Project description:The SARS-CoV-2 has already caused over 523 million COVID-19 cases and 6.27 million deaths worldwide. COVID-19 leads to a severe acute respiratory syndrome, a hyperinflammatory response, and widespread multi-organ damage. Common symptoms of COVID-19 include fever, cough, fatigue, shortness of breath, and loss of taste and smell. Here we offer an in-depth analysis of the transcriptional response to SARS-CoV-2. We performed RNA-seq analysis of lung tissues from three COVID-19 patients.

2022-09-07 | GSE203401 | GEO

Poor Quantitative Concordance of Proteomic Data between Autopsy Samples and Fresh Frozen Samples from Human Coronary Arteries

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.

2025-06-09 | PXD052071 | Pride

Non-Small Cell Lung Cancer patients undergoing radical radiotherapy

Project description:Currently there is no predictive marker with clinical utility to guide treatment decisions in NSCLC patients undergoing radiotherapy. Identification of such markers would allow treatment options to be considered for more effective therapy. To enable the identification of appropriate protein biomarkers, plasma samples were collected from patients with non-small cell lung cancer before and during radiotherapy for longitudinal comparison following a protocol that carries sufficient power for effective discovery proteomics. Plasma samples from patients pre- and during radiotherapy who had survived >18 months were compared to the same time points from patients who survived <14 months using an 8 channel isobaric tagging tandem mass spectrometry discovery proteomics platform.

2018-10-19 | PXD001052 | Pride

Shotgun proteomics of lung tumors and normal tumor-adjacent tissue of non-small cell lung cancer patients

Project description:Lung tumors, as well as normal tumor-adjacent (NTA) tissue of non-small cell lung cancer (NSCLC) patients, were collected and subjected label-free quantitation shotgun proteomics in data-independent mode to identify differences between the tumors and adjacent tissue. By employing in-depth proteomics, we identified several pathways that are up- or downregulated in the tumors of non-small cell lung cancer patients.

2023-11-27 | PXD046998 | Pride

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HumanRef-v3 samples]

Project description:We performed an expression profiling study of 168 primary breast tumors, lymph node metastases, and autopsy samples of primary breast tumours and metastases to liver, chest wall, lymph node, lung, and spleen, as well as positive and negative RNA controls, with technical replicates, to assess quality control methodology and probe-level reproducibility of the Illumina DASL microarray assay. The experiment included both Illumina DASL HumanRef-v3 and DASL HT-12; this series includes only the 120 HumanRef-v3 samples .

2012-10-02 | GSE32489 | GEO

Expression profiling of formalin-fixed, paraffin-embedded (FFPE) breast cancer metastases of the lymph node and autopsy tissues [DASL HT-12 samples]

2012-10-02 | GSE32488 | GEO