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Lookup NU author(s): Professor Bobby McFarlandORCiD, Professor Robert TaylorORCiD
This work is licensed under a Creative Commons Attribution 4.0 International License (CC BY 4.0).
© The Author(s) 2025.Background: Only half of individuals with suspected rare diseases receive a genetic diagnosis following genomic testing. A genetic diagnosis allows access to appropriate care, restores reproductive confidence and reduces the number of potentially unnecessary interventions. A major barrier is the lack of disease agnostic functional tests suitable for implementation in routine diagnostics that can provide evidence supporting pathogenicity of novel variants, especially those refractory to RNA sequencing. Methods: Focusing on mitochondrial disease, we describe an untargeted mass-spectrometry based proteomics pipeline that can quantify proteins encoded by > 50% of Mendelian disease genes and > 80% of known mitochondrial disease genes in clinically relevant sample types, including peripheral blood mononuclear cells (PBMCs). In total we profiled > 90 individuals including undiagnosed individuals suspected of mitochondrial disease and a supporting cohort of disease controls harbouring pathogenic variants in nuclear and mitochondrial genes. Proteomics data were benchmarked against pathology accredited respiratory chain enzymology to assess the performance of proteomics as a functional test. Proteomics testing was subsequently applied to individuals with suspected mitochondrial disease, including a critically ill infant with a view toward rapid interpretation of variants identified in ultra-rapid genome sequencing. Results: Proteomics testing provided evidence to support variant pathogenicity in 83% of individuals in a cohort with confirmed mitochondrial disease, outperforming clinical respiratory chain enzymology. Freely available bioinformatic tools and criteria developed for this study (https://rdms.app/) allow mitochondrial dysfunction to be identified in proteomics data with high confidence. Application of proteomics to undiagnosed individuals led to 6 additional diagnoses, including a mitochondrial phenocopy disorder, highlighting the disease agnostic nature of proteomics. Use of PBMCs as a sample type allowed rapid return of proteomics data supporting pathogenicity of novel variants identified through ultra-rapid genome sequencing in as little as 54 h. Conclusions: This study provides a framework to support the integration of a single untargeted proteomics test into routine diagnostic practice for the diagnosis of mitochondrial and potentially other rare genetic disorders in clinically actionable timelines, offering a paradigm shift for the functional validation of genetic variants.
Author(s): Hock DH, Caruana NJ, Semcesen LN, Lake NJ, Formosa LE, Amarasekera SSC, Stait T, Tregoning S, Frajman LE, Bournazos AM, Robinson DRL, Ball M, Reljic B, Ryder B, Wallis MJ, Vasudevan A, Beck C, Peters H, Lee J, Tan NB, Freckmann M-L, Harris M, Martin EM, McGrath P, Atthow C, Elbaum Y, MacArthur DG, Balasubramaniam S, Siira SJ, Simons C, Sallevelt SCEH, Ghaoui R, Davis RL, Murray S, Coman D, Stojanovski D, Filipovska A, Karlaftis V, Attard C, Monagle P, Samarasinghe A, Brown R, Bi W, Lek M, McFarland R, Taylor RW, Ryan MT, Cooper ST, Stark Z, Christodoulou J, Compton AG, Thorburn DR, Stroud DA
Publication type: Article
Publication status: Published
Journal: Genome Medicine
Year: 2025
Volume: 17
Issue: 1
Online publication date: 22/05/2025
Acceptance date: 02/04/2025
Date deposited: 09/06/2025
ISSN (electronic): 1756-994X
Publisher: BioMed Central Ltd
URL: https://doi.org/10.1186/s13073-025-01467-z
DOI: 10.1186/s13073-025-01467-z
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