Project description:In this study, through coupling of our ISDoT tissue decellularisation technology with quantitative mass spectrometry, we explored the changing tumour matrisome during mammary tumourigenesis in the PyMT breast cancer model compared to age-matched healthy control mammary gland
Project description:We explored the prognostic impact of the dynamic contrast enhanced MR imaging (DCE-MRI) parameter ABrix in cervical cancer combined with global gene expression data to reveal the underlying molecular phenotype of the parameter and construct a gene signature that reflected ABrix. Based on 78 cervical cancer patients subjected to curative chemoradiotherapy, we identified a prognostic ABrix parameter by pharmacokinetic analysis of DCE-MR images based on the Brix model, where tumors with low ABrix appeared to be most aggressive. Gene set enrichment analysis of 46 tumors with pairwise DCE-MRI and gene expression data showed a significant correlation between ABrix and the hypoxia gene sets, whereas gene sets related to proliferation, radioresistance, and wound healing were not significant. Hypoxia gene sets specific for cervical cancer created in cell culture experiments, including targets of the hypoxia inducible factor (HIF1M-NM-1) and the unfolded protein response (UPR), were the most significant. In the remaining 32 tumors, low ABrix was associated with upregulation of HIF1M-NM-1 protein expression, as assessed by immunohistochemistry, consistent with increased hypoxia. Based on the hypoxia gene sets, a signature of 31 genes that were upregulated in tumors with low ABrix was constructed. This DCE-MRI hypoxia gene signature showed prognostic impact in an independent validation cohort of 109 patients. Gene expression correlating with the DCE-MRI parameter ABrix were identified in 46 patients (DCE-MRI cohort) and used to find a hypoxia gene signature. The prognsotic impact of the gene signature was validated in an independent cohort of 109 patients (validation chort). Cell culture experiments were performed to generate cervical cancer specific gene lists associated with hypoxia (GSM897799 - GSM897804).
Project description:In Eco-Metabolomics, non-model organisms are typically studied in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such data involve, among others, complex ecological experiment designs, peak detection parameter settings and high variation of metabolite profiles of different species. Here, we present a representative dataset generated from 108 samples of 9 bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry (LC/MS) acquisition method. With this dataset, we address the challenges in data processing focusing on data import, analytical quality control and peak detection. We expect that this representative dataset will encourage researchers to conduct subsequent Eco-Metabolomics studies.
Project description:We report a new but determining pathway of mRNA quality control by transcription-translation coupling (TTC), which inhibits the generation of untranslatable mRNAs from the promoter-proximal region when transcription is decoupled from translation. Single-molecule mRNA FISH shows that the 5’ end-proximal regions of mRNA, of which amount reflects transcription initiation, are not generated without translation. The decoupling between transcription and translation results in the occupancy of RNAPs only within 250 base pairs from the transcription start site. It is further supported by the observation that RNAP decoupled with translation elongates mRNA only 80-90 bp on average in vivo. We show that the length of RNAP elongation before coupling with the ribosome (i.e., 5’-UTR length) determines the mRNA expression level. Our results demonstrate that the ribosome-coupling near the promoter-proximal region, within 100 bp from the transcription start site, functions as an mRNA-quality control, critical for the efficient synthesis of translatable mRNAs by RNAPs. The limited processivity of RNAP before coupling with ribosome provides a potential explanation of the natural distribution of 5’-UTR lengths in E. coli, where longer than 100 bp 5’-UTRs are rare.
Project description:The data set provided is used to demonstrate a complete, reproducible LC-MS data preprocessing workflow using *xcms*, illustrated with a small untargeted LC-MS metabolomics data set. Special emphasis is placed on the best practices for data handling, parameter optimization, and quality control.
Project description:The data set provided is used to demonstrate a complete, reproducible LC-MS data preprocessing workflow using *xcms*, illustrated with a small untargeted LC-MS metabolomics data set. Special emphasis is placed on the best practices for data handling, parameter optimization, and quality control.
Project description:We explored the prognostic impact of the dynamic contrast enhanced MR imaging (DCE-MRI) parameter ABrix in cervical cancer combined with global gene expression data to reveal the underlying molecular phenotype of the parameter and construct a gene signature that reflected ABrix. Based on 78 cervical cancer patients subjected to curative chemoradiotherapy, we identified a prognostic ABrix parameter by pharmacokinetic analysis of DCE-MR images based on the Brix model, where tumors with low ABrix appeared to be most aggressive. Gene set enrichment analysis of 46 tumors with pairwise DCE-MRI and gene expression data showed a significant correlation between ABrix and the hypoxia gene sets, whereas gene sets related to proliferation, radioresistance, and wound healing were not significant. Hypoxia gene sets specific for cervical cancer created in cell culture experiments, including targets of the hypoxia inducible factor (HIF1α) and the unfolded protein response (UPR), were the most significant. In the remaining 32 tumors, low ABrix was associated with upregulation of HIF1α protein expression, as assessed by immunohistochemistry, consistent with increased hypoxia. Based on the hypoxia gene sets, a signature of 31 genes that were upregulated in tumors with low ABrix was constructed. This DCE-MRI hypoxia gene signature showed prognostic impact in an independent validation cohort of 109 patients.
Project description:Synthetic circuits embedded in host-cells compete with cellular processes for limited intracellular resources. We show how funneling of cellular resources, after global transcriptome degradation by the sequence-dependent endoribonuclease MazF, to a synthetic circuit can increase production. Target genes are protected from MazF activity by recoding the gene sequence to eliminate recognition sites, while preserving the amino acid sequence. The expression of a protected fluorescent reporter and flux of a high-value metabolite are significantly enhanced using this genome-scale control strategy. Proteomics measurements discover a host factor in need of protection to improve resource redistribution activity. A computational model demonstrates that the MazF mRNA-decay feedback loop enables proportional control of MazF in an optimal operating regime. Transcriptional profiling of MazF-induced cells elucidates the dynamic shifts in transcript abundance and discovers regulatory design elements. Together, our results suggest that manipulation of cellular resource allocation is a key control parameter for synthetic circuit design.