Project description:Adult cardiac progenitor/stem cells (CPC/CSC) are multipotent resident populations involved in cardiac homeostasis and heart repair. Assisted by complementary RNAseq analysis, we defined the proteome fraction associable to specific CPC functions by comparison with human mesenchymal stem cells (MSC), the reference population for cell therapy. Label-free proteomics analysis identified 526 proteins expressed differentially in CPC. Quantitative iTRAQ analysis confirmed differential expression of a substantial proportion of these proteins expressed specifically in CPC relative to MSC. Systems biology analysis defined a clear overrepresentation of several categories related to enhanced angiogenic potential. The CPC plasma membrane compartment is comprised by 1595 proteins including a minimal signature of 167 proteins expressed preferentially in CPC. Of these core CPC functions, we selected a panel of 15 predicted cell surface markers and validated high differential expression of CDH5, CD200 and F11R in CPC.
Project description:To understand the relationship between protein expression and mRNA translation during primary hepatocytes dedifferentiation, we have employed transcriptome microarrayas a discovery platform. Rat primary hepatocytes were isolated by the method of two-step enzymes perfusion and then cultured on mono-layer in vitro. Samples at 0h( just after perfusion, before planking) , 6h, 12h ,24h and 48h were collected. Integrative analysis of transcriptome and whole cell proteomics (WCP) leaded us to realize the poor correlation of them. This discovery made us realize that targeting mRNA was far from enough in illustrating this process. It would provide new insights from the aspects of post-translational modifications(PTMs).Post-translational modifications play important role in numorous biological and pathological process, but a few reports are related to primary hepatocytes dedifferentiation process, and there is still no integrative proteomics analysis in this field yet. In this study, we perform ubiquitinome phosphorylated proteome, whole cell proteome and transcriptome simultaneously during the five different time points of dedifferentiation in vitro quantified over 6000 modified sites mapping to over 2000 proteins. And comprehensive analysis of these datasets provides novel insight in this field.
Project description:Fatal COVID-19 is often complicated by hypoxemic respiratory failure and acute respiratory distress syndrome (ARDS). Mechanisms governing lung injury and repair in ARDS remain poorly understood because there are no biomarker-targeted therapeutics for patients with ARDS. We hypothesized that plasma proteomics may uncover unique biomarkers that correlate with disease severity in COVID-19 ARDS. We analyzed the circulating plasma proteome from 32 patients with ARDS and COVID-19 using an aptamer-based platform, which measures 7289 proteins, and correlated protein measurements with sequential organ failure assessment (SOFA) scores at 2 time points (Days 1 and 7 following ICU admission). We compared differential protein abundance and SOFA scores at each individual time point and identified 119 proteins at Day 1 and 46 proteins at Day 7 that correlated with patient SOFA scores. We modeled the relationship between dynamic protein abundance and changes in SOFA score between Days 1 and 7 and identified 39 proteins that significantly correlated with changes in SOFA score. Using Ingenuity Pathway Analysis, we identified increased ephrin signaling and acute phase response signaling correlated with increased SOFA scores over time, while pathways related to pulmonary fibrosis signaling and wound healing had an inverse relationship with SOFA scores between Days 1 and 7. These findings suggest that persistent inflammation may drive worsened disease severity, while repair processes correlate with improvements in organ dysfunction over time. This approach is generalizable to more diverse ARDS cohorts for identification of protein biomarkers and disease mechanisms as we strive towards targeted therapies in ARDS.
Project description:Prokaryotes are, due to their moderate complexity, particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant and membrane localized, we could eliminate their initial under-representation compared to the estimated endpoint. A total of 1,250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and around 90% of the expressed protein-coding genes. Genes, whose transcripts were detected, but not their corresponding protein products, were found highly enriched in several genomic islands. Additionally, genes that lacked an ortholog and a functional annotation were not detected at the protein level, and possibly include over-predicted genes in genome annotations. Furthermore, a dramatic membrane proteome re-organization was observed including differential regulation of autotransporters, adhesins and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor. Transcriptome and proteome analysis of B.henselae in two conditions and duplicates: uninduced and induced for host invasion.