Zimmermman, Johannes, Kaleta, Christoph, Chrysostomou, Despoina, Marchesi, Julian, W. Zatorska, Michalina, Barr, Alexis, Quintaneiro, Leonor, Cabreiro, Filipe, Martinez-Martinez, Daniel, Peres, Tanara, Kramer, Holger, Best, Lena, Marinos, Georgios, B. Mokochinski, Joao
[
International Worm Meeting,
2021]
Microbiota derived metabolites have been shown to influence cancer susceptibility, tumour progression and therapy outcome. Diet is a major environmental factor influencing gut microbiota composition, dictating the abundance of potential oncometabolites. The complex interactions between diet and the microbiota need to be clarified so that dietary intake may be shaped to influence disease outcome. Having previously demonstrated the impact of bacterial metabolism in 5-fluorouracil (5-FU) cancer drug efficacy, we set out to investigate the role of nutrition in host-microbe responses to this drug, an antimetabolite widely used for colorectal cancer (CRC) chemotherapy. Host-microbe-drug-nutrient interaction and its influence on drug efficacy were assessed using a high-throughput 4-way screening approach. To understand gene-nutrient interactions at the bacterial level that regulate the effect of a drug on host physiology, genetically modified E. coli from the Keio deletion library were used to probe the role of bacterial metabolic pathways in 5-FU effects in a nutrient-dependent manner. We found that glycolytic nutrients, including sugars, importantly antagonise the toxic effects of 5-FU action on the host. Sugars induce a shift in metabolic pathways that favour the production of nucleotides, specifically UMP and UTP derived from the activation of pyrimidine de novo biosynthesis pathway in bacteria, counteracting pro-drug activation through the salvage pathway. We also found that bacterial mutations in the TCA cycle and pyruvate metabolism decrease drug efficacy in amino acid-based media. A combination of bacterial genetic work and metabolomics has revealed the presence of a novel bacterial metabolite with the capacity to increase 5-FU drug efficacy in both C. elegans and human cancer cells. Importantly, flux balance analysis of the cancer associated microbiota predicts an increased production of this metabolite in several organs. In particular, investigations of the gut microbiome from four independent human CRC cohorts shows an increased production of this metabolite, compared to healthy patients, further implicating this metabolite in drug cancer therapy. These findings highlight the potential of manipulating gut microbiota through diet to improve cancer therapy outcome.
[
European Worm Meeting,
2006]
Julian Ceron and Sander van den Heuvel. We have initiated a functional genomics approach aimed at defining an interaction network for splicing-related components. The spliceosome contains a highly conserved collection of snRNPs (snRNAs and associated proteins) and many other protein factors recruited to pre-mRNA to carry out splicing. In addition, recent reports have implicated splicing factors in regulating gene expression through mechanisms different from splicing. How the different factors interact to carry out the various functions remains largely unknown.. To create a C. elegans dataset of spliceosome proteins, we used a collection of 254 human spliceosome proteins recently reviewed (Barbosa-Morais et al, 2006) to search for C. elegans orthologs in the InParanoid database. As a result, we found 164 C. elegans genes orthologous to human spliceosome genes that were further used in our functional genomics analysis.. Combining genomics information available in web-based resources, we are generating a platform to assemble a Spliceosome functional map in C. elegans. This information includes phenotypes observed in genome-wide RNAi screens (Phenome), large-scale identification of protein-protein interactions (Interactome), extensive characterization of expression profiles (Localizome) and transcriptional profiles obtained in microarray-based mRNA expression studies (Transcriptome). As splicing factors are evolutionarily highly conserved, this approach will provide a valuable resource for a better understanding of how molecules and pathways interrelate in the control of gene expression, and how alterations in the splicing system may lead to disease.