Oral Presentation 28th Annual Lorne Proteomics Symposium 2023

Utility of quantitative proteomics in solving rare disease diagnosis (#11)

Daniella Hock 1 , Liana Semcesen 1 , Nikeisha Caruana 1 , Alison Compton 2 3 , Sumudu Amarasekera 2 3 , Tegan Stait 3 , John Christodoulou 2 3 , David Thorburn 2 3 , David Stroud 1 3
  1. Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia, Bio21, Melbourne
  2. Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia, Paediatrics, Melbourne
  3. Murdoch Children’s Research Institute, Royal Children’s Hospital, Melbourne, VIC, Australia, MCRI, Melbourne

Diagnostic yields from exome (ES) or genome sequencing (GS) in suspected rare diseases are typically ~50% of the cases. Large numbers of candidate genes with variable genotype-phenotype correlations complicate variant curation and diagnosis, leading to some patients and families waiting for decades for a definitive diagnosis. Delayed diagnosis not only places a burden in public health systems but also prevents any possible patient intervention. Undiagnosed patients can have zero to tens of candidate variants that may warrant functional follow-up to determine genetic diagnosis. Label Free Quantitation (LFQ) and TMT-based proteomics were used to analyse primary fibroblasts from a retrospective cohort (N=10) of patients suspected of rare mitochondrial disease where ES/GS were inconclusive. We also comprehensively analysed (N=26) primary fibroblasts from diagnosed mitochondrial disease patients using LFQ Data Independent Acquisition (DIA) to validate and investigate the broad utility and limitations of the technique in the clinical setting. We achieved 80% diagnostic rate in the retrospective cohort with most variant types being intronic1, missense and copy number2 variants. We also showed that proteomics was more sensitive and specific in detecting protein defects compared to classical enzymology test, currently the only accredited test for confirmation of mitochondrial disease in Australia. Including the retrospective cohort, our quantitative proteomic approaches have helped achieve a genetic diagnosis for 30+ rare disease patients3, 4, and contributed to the identification of 5 new disease genes that can allow faster diagnosis for future cases. Mass spectrometry-based quantitative proteomics has the potential to identify the functional impact of genetic variants by quantifying thousands of proteins in a single test, being a suitable approach for clinical accreditation and use in functional investigation of ES/GS inconclusive cases.

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  3. 3. Van Bergen, N.J. et al. Mutations in the exocyst component EXOC2 cause severe defects in human brain development. J Exp Med 217 (2020).
  4. 4. Van Bergen, N.J. et al. Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function. Int J Mol Sci 23 (2022).