Project description:Aim: To discovery biomarkers in JIA base on gene expression from RNA sequencing on PBMC Method: Paired-end Ilumina sequencing to capture gene expression of PBMC from JIA individuals and healthy controls Results:sample heterogeneity makes RNA sequencing on PBMC unsuitable as a first-step method for screening biomarker candidates in JIA
Project description:ARN sample of PBMC from mouse were obtened at 6 times points: 1h, 1h30, 3h, 4h, 18H, 24h, after injection of oleic acid or physiological serum PBMC total RNAs from mouse injected with acid oleic or physiological serum were profiled after hybridization with Agilent SurePrint G3 Mouse GE 8x60K Microarray to identify genes with differential expression
Project description:Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease that displays a significant gender difference in terms of incidence and severity. However, the underlying mechanisms accounting for sexual dimorphism remain unclear. To reveal the heterogeneity in the pathogenesis of SLE between male and female patients. PBMC were collected from 15 patients with SLE (7 males, 8 females) and 15 age-matched healthy controls (7 males, 8 females) for proteomic analysis. Enrichment analysis of proteomic data revealed that type I interferon signaling and neutrophil activation networks mapped to both male and female SLE, while male SLE has a higher level of neutrophil activation compared with female SLE. Our findings define gender heterogeneity in the pathogenesis of SLE and may facilitate the development of gender-specific treatments.
Project description:Benchmarking Proteomics Quantitation in DIA-type data using real patient material to create a benchmark dataset comprising inter-patient heterogeneity
Project description:Large scale proteomic profiling of cell lines can yield valuable insights into the molecular signatures attributed to variable genotypes or induced perturbations. Specifically, the ability to perform deep and rapid proteome analysis of pharmacologically modulated cells could generate drug-protein associations for large libraries of compounds that predict mechanism of action and enable rational drug design. Although isobaric labelling has greatly increased the throughput of proteomic analysis at deep coverage, the commonly used sample preparation workflows often require complex time-consuming steps and/or costly consumables, limiting their suitability for large scale studies. Here, we present a simplified and cost effective one-pot reaction sample preparation workflow in a 96-well plate format with manual parallel processing (SimPLIT), that minimizes processing steps and reduces technical variability. The workflow is based on a sodium deoxycholate lysis buffer and a single detergent clean-up step after peptide labeling, followed by quick off-line fractionation and MS2 analysis. The simplified workflow demonstrates high reproducibility and provides improved proteome representation compared to alternative approaches. We showcase the large-scale applicability of the workflow by investigating proteomic heterogeneity in a panel of colorectal cancer cell lines and by performing target discovery for a set of molecular glue degraders in different cell lines, in a 96-sample assay. Using this workflow, we report a subset of frequently dysregulated proteins in colorectal cancer cells and uncover cell-dependent protein degradation profiles of seven cereblon E3 ligase modulators (CRL4CRBN). Overall, SimPLIT is a robust method that can be easily implemented in most proteomics laboratories for medium-to-large scale TMT-based studies involving deep profiling of cell lines.
Project description:Large scale proteomic profiling of cell lines can yield valuable insights into the molecular signatures attributed to variable genotypes or induced perturbations. Specifically, the ability to perform deep and rapid proteome analysis of pharmacologically modulated cells could generate drug-protein associations for large libraries of compounds that predict mechanism of action and enable rational drug design. Although isobaric labelling has greatly increased the throughput of proteomic analysis at deep coverage, the commonly used sample preparation workflows often require complex time-consuming steps and/or costly consumables, limiting their suitability for large scale studies. Here, we present a simplified and cost effective one-pot reaction sample preparation workflow in a 96-well plate format with manual parallel processing (SimPLIT), that minimizes processing steps and reduces technical variability. The workflow is based on a sodium deoxycholate lysis buffer and a single detergent clean-up step after peptide labeling, followed by quick off-line fractionation and MS2 analysis. The simplified workflow demonstrates high reproducibility and provides improved proteome representation compared to alternative approaches. We showcase the large-scale applicability of the workflow by investigating proteomic heterogeneity in a panel of colorectal cancer cell lines and by performing target discovery for a set of molecular glue degraders in different cell lines, in a 96-sample assay. Using this workflow, we report a subset of frequently dysregulated proteins in colorectal cancer cells and uncover cell-dependent protein degradation profiles of seven cereblon E3 ligase modulators (CRL4CRBN). Overall, SimPLIT is a robust method that can be easily implemented in most proteomics laboratories for medium-to-large scale TMT-based studies involving deep profiling of cell lines.