Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters.

Homology search and phylogenetic analysis have commonly been used to annotate gene function, although they are prone to error. We hypothesize that the power of homology search in functional annotation depends on the coupling of sequence variation to functional diversification, and we herein focus on the SoLute Carrier (SLC25) family of mitochondrial metabolite transporters to survey this coupling in a family-wide manner. The SLC25 family is the largest family of mitochondrial metabolite transporters in eukaryotes that translocate ligands of different chemical properties, ranging from nucleotides, amino acids, carboxylic acids and cofactors, presenting adequate experimentally validated functional diversification in ligand transport. Here, we combine phylogenetic analysis to profile SLC25 transporters across common eukaryotic model organisms, from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, to Homo sapiens, and assess their sequence adaptations to the transported ligands within individual subfamilies. Using several recently studied and poorly characterized SLC25 transporters, we discuss the potentials and limitations of phylogenetic analysis in guiding functional characterization.

Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS.

The SLC25 carrier family consists of 53 transporters that shuttle nutrients and co-factors across mitochondrial membranes. The family is highly redundant and their transport activities coupled to metabolic state. Here, we use a pooled, dual CRISPR screening strategy that knocks out pairs of transporters in four metabolic states - glucose, galactose, OXPHOS inhibition, and absence of pyruvate - designed to unmask the inter-dependence of these genes. In total, we screen 63 genes in four metabolic states, corresponding to 2016 single and pair-wise genetic perturbations. We recover 19 gene-by-environment (GxE) interactions and 9 gene-by-gene (GxG) interactions. One GxE interaction hit illustrates that the fitness defect in the mitochondrial folate carrier (SLC25A32) KO cells is genetically buffered in galactose due to a lack of substrate in de novo purine biosynthesis. GxG analysis highlights a buffering interaction between the iron transporter SLC25A37 (A37) and the poorly characterized SLC25A39 (A39). Mitochondrial metabolite profiling, organelle transport assays, and structure-guided mutagenesis identify A39 as critical for mitochondrial glutathione (GSH) import. Functional studies reveal that A39-mediated glutathione homeostasis and A37-mediated mitochondrial iron uptake operate jointly to support mitochondrial OXPHOS. Our work underscores the value of studying family-wide genetic interactions across different metabolic environments.

A Socio-Technical Exploration for Reducing & Mitigating the Risk of Retained Foreign Objects.

A Retained Foreign Object (RFO) is a fairly infrequent but serious adverse event. An accurate rate of RFOs is difficult to establish due to underreporting but it has been estimated that incidences range between 1/1000 and 1/19,000 procedures. The cost of a RFO incident may be substantial and three-fold: (i) the cost to the patient of physical and/or psychological harm; (ii) the reputational cost to an institution and/or healthcare provider; and (iii) the financial cost to the taxpayer in the event of a legal claim. This Health Research Board-funded project aims to analyse and understand the problem of RFOs in surgical and maternity settings in Ireland and develop hospital-specific foreign object management processes and implementation roadmaps. This project will deploy an integrated evidence-based assessment methodology for social-technical modelling (Supply, Context, Organising, Process & Effects/ SCOPE Analysis Cube) and bow tie methodologies that focuses on managing the risks in effectively implementing and sustaining change. It comprises a multi-phase research approach that involves active and ongoing collaboration with clinical and other healthcare staff through each phase of the research. The specific objective of this paper is to present the methodological approach and outline the potential to produce generalisable results which could be applied to other health-related issues.