A Novel Multi-Network Approach Reveals Tissue-Specific Cellular Modulators of Fibrosis in Systemic Sclerosis

Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology.We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues. We used this signature to query tissue-specific functional genomic networks. We performed novel network analyses to contrast the skin and lung microenvironments and to assess the functional role of the inflammatory and fibrotic genes in each organ. Lastly, we tested the expression of macrophage activation state-associated gene sets for enrichment in skin and lung using a Wilcoxon rank sum test

Identification of Cell Cycle–Regulated Genes Periodically Expressed in U2OS Cells and their Regulation by FOXM1 and E2F Transcription Factors

We identify the cell cycle–regulated mRNA transcripts genome-wide in the osteosarcoma-derived U2OS cell line. This results in 2140 transcripts mapping to 1871 unique cell cycle–regulated genes that show periodic oscillations across multiple synchronous cell cycles. We identify genomic loci bound by the G2/M transcription factor FOXM1 by chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) and associate these with cell cycle–regulated genes. FOXM1 is bound to cell cycle–regulated genes with peak expression in both S phase and G2/M phases. We show that ChIP-seq genomic loci are responsive to FOXM1 using a real-time luciferase assay in live cells, showing that FOXM1 strongly activates promoters of G2/M phase genes and weakly activates those induced in S phase. Analysis of ChIP-seq data from a panel of cell cycle transcription factors (E2F1, E2F4, E2F6, and GABPA) from the Encyclopedia of DNA Elements and ChIP-seq data for the DREAM complex finds that a set of core cell cycle genes regulated in both U2OS and HeLa cells are bound by multiple cell cycle transcription factors. These data identify the cell cycle–regulated genes in a second cancer-derived cell line and provide a comprehensive picture of the transcriptional regulatory systems controlling periodic gene expression in the human cell division cycle

Gene Expression Changes Reflect Clinical Response in a Placebo-Controlled Randomized Trial of Abatacept in Patients with Diffuse Cutaneous Systemic Sclerosis

Systemic sclerosis is an autoimmune disease characterized by inflammation and fibrosis of the skin and internal organs. We sought to assess the clinical and molecular effects associated with response to intravenous abatacept in patients with diffuse cutaneous systemic

Correlation Between Aspartate Aminotransferase to Platelet Ratio Index Score and the Degree of Esophageal Varices with Liver Cirrhosis

Background: Esophageal varices is the most common complication in liver cirrhosis. Bleeding varices is a serious complication causing increased mortality rate. In anticipation of those complications, the role of screening test is essential. Endoscopy is the standard method for assessing esophageal varices, but it carries certain risks for patients if it is contraindicated. Moreover, it is an invasive, expensive and uncomfortable procedure. Accordingly, a non-invasive method, aspartat aminotransferase to platelet ratio index (APRI) score, has been developed for evaluating esophageal varices. Method: An analytic cross-sectional observational study was conducted in patients with liver cirrhosis who underwent endoscopy between March 2011 and August 2012. Data were obtained from medical records of hospitalized patients in Mohammad Hoesin General Hospital. The degree of esophageal varices was assessed based on endoscopic findings and APRI score. Spearman test was performed to analyze the correlation between APRI score and the degree of esophageal varices.Results: There were 55 patients, 30 (54.5%) male and 25 (45.5%) female patients, with a range of age between 15-70 years and a mean value of age of 47.09 ± 12.8. APRI score < 0.5 was found in 21.81% subjects, APRI score of 0.5-1.5 was obtained in 41.81% subjects and APRI score > 1.5 was noted in 36.36% subjects with a mean value of 2.32 ± 3.92. There was a correlation between APRI score and degree of esophageal varices with p = 0.011 Conclusion: APRI score can indirectly predict esophageal varices in patients with liver cirrhosis

Regulator combinations identify systemic sclerosis patients with more severe disease

Systemic sclerosis (SSc) is a heterogeneous autoimmune disorder that results in skin fibrosis, autoantibody production, and internal organ dysfunction. We previously identified 4 “intrinsic” subsets of SSc based upon skin gene expression that are found across organ systems. Gene expression regulators that underlie the SSc-intrinsic subsets, or are associated with clinical covariates, have not been systematically characterized. Here, we present a computational framework to calculate the activity scores of gene expression regulators and identify their associations with SSc clinical outcomes. We found that regulator activity scores can reproduce the intrinsic molecular subsets, with distinct sets of regulators identified for inflammatory, fibroproliferative, limited, and normal-like samples. Regulators most highly correlated with modified Rodnan skin score (MRSS) also varied by intrinsic subset. We identified subgroups of patients with fibroproliferative and inflammatory SSc with more severe pathophenotypes, such as higher MRSS and increased likelihood of interstitial lung disease (ILD). Using an independent cohort, we show that the group with more severe ILD was more likely to show forced vital capacity decline over a period of 36–54 months. Our results demonstrate an association among the activation of regulators, gene expression subsets, and clinical variables that can identify patients with SSc with more severe disease

Viewpoint

Entire output for the 106 pathway signature in improvers from gene set enrichment analysis (GSEA). (PDF 367 kb

Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression in systemic sclerosis skin

Abstract Background Infectious agents have long been postulated to be disease triggers for systemic sclerosis (SSc), but a definitive link has not been found. Metagenomic analyses of high-throughput data allows for the unbiased identification of potential microbiome pathogens in skin biopsies of SSc patients and allows insight into the relationship with host gene expression. Methods We examined skin biopsies from a diverse cohort of 23 SSc patients (including lesional forearm and non-lesional back samples) by RNA-seq. Metagenomic filtering and annotation was performed using the Integrated Metagenomic Sequencing Analysis (IMSA). Associations between microbiome composition and gene expression were analyzed using single-sample gene set enrichment analysis (ssGSEA). Results We find the skin of SSc patients exhibits substantial changes in microbial composition relative to controls, characterized by sharp decreases in lipophilic taxa, such as Propionibacterium, combined with increases in a wide range of gram-negative taxa, including Burkholderia, Citrobacter, and Vibrio. Conclusions Microbiome dysbiosis is associated with disease duration and increased inflammatory gene expression. These data provide a comprehensive portrait of the SSc skin microbiome and its association with local gene expression, which mirrors the molecular changes in lesional skin

Bridges between components of the network.

<p>Several genes bridge the component subnetworks of the molecular network. <i>PLAUR</i> is a gene that contains SSc-associated polymorphisms that forms a bridge between the interferon subnetwork and TGFβ/ECM subnetwork. The gene <i>RAC2</i> is a bridge between the interferon and M2 macrophage subnetworks. The genes <i>LCP2</i> and <i>CXCR4</i> are bridges between the M2 macrophage subnetwork and the adaptive immunity subnetwork. There are also several paths through <i>GRB10</i> to <i>ADAP2</i> between the M2 macrophage subnetwork and the adaptive immunity subnetwork. The genes <i>CD14</i> and <i>THY1</i> (<i>CD90</i>) are bridges between the M2 macrophage subnetwork and the TGFβ/ECM subnetwork. The genes <i>IRAK1</i> and <i>PXK</i> are bridges between the TGFβ/ECM subnetwork and the cell proliferation subnetwork.</p