Theoretical open-loop model of respiratory mechanics in the extremely preterm infant

Non-invasive ventilation is increasingly used for respiratory support in preterm infants, and is associated with a lower risk of chronic lung disease. However, this mode is often not successful in the extremely preterm infant in part due to their markedly increased chest wall compliance that does not provide enough structure against which the forces of inhalation can generate sufficient pressure. To address the continued challenge of studying treatments in this fragile population, we developed a nonlinear lumped-parameter model of respiratory system mechanics of the extremely preterm infant that incorporates nonlinear lung and chest wall compliances and lung volume parameters tuned to this population. In particular we developed a novel empirical representation of progressive volume loss based on compensatory alveolar pressure increase resulting from collapsed alveoli. The model demonstrates increased rate of volume loss related to high chest wall compliance, and simulates laryngeal braking for elevation of end-expiratory lung volume and constant positive airway pressure (CPAP). The model predicts that low chest wall compliance (chest stiffening) in addition to laryngeal braking and CPAP enhance breathing and delay lung volume loss. These results motivate future data collection strategies and investigation into treatments for chest wall stiffening.Comment: 22 pages, 5 figure

Pan-cancer analysis reveals recurrent BCAR4 gene fusions across solid tumors

UNLABELLED: Chromosomal rearrangements often result in active regulatory regions juxtaposed upstream of an oncogene to generate an expressed gene fusion. Repeated activation of a common downstream partner-with differing upstream regions across a patient cohort-suggests a conserved oncogenic role. Analysis of 9,638 patients across 32 solid tumor types revealed an annotated long noncoding RNA (lncRNA), Breast Cancer Anti-Estrogen Resistance 4 (BCAR4), was the most prevalent, uncharacterized, downstream gene fusion partner occurring in 11 cancers. Its oncogenic role was confirmed using multiple cell lines with endogenous BCAR4 gene fusions. Furthermore, overexpressing clinically prevalent BCAR4 gene fusions in untransformed cell lines was sufficient to induce an oncogenic phenotype. We show that the minimum common region to all gene fusions harbors an open reading frame that is necessary to drive proliferation. IMPLICATIONS: BCAR4 gene fusions represent an underappreciated class of gene fusions that may have biological and clinical implications across solid tumors

DANSR: A tool for the detection of annotated and novel small RNAs

Existing small noncoding RNA analysis tools are optimized for processing short sequencing reads (17-35 nucleotides) to monitor microRNA expression. However, these strategies under-represent many biologically relevant classes of small noncoding RNAs in the 36-200 nucleotides length range (tRNAs, snoRNAs, etc.). To address this, we developed DANSR, a tool for the detection of annotated and novel small RNAs using sequencing reads with variable lengths (ranging from 17-200 nt). While DANSR is broadly applicable to any small RNA dataset, we applied it to a cohort of matched normal, primary, and distant metastatic colorectal cancer specimens to demonstrate its ability to quantify annotated small RNAs, discover novel genes, and calculate differential expression. DANSR is available as an open source tool

Cytoskeletal Regulation of the Myofibroblast Phenotype: Central Effects on the Primary Cilium and Redox State

The myofibroblast is a contractile cell which arises from progenitors to elicit wound healing. Dysregulation of these events are the basis of fibrosis, a feature of chronic kidney disease. During myofibroblast transition (MyT) there is the activation of a myogenic program in progenitor cells. This includes reorganization of the actin cytoskeleton in generation of stress fibres. Stabilization of the actin cytoskeleton mobilizes the Myocardin Related Transcription Factor (MRTF) which influences cell fate through expression of the CArGome, a group of myogenic genes containing CArG elements. Here we report that MyT is also characterized by changes in the tubulin network, namely alterations in the primary cilium. The cilium is a cellular antennae and emergence of the myofibroblast results in deciliation both in-vitro and in-vivo, causing a phenotypic shift. Contractility, by myosin, underlies axoneme abscission. During MyT myosin expression is induced by MRTF, while phosphorylation is dependent upon Reactive Oxygen Species (ROS) from the NADPH oxidase Nox4. Nox4 is a permissive, fibrotic factor and dependent upon the TGFβ effecter Smad3. Analysis of the Nox4 promoter revealed a CArG element present raising the potential of regulation by MRTF. In the second part of my thesis, we demonstrate that Nox4 promoter activation, mRNA levels, and protein expression are all dependent upon MRTF. Thus mobilization of MRTF during myofibroblast generation manifests in alteration of the primary cilium through expression and activation of myosin by Nox4 derived ROS. Finally, we extrapolate our core findings and apply it to the context of mitosis. The primary cilium is derived from the mother centriole and must be reabsorbed prior to cell division. This is dependent on signaling involving HEF1, Aurora Kinasa A and HDAC6. We demonstrate that these genes contain CArG elements and further that HEF1 expression is dependent upon MRTF. Suppression of MRTF via siRNA is sufficient to block cilium reabsorption and arrest the cell cycle. We define MRTF as a regulator of the primary cilium via two different pathways: It enables scission by promoting contractility and is necessary for reabsorption by regulating HEF1. Its novel role in HEF1 expression, distinguishes MRTF as a permissive mitogenic factor.Ph.D

Aggregate parameters and output states targeted during simulations.

<p>Aggregate parameters and output states targeted during simulations.</p

Breath-to-breath dynamic lung compliance and tidal volume.

<p>Depicted are high and low <i>C</i>_<i>w</i> conditions, with simulated CPAP triggered in the high <i>C</i>_<i>w</i> condition when recruited fraction dropped 10%, 5%, and 3%.</p

Lung, chest wall, and total respiratory system compliance curves for high <i>C</i>_<i>w</i> (left) and low <i>C</i>_<i>w</i> (right).

<p>Curves are described by Eqs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198425#pone.0198425.e016" target="_blank">(9)</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198425#pone.0198425.e017" target="_blank">(10)</a> and parameterized using the procedures described in <b>Parameterization</b>. Tidal breathing loops with normal <i>R</i>_<i>u</i> (grey) and increased <i>R</i>_<i>u</i> (black) are superimposed for each condition over the lung compliance curve and larger in each inset to display hysteresis.</p

Initial conditions.

<p>Initial conditions.</p

Lumped-parameter respiratory mechanics model, in both volume-pressure (panel A) and electrical (panel B) system analogs.

<p>Each non-rigid compartment has a volume <i>V</i> (black), pressure <i>P</i>, (black) and associated compliance <i>C</i> (green, for emphasis) that is a function of the transmural pressures (purple) across the compartment boundaries. Air flows (red) across resistances <i>R</i> and inertance <i>I</i> (blue) are positive in the direction of the arrows. Circular yellow arrows indication direction of loop summations in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0198425#pone.0198425.e009" target="_blank">Eq (3)</a>. Subscripts: airway opening <i>ao</i>, upper <i>u</i>, collapsible <i>c</i>, small peripheral <i>s</i>, alveolar <i>A</i>, viscoelastic <i>ve</i>, lung elastic <i>el</i>, transmural <i>tm</i>, pleural <i>pl</i>, chest wall <i>cw</i>, muscle <i>mus</i>.</p

Simulations and time to failure (TTF, in hours), defined as 90% volume loss.

<p>Simulations and time to failure (TTF, in hours), defined as 90% volume loss.</p