Tagless LysoIP method for molecular profiling of lysosomal content in clinical samples

Daniel Saarela, Paweł Lis, Sara Gomes, Raja Nirujogi, Wentao Dong, Eshaan S. Rawat, Sophie Glendinning, Karolina Zeneviciute, Enrico Bagnoli, Rotimi Fasimoye, Cindy Lin, Kwamina Nyame, Fanni A. Boros, Friederike Zunke, Fred Lamoliatte, Sadik Elshani, Matthew Jaconelli, Judith J. M. Jans Jans, Margriet A. Huisman, Christian PosernLena M. Westermann Westermann, Angela Schulz, Peter M. van Hasselt, Dario Alessi (Lead / Corresponding author), Monther Abu-Remaileh (Lead / Corresponding author), Esther Sammler (Lead / Corresponding author)

Research output: Working paper/PreprintPreprint

Abstract

Lysosomes are implicated in a wide spectrum of human diseases including monogenic lysosomal storage disorders (LSDs), age-associated neurodegeneration and cancer. Profiling lysosomal content using tag-based lysosomal immunoprecipitation (LysoTagIP) in cell and animal models allowed major discoveries in the field, however studying lysosomal dysfunction in human patients remains challenging. Here, we report the development of the “tagless LysoIP method” to enable rapid enrichment of lysosomes, via immunoprecipitation, using the endogenous integral lysosomal membrane protein TMEM192, directly from clinical samples and human cell lines (e.g. induced Pluripotent Stem Cell (iPSCs) derived neurons). Isolated lysosomes are intact and suitable for subsequent multimodal omics analyses. To validate our approach, we employed the tagless LysoIP to enrich lysosomes from peripheral blood mononuclear cells (PBMCs) derived from fresh blood from patients with CLN3 disease, a neurodegenerative LSD. Metabolic profiling of isolated lysosomes showed massive accumulation of glycerophosphodiesters (GPDs) in patients’ lysosomes. Interestingly, a patient with a milder phenotype and genotype displayed lower accumulation of lysosomal GPDs, consistent with their potential role as disease biomarkers. Altogether, the tagless LysoIP provides a framework to study native lysosomes from patient samples, identify novel biomarkers and discover human-relevant disease mechanisms.
Original languageEnglish
PublisherBioRxiv
Number of pages31
DOIs
Publication statusPublished - 27 May 2024

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