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

TY - UNPB

T1 - Tagless LysoIP method for molecular profiling of lysosomal content in clinical samples

AU - Saarela, Daniel

AU - Lis, Paweł

AU - Gomes, Sara

AU - Nirujogi, Raja

AU - Dong, Wentao

AU - Rawat, Eshaan S.

AU - Glendinning, Sophie

AU - Zeneviciute, Karolina

AU - Bagnoli, Enrico

AU - Fasimoye, Rotimi

AU - Lin, Cindy

AU - Nyame, Kwamina

AU - Boros, Fanni A.

AU - Zunke, Friederike

AU - Lamoliatte, Fred

AU - Elshani, Sadik

AU - Jaconelli, Matthew

AU - Jans, Judith J. M.

AU - Huisman, Margriet A.

AU - Posern, Christian

AU - Westermann, Lena M. Westermann

AU - Schulz, Angela

AU - van Hasselt, Peter M.

AU - Alessi, Dario

AU - Abu-Remaileh, Monther

AU - Sammler, Esther

N1 - The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.

PY - 2024/5/27

Y1 - 2024/5/27

N2 - 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.

AB - 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.

U2 - 10.1101/2024.05.17.594681

DO - 10.1101/2024.05.17.594681

M3 - Preprint

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

PB - BioRxiv

ER -