Tagless LysoIP for immunoaffinity enrichment of native lysosomes from 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; Margriet A. Huisman; Christian Posern; Lena M. Westermann; Angela Schulz; Peter M. van Hasselt; Dario Alessi; Monther Abu-Remaileh; Esther Sammler

doi:10.1172/JCI183592

Tagless LysoIP for immunoaffinity enrichment of native lysosomes from 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
, Margriet A. Huisman
, Christian Posern

Lena M. 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: Contribution to journal › Article › peer-review

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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 has substantially moved the field forward, but studying lysosomal dysfunction in human patients remains challenging. Here, we report the development of the 'tagless LysoIP' method, designed to enable the 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 derived neurons). Isolated lysosomes were intact and suitable for subsequent multimodal omics analyses. To validate our approach, we applied the tagless LysoIP to enrich lysosomes from peripheral blood mononuclear cells derived from fresh blood of healthy donors and patients with CLN3 disease, an autosomal recessive neurodegenerative LSD. Metabolic profiling of isolated lysosomes revealed 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 disease biomarkers, and discover human-relevant disease mechanisms.

Original language	English
Article number	e183592
Number of pages	15
Journal	Journal of Clinical Investigation
Volume	135
Issue number	4
Early online date	26 Dec 2024
DOIs	https://doi.org/10.1172/JCI183592
Publication status	Published - 17 Feb 2025

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SDG 3 Good Health and Well-being

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10.1172/JCI183592Licence: CC BY

Final published version
Copyright: © 2024, Saarela et al. This is an open access article published under the terms of the Creative Commons Attribution 4.0 International License.
Final published version, 2.13 MBLicence: CC BY

Cite this

Saarela, D., Lis, P., Gomes, S., Nirujogi, R., Dong, W., Rawat, E. S., Glendinning, S., Zeneviciute, K., Bagnoli, E., Fasimoye, R., Lin, C., Nyame, K., Boros, F. A., Zunke, F., Lamoliatte, F., Elshani, S., Jaconelli, M., Jans, J. J. M., Huisman, M. A., ... Sammler, E. (2025). Tagless LysoIP for immunoaffinity enrichment of native lysosomes from clinical samples. Journal of Clinical Investigation, 135(4), Article e183592. https://doi.org/10.1172/JCI183592

@article{ecb6aa445d3644fe820ba790dba12cf8,

title = "Tagless LysoIP for immunoaffinity enrichment of native lysosomes from clinical samples",

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 has substantially moved the field forward, but studying lysosomal dysfunction in human patients remains challenging. Here, we report the development of the 'tagless LysoIP' method, designed to enable the 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 derived neurons). Isolated lysosomes were intact and suitable for subsequent multimodal omics analyses. To validate our approach, we applied the tagless LysoIP to enrich lysosomes from peripheral blood mononuclear cells derived from fresh blood of healthy donors and patients with CLN3 disease, an autosomal recessive neurodegenerative LSD. Metabolic profiling of isolated lysosomes revealed 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 disease biomarkers, and discover human-relevant disease mechanisms.",

author = "Daniel Saarela and Pawe{\l} Lis and Sara Gomes and Raja Nirujogi and Wentao Dong and Rawat, \{Eshaan S.\} and Sophie Glendinning and Karolina Zeneviciute and Enrico Bagnoli and Rotimi Fasimoye and Cindy Lin and Kwamina Nyame and Boros, \{Fanni A.\} and Friederike Zunke and Fred Lamoliatte and Sadik Elshani and Matthew Jaconelli and Jans, \{Judith J. M.\} and Huisman, \{Margriet A.\} and Christian Posern and Westermann, \{Lena M.\} and Angela Schulz and \{van Hasselt\}, \{Peter M.\} and Dario Alessi and Monther Abu-Remaileh and Esther Sammler",

note = "Copyright: {\textcopyright} 2024, Saarela et al.",

year = "2025",

month = feb,

day = "17",

doi = "10.1172/JCI183592",

language = "English",

volume = "135",

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Saarela, D, Lis, P , Gomes, S , Nirujogi, R, Dong, W, Rawat, ES, Glendinning, S, Zeneviciute, K, Bagnoli, E , Fasimoye, R, Lin, C, Nyame, K, Boros, FA, Zunke, F, Lamoliatte, F , Elshani, S , Jaconelli, M, Jans, JJM, Huisman, MA, Posern, C, Westermann, LM, Schulz, A, van Hasselt, PM, Alessi, D, Abu-Remaileh, M & Sammler, E 2025, 'Tagless LysoIP for immunoaffinity enrichment of native lysosomes from clinical samples', Journal of Clinical Investigation, vol. 135, no. 4, e183592. https://doi.org/10.1172/JCI183592

TY - JOUR

T1 - Tagless LysoIP for immunoaffinity enrichment of native lysosomes from 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.

AU - Schulz, Angela

AU - van Hasselt, Peter M.

AU - Alessi, Dario

AU - Abu-Remaileh, Monther

AU - Sammler, Esther

PY - 2025/2/17

Y1 - 2025/2/17

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 has substantially moved the field forward, but studying lysosomal dysfunction in human patients remains challenging. Here, we report the development of the 'tagless LysoIP' method, designed to enable the 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 derived neurons). Isolated lysosomes were intact and suitable for subsequent multimodal omics analyses. To validate our approach, we applied the tagless LysoIP to enrich lysosomes from peripheral blood mononuclear cells derived from fresh blood of healthy donors and patients with CLN3 disease, an autosomal recessive neurodegenerative LSD. Metabolic profiling of isolated lysosomes revealed 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 disease 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 has substantially moved the field forward, but studying lysosomal dysfunction in human patients remains challenging. Here, we report the development of the 'tagless LysoIP' method, designed to enable the 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 derived neurons). Isolated lysosomes were intact and suitable for subsequent multimodal omics analyses. To validate our approach, we applied the tagless LysoIP to enrich lysosomes from peripheral blood mononuclear cells derived from fresh blood of healthy donors and patients with CLN3 disease, an autosomal recessive neurodegenerative LSD. Metabolic profiling of isolated lysosomes revealed 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 disease biomarkers, and discover human-relevant disease mechanisms.

UR - https://www.scopus.com/pages/publications/85218129107

U2 - 10.1172/JCI183592

DO - 10.1172/JCI183592

M3 - Article

C2 - 39724071

SN - 0021-9738

VL - 135

JO - Journal of Clinical Investigation

JF - Journal of Clinical Investigation

IS - 4

M1 - e183592

ER -

Tagless LysoIP for immunoaffinity enrichment of native lysosomes from clinical samples

Abstract

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ASAP - Mapping the LRRK2 Signalling Pathway and its Interplay with other Parkinson's Disease Components

Bench-to-Bedside Parkinson's Disease Research: Biomarkers in LRRK2 (NHS Research Scotland (NRS) and Scottish Universities Scottish Senior Clinical Academic Fellowship Scheme)

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Tagless LysoIP for immunoaffinity enrichment of native lysosomes from clinical samples

Abstract

UN SDGs

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ASAP - Mapping the LRRK2 Signalling Pathway and its Interplay with other Parkinson's Disease Components

Bench-to-Bedside Parkinson's Disease Research: Biomarkers in LRRK2 (NHS Research Scotland (NRS) and Scottish Universities Scottish Senior Clinical Academic Fellowship Scheme)

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