Project description:Gene expression profiling of CMS4 colon cancer treated with Imatinib in the ImPACCT study. Fresh-frozen biopsies were taken during diagnostic colonoscopy for CMS4 identification. Five patients gave informed consent for two week of neoadjuvant Imatinib therapy prior to removal of the primary tumor. Fresh-frozen samples were taken from surgically resected colon cancer specimens.
Project description:To identify aberrantly expressed long intergenic noncoding RNAs (lincRNAs) in muscle-invasive bladder cancer tissues compared with normal adjacent tissues, we have employed microarray expression profiling as a discovery platform to identify lincRNAs that may play important roles in bladder cancer progression. Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were obtained during surgical resection, and total RNA was extracted for microarray analysis.
Project description:To identify aberrantly expressed long intergenic noncoding RNAs (lincRNAs) in bladder cancer tissues compared with normal adjacent tissues, we have employed microarray expression profiling as a discovery platform to identify lincRNAs that may play important roles in bladder cancer origin and progression. Samples of fresh frozen cancer tissues, together with normal adjacent tissues (3 cm away from the tumor), were obtained during surgical resection, and total RNA was extracted for microarray analysis.
Project description:Proteomic analyses of human tissues are sometimes conducted on autopsy samples. However, no comparative analysis between proteomic data derived from autopsy samples and fresh frozen samples has been undertaken, nor has there been an assessment of the post-mortem interval (PMI) influences on protein quantification. In the current study, 94 human left anterior descending (LAD) coronary artery were collected from deceased patients. Proteins were analysed using nanoflow liquid chromatography-tandem mass spectrometry. Data were processed with Proteome Discoverer and Mascot. The correlations between the protein abundances and the PMI were calculated. DAVID software was used for pathway and GO annotation enrichment. Among consistently quantified proteins, approximately 40% of the protein abundances exhibited significant correlations with PMI, most of which being inverse. Notably, smooth muscle cell markers displayed substantial reduction with prolonged PMI. Conversely, positive correlations with PMI were observed for immunoglobulins, coagulation factors, and complement factors, including coagulation factor XII, plasminogen, and lactotransferrin. Comparative analyses of sex differences between autopsy LAD samples and fresh-frozen LAD samples (n=65) showed no concordance in protein quantification. However, a robust correlation was observed within a sex comparison conducted between fresh-frozen carotid endarterectomies (CEA) from 2 different cohorts (n=104 and n=200). This study represents the first large-scale proteomics investigation into the influence of PMI on the protein composition of human vasculature. We observed significant correlations with PMI for nearly 40% of the consistently quantified proteins. Our findings underscore potential discrepancies in the quantitative accuracy of proteomics data derived from autopsy samples. Consequently, results obtained from post-mortem specimens may not be reproducible in fresh-frozen samples.
Project description:This dataset was applied to evaluate the performance of a deep learning framework, FFPERescuer, specifically designed to reconstruct gene expression profiles from RNA sequencing data derived from FFPE (formalin-fixed, paraffin-embedded) tumor tissues. The dataset includes a total of 12 RNA-Seq samples, comprising 10 FFPE tumor tissue samples from colorectal cancer (CRC) cases collected in Amsterdam, the Netherlands, with 2 duplicate samples included for reproducibility assessment. The corresponding gene expression profiles from fresh-frozen tumor tissues for these 10 cases are available in the dataset GSE33113, generated using microarray technology.