Biology subjects

Collier, J. J.

Publications and source records attributed to Collier, J. J..

3 recordsLinked to original sources

bioRxiv2024

RTN4IP1 is essential for the final stages of mitochondrial complex I assembly and coenzyme Q biosynthesis

A biochemical deficiency of mitochondrial complex I (CI) underlies [~]30% of cases of primary mitochondrial disease, yet the inventory of molecular machinery required for CI assembly remains incomplete. We previously characterised patients with isolated CI deficiency caused by segregating variants in RTN4IP1, encoding a mitochondrial NAD(P)H oxidoreductase. Here, we demonstrate that RTN4IP1 deficiency causes a CI assembly defect in both patient fibroblasts and knockout cells, and report that RTN4IP1 is a bona fide CI assembly factor. Complexome profiling revealed accumulation of unincorporated ND5-module and impaired N-module production. RTN4IP1 patient fibroblasts also exhibited defective coenzyme Q biosynthesis, substantiating this emerging function of RTN4IP1. Thus, our data reveal RTN4IP1 plays an essential role in both the terminal stages of CI assembly and in coenzyme Q metabolism, and that pathogenic RTN4IP1 variants impair both functions in patients with mitochondrial disease.

cell biology↗

bioRxiv2023

Parkinson's genes orchestrate pyroptosis through selective trafficking of mtDNA to leaky lysosomes

Inflammation is an age-related factor that underlies numerous human disorders. A key driver of inflammation is the release of mitochondrial DNA (mtDNA), which binds and activates cytosolic sensors. This induces transcriptional responses and, ultimately, pyroptotic cell death. The main challenge has been to understand how mtDNA can cross the two mitochondrial membranes to access the cytosol. Through a genome-wide CRISPR knockout screen we identified a new pyroptotic pathway defined by mtDNA exit within mitochondrial-derived vesicles that are delivered to lysosomes. Critically, breach of lysosomes allows mtDNA to access cytosol, requiring multiple Parkinsons Disease-related proteins and Gasdermin pores, identified in the screen. These data place mitochondria-to-lysosome transport as a driver of pyroptosis and link multiple PD proteins along a common pathway. One sentence summaryParkinsons disease-related proteins regulate pyroptosis

cell biology↗

bioRxiv2021

Detection of pathogenic splicing events from RNA-sequencing data using dasper

Although next-generation sequencing technologies have accelerated the discovery of novel gene-to-disease associations, many patients with suspected Mendelian diseases still leave the clinic without a genetic diagnosis. An estimated one third of these patients will have disorders caused by mutations impacting splicing. RNA-sequencing has been shown to be a promising diagnostic tool, however few methods have been developed to integrate RNA-sequencing data into the diagnostic pipeline. Here, we introduce dasper, an R/Bioconductor package that improves upon existing tools for detecting aberrant splicing by using machine learning to incorporate disruptions in exon-exon junction counts as well as coverage. dasper is designed for diagnostics, providing a rank-based report of how aberrant each splicing event looks, as well as including visualization functionality to facilitate interpretation. We validate dasper using 16 patient-derived fibroblast cell lines harbouring pathogenic variants known to impact splicing. We find that dasper is able to detect pathogenic splicing events with greater accuracy than existing LeafCutterMD or z-score approaches. Furthermore, by only applying a broad OMIM gene filter (without any variant-level filters), dasper is able to detect pathogenic splicing events within the top 10 most aberrant identified for each patient. Since using publicly available control data minimises costs associated with incorporating RNA-sequencing into diagnostic pipelines, we also investigate the use of 504 GTEx fibroblast samples as controls. We find that dasper leverages publicly available data effectively, ranking pathogenic splicing events in the top 25. Thus, we believe dasper can increase diagnostic yield for a pathogenic splicing variants and enable the efficient implementation of RNA-sequencing for diagnostics in clinical laboratories.

bioinformatics↗