Project description:Analyses of new genomic, transcriptomic or proteomic data commonly result in trashing many unidentified data escaping the ‘canonical’ DNA-RNA-protein scheme. Testing systematic exchanges of nucleotides over long stretches produces inversed RNA pieces (here named “swinger” RNA) differing from their template DNA. These may explain some trashed data. Here analyses of genomic, transcriptomic and proteomic data of the pathogenic Tropheryma whipplei according to canonical genomic, transcriptomic and translational 'rules' resulted in trashing 58.9% of DNA, 37.7% RNA and about 85% of mass spectra (corresponding to peptides). In the trash, we found numerous DNA/RNA fragments compatible with “swinger” polymerization. Genomic sequences covered by «swinger» DNA and RNA are 3X more frequent than expected by chance and explained 12.4 and 20.8% of the rejected DNA and RNA sequences, respectively. As for peptides, several match with “swinger” RNAs, including some chimera, translated from both regular, and «swinger» transcripts, notably for ribosomal RNAs. Congruence of DNA, RNA and peptides resulting from the same swinging process suggest that systematic nucleotide exchanges increase coding potential, and may add to evolutionary diversification of bacterial populations.
Project description:The purpose of this study is the investigation of new host-microbiome interactions promoting adenoma formation and adenocarcinoma progression. For that purpose, the investigators will collect saliva, stool and colon biopsy specimens from patients referred to colonoscopy or surgical resection of colorectal tumor. Besides, a questionnaire about diet, lifestyle and medical history will be collected. Sample analysis will involve simultaneous characterization of host and microbiota genomic and transcriptomic components.
Project description:NO-CUT is a one-stage phase II trial seeking to establish whether an oxaliplatin-based chemotherapy preceding standard neo-adjuvant fluoropyrimidines-based chemo radiotherapy, can safely spare demolitive surgical intervention in patients with operable rectal cancer, without increasing the risk of distant relapse. The trial also has a translational component aimed at establishing whether selected genomic, epigenetic, and transcriptomic markers are predictive of tumor and patient outcome.
Project description:Fresh-frozen meningioma tissues of varying WHO grades were analyzed by shotgun DDA proteomics. The proteomic profiles were compared and reflected a set of new clinical subtypes derived from genomic, epigenomic and transcriptomic data which improved risk stratification.
Project description:Characterizing tumor-specific neoantigen peptides, which are derived from genomic or transcriptomic aberrations and presented to the immune system, is essential for studies in immuno-oncology. To facilitate this process, the modular iPepGen immunopeptidogenomics pipeline offers several key functions: (1) Neoantigen prediction and generation of a protein database from genomic or transcriptomic sequencing data; (2) Peptide identification; (3) Verification using immunopeptidomic mass spectral data; (4) Neoantigen classification and visualization; and (5) Candidate prioritization for further research. The pipeline is easily accessible through a publicly available, scalable cloud-based gateway and includes online interactive training materials. This streamlines adoption by cancer researchers, particularly those who may lack advanced computational expertise and resources for immunopeptidogenomic analysis.
