Biology subjects

Kipura, T.

Publications and source records attributed to Kipura, T..

3 recordsLinked to original sources

bioRxiv2024

GEMCAT - A new algorithm for gene expression-based prediction of metabolic alterations

The conclusive interpretation of multi-omics datasets obtained from high throughput approaches is an important prerequisite to understand disease-related physiological changes and to predict biomarkers in body fluids. We here present a Gene Expression-based Metabolite Centrality Analysis Tool, GEMCAT, a new genome scale metabolic modelling algorithm. GEMCAT enables integration of transcriptomics or proteomics data to predict changes in metabolite concentrations which can be verified by targeted metabolomics. In addition, GEMCAT allows to trace measured and predicted metabolic changes back to the underlying alterations in gene expression or proteomics and thus enables functional interpretation and integration of multi-omics data. We demonstrate the predictive capacity of GEMCAT on two datasets, one using RNA sequencing data and metabolomics from an engineered human cell line with a functional deletion of the mitochondrial NAD-transporter and another using proteomics and metabolomics measurements from patients with inflammatory bowel disease.

bioinformatics↗

bioRxiv2024

Automated liquid handling extraction and rapid quantification of underivatized amino acids and tryptophan metabolites from human serum and plasma using dual-column U(H)PLC-MRM-MS and its application to prostate cancer study.

Free amino acids (AAs) and their metabolites are important building blocks, energy sources and signaling molecules associated with various pathological phenotypes. The quantification of AA and tryptophan (TRP) metabolites in human serum and plasma is therefore of great diagnostic interest. Robust and reproducible sample extraction and processing workflows as well as rapid, sensitive absolute quantification of AA and TRP metabolites are required to identify candidate biomarkers and to improve current screening methods. We developed a validated semi-automated extraction and sample processing workflow using a robotic liquid handling platform and a rapid method for the absolute quantification of 20 free, underivatized AAs and 6 TRP metabolites using dual-column U(H)PLC-MRM-MS. The automated extraction and sample preparation workflow is designed for use in a 96-well plate format, allowing robust and reproducible high sample throughput without the need for further SPE, evaporation and/or buffer exchange. Samples extracted from serum and/or plasma in 96-well plates can be transferred directly to the U(H)PLC autosampler. The dual-column U(H)PLC-MRM-MS method, using a mixed- mode reversed-phase anion exchange column with formic acid as mobile phase modifier and a high- strength silica reversed-phase column with difluoroacetic acid as mobile phase additive, provided absolute quantification with nanomolar lower limits of quantification (LLOQ) for all metabolites except glycine (LLOQ: 2.46 {micro}M) in only 7.9 minutes. The semi-automated extraction workflow and dual-column U(H)PLC-MRM-MS method was applied to a human prostate cancer study and was shown to discriminate between treatment regimens and to identify amino acids responsible for the statistical separation between healthy controls and prostate cancer patients on active surveillance.

biochemistry↗

bioRxiv2023

Tryptophan stress activates EGFR-RAS-signaling to MTORC1 and p38/MAPK to sustain translation and AHR-dependent autophagy

Tumours face tryptophan (Trp) depletion, but the mechanisms sustaining protein biosynthesis under Trp stress remain unclear. We report that Trp stress increases the levels of the translation repressor EIF4EBP1. Yet, at the same time, EIF4EBP1 is selectively phosphorylated by the metabolic master regulator MTORC1 kinase, preventing EIF4EBP1 from inhibiting translation. MTORC1 activity under Trp stress is unexpected because the absence of amino acids is typically linked with MTORC1 inhibition. EIF4EBP1-sensitive translation in Trp starved cells is sustained by EGFR and RAS signalling to MTORC1. Via this mechanism, Trp stress enhances the synthesis and activity of the aryl hydrocarbon receptor (AHR). This is noteworthy as Trp catabolites are known to activate AHR, and therefore Trp stress was previously considered to inhibit AHR. Trp stress-induced AHR enhances the expression of key regulators of autophagy, which sustains intracellular Trp levels and Trp-charged tRNAs for translation. Hence, Trp stress switches MTORC1 from its established inhibitory function into an enhancer of autophagy, acting through AHR. The clinical potential of this fundamental mechanism is highlighted by the activity of the mTORC1-AHR pathway and an autophagy signature in 20% of glioblastoma patients, opening up new avenues for cancer therapy.

biochemistry↗