Project description:Analysis of targets organs might help to get new insights into the pathogenesis of autoimmune diseases. We used global gene expression profiling of minor salivary glands to identify distinct patterns of gene expression in patients with primary Sjögrens syndrome (pSS), a frequent and prototype systemic autoimmune disease. Gene expression signature allowed to distinguish most patients with pSS from healthy controls
Project description:Even though autoimmune diseases are heterogeneous, believed to result from the interaction between genetic and environmental components, patients with these disorders exhibit reproducible patterns of gene expression in their peripheral blood mononuclear cells. A portion of this gene expression profile reflects family resemblance rather than the actual presence of an autoimmune disease. Here we wanted to identify that portion of this gene expression pattern that is independent of family resemblance and determine if it is a product of disease duration, disease onset, or other factors. By increasing the number of autoimmune samples in our analysis and employing supervised clustering algorithms, we identified 100 genes whose expression profiles are shared in individuals with various autoimmune diseases but are not shared by first-degree relatives of individuals with autoimmune disease or by controls. Individuals with early disease (1 yr after onset) and established disease (10 yr after onset) exhibit a near identical expression pattern suggesting that this unique profile reflects disease onset rather than disease duration. supervised gene expression profiling were performed to a cohort sample pool: control individuals(8), unaffected family members of autoimmune diseases patients (8), and individuals with autoimmune diseases (54). we try to identify a gene expression signatures that were exclusively associated with autoimmune diseases but not infulenced by genetic components
Project description:Even though autoimmune diseases are heterogeneous, believed to result from the interaction between genetic and environmental components, patients with these disorders exhibit reproducible patterns of gene expression in their peripheral blood mononuclear cells. A portion of this gene expression profile reflects family resemblance rather than the actual presence of an autoimmune disease. Here we wanted to identify that portion of this gene expression pattern that is independent of family resemblance and determine if it is a product of disease duration, disease onset, or other factors. By increasing the number of autoimmune samples in our analysis and employing supervised clustering algorithms, we identified 100 genes whose expression profiles are shared in individuals with various autoimmune diseases but are not shared by first-degree relatives of individuals with autoimmune disease or by controls. Individuals with early disease (1 yr after onset) and established disease (10 yr after onset) exhibit a near identical expression pattern suggesting that this unique profile reflects disease onset rather than disease duration. Keywords: gene expression signatures
Project description:Autoimmune Hepatitis (AIH) and Primary Biliary Cholangitis (PBC) are autoimmune diseases that target the liver in which the immune system produces an inappropriate response to self-antigens resulting in inflammation, damage, and dysfunction of hepatic tissues. Despite progress in the understanding of the etiopathogenesis and in the diagnostic and therapeutic approach of these diseases, critical issues remain concerning the early diagnosis of affected individuals. The present study aims to detect and characterize by a gel-based bottom-up proteomic approach the acid-insoluble fraction of salivary proteome from patients affected by AIH and PBC with respect to healthy controls (HCs). The study was performed on the salivary acid-insoluble proteins after in-gel digestion starting from: i) the entire SDS-PAGE lane; ii) a portion of the SDS-PAGE at lowest molecular weight (MW </= 25 kDa).
Project description:This study constructed a proteomics atlas for old and young rheumatism patients and revealed SASPs present in individuals with three specific autoimmune diseases. Although we found several shared aging targets in healthy individuals and autoimmune patients, proteomics markers specific to different autoimmune disorders could still be identified.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
