13 folds greater than when no CFF exists. Reversing the CFF so that it opposed the drug diffusion gradient significantly impairs drug penetration. In conclusion, a novel in vitro model for assessing the impact of CFF on drug delivery has been developed. This model could be used to evaluate strategies designed to increase drug delivery to solid tumours by modifying the CFF.

Tissues arising late in evolutionary time, such as lung alveoli that are unique to air breathing organisms, have been challenging to generate in vitro from pluripotent stem cells (PSCs), in part because there are limited lower organism model systems available to provide the necessary developmental roadmaps to guide in vitro differentiation. Furthermore, pulmonary alveolar epithelial type II cell (AEC2) dysfunction has been implicated as a primary cause of pathogenesis in many poorly understood lung diseases that lack effective therapies, including interstitial lung disease (ILD) and emphysema. Here we report the successful directed differentiation in vitro of human PSCs into AEC2s, the facultative progenitors of lung alveoli. Using gene editing to engineer multicolored fluorescent reporter PSC lines (NKX2-1GFP;SFTPCtdTomato), we track and purify human SFTPC+ alveolar progenitors as they emerge from NKX2-1+ endodermal developmental precursors in response to stimulation of Wnt and FGF signaling. Purified PSC-derived SFTPC+ cells are able to form monolayered epithelial spheres (“alveolospheres”) in 3D cultures without the need for mesenchymal co-culture support, exhibit extensive self-renewal capacity, and display additional canonical AEC2 functional capacities, including innate immune responsiveness, the production of lamellar bodies able to package surfactant, and the ability to undergo squamous cell differentiation while upregulating type 1 alveolar cell markers. Guided by time-series global transcriptomic profiling we find that AEC2 maturation involves downregulation of Wnt signaling activity, and the highest differentially expressed transcripts in the resulting SFTPC+ cells encode genes associated with lamellar body and surfactant biogenesis. Finally, we apply this novel model system to generate patient-specific AEC2s from induced PSCs (iPSCs) carrying homozygous surfactant mutations (SFTPB121ins2), and we employ footprint-free CRISPR-based gene editing to observe that correction of this genetic lesion restores surfactant processing in the cells responsible for their disease. Thus we provide an approach for disease modeling and future functional regeneration of a cell type unique to air-breathing organisms.

No description available.

No description available.

Ce mémoire de maîtrise porte sur le développement de microaiguilles hydrogels pour la capture et la détection précoce de biomarqueurs protéiques spécifiques du liquide interstitiel cutané. Le diagnostic précoce d’une maladie et le suivi préventif des paramètres biologiques peuvent effectivement améliorer les traitements et auront un rôle plus important dans les années à venir. Cependant, des obstacles considérables à cette approche persistent, en particulier la nature hautement invasive et perturbatrice des analyses biologiques. Se rendre dans une clinique et subir un prélèvement invasif de sang (ou de liquide biologique) sont des défis considérables par rapport aux traitements courants, qui consistent souvent en des médicaments qui peuvent être pris sans douleur à la maison. Une solution à ces problèmes peut être trouvée dans l'invention de méthodes peu invasives pour le diagnostic et l'analyse des soins de santé, idéalement celles qui peuvent être utilisées à domicile sans nécessiter de personnel formé. À cet égard, les micro-aiguilles (MNs) démontrent un énorme potentiel car leur petite taille garantit qu’elles sont relativement simples et presque indolores. De plus, leur nature simple et à usage unique permet potentiellement une administration à domicile par le patient. Les micro-aiguilles d'hydrogel présentent des caractéristiques bénéfiques à des fins de diagnostic compte tenu de leurs propriétés de gonflement qui permettent d'absorber les fluides corporels tels que le liquide interstitiel (ISF) et de capturer les biomarqueurs. Ces caractéristiques remarquables ont poussé les scientifiques à utiliser des micro-aiguilles d'hydrogel pour des applications de diagnostic. Afin de fournir un contexte pour le développement de cette technologie, cette thèse commence par un examen des principes et des avancées récentes dans le domaine des applications diagnostiques des MN (Chapitre 1). Par la suite, des sections expérimentales, de résultats et de discussion seront présentes sur la fonctionnalisation de l'hydrogel avec des anticorps pour la détection de biomarqueurs spécifiques (Chapitre 2). Le dernier chapitre aborde la conclusion générale et les perspectives d'avenir de cette approche (Chapitre 3). / This master’s thesis focuses on the development of hydrogel microneedles (HMNs) for capture and early detection of specific protein biomarkers form the skin interstitial fluid. Early disease diagnosis and preventative monitoring of biological parameters can effectively improve medical results and anticipate playing a more important part in the forthcoming years. However, considerable barriers to this approach persist, specifically the highly invasive and disruptive nature of biological analyses. Visiting clinics and undergoing invasive blood (or biological fluid) sampling are considerable challenges in comparison with common treatments, which often consist of drugs that may be taken painlessly at home. A solution to these concerns can be found in the invention of minimally invasive methods for diagnostics and healthcare analyzing, ideally ones that may be utilized at home without the requirement for trained staff. In this regard, microneedles (MNs) demonstrate tremendous potential as their small size ensures that they are relatively straightforward and almost painless. Also, their simple and single-use nature potentially permits at-home administration by the patient. HMNs demonstrate beneficial features for the diagnosis purposes considering the swelling properties of them which give the chance of absorbing body fluids such as ISF and capture of the biomarkers. These remarkable features have driven scientists to employ HMNs for diagnostic applications. To provide background for the development of this technology, this thesis begins with a review of the principles and recent advances in the field of diagnostic applications of MNs (Chapter 1). Subsequently, experimental, result, and discussion sections will be present about the functionalization of hydrogel with a model antibody for specific biomarkers detection (Chapter 2). The last chapter discusses the general conclusion and future prospects of this approach (Chapter 3).