Systematic Comparison of Strategies for the Enrichment of Lysosomes by Data Independent Acquisition

In mammalian cells, the lysosome is the main organelle for the degradation of macromolecules and the recycling of their building blocks. Correct lysosomal function is essential, and mutations in every known lysosomal hydrolase result in so-called lysosomal storage disorders, a group of rare and often fatal inherited diseases. Furthermore, it is becoming more and more apparent that lysosomes play also decisive roles in other diseases, such as cancer and common neurodegenerative disorders. This leads to an increasing interest in the proteomic analysis of lysosomes for which enrichment is a prerequisite. In this study, we compared the four most common strategies for the enrichment of lysosomes using data-independent acquisition. We performed centrifugation at 20,000 × g to generate an organelle-enriched pellet, two-step sucrose density gradient centrifugation, enrichment by superparamagnetic iron oxide nanoparticles (SPIONs), and immunoprecipitation using a 3xHA tagged version of the lysosomal membrane protein TMEM192. Our results show that SPIONs and TMEM192 immunoprecipitation outperform the other approaches with enrichment factors of up to 118-fold for certain proteins relative to whole cell lysates. Furthermore, we achieved an increase in identified lysosomal proteins and a higher reproducibility in protein intensities for label-free quantification in comparison to the other strategies

Systematic Comparison of Strategies for the Enrichment of Lysosomes by Data Independent Acquisition

In mammalian cells, the lysosome is the main organelle for the degradation of macromolecules and the recycling of their building blocks. Correct lysosomal function is essential, and mutations in every known lysosomal hydrolase result in so-called lysosomal storage disorders, a group of rare and often fatal inherited diseases. Furthermore, it is becoming more and more apparent that lysosomes play also decisive roles in other diseases, such as cancer and common neurodegenerative disorders. This leads to an increasing interest in the proteomic analysis of lysosomes for which enrichment is a prerequisite. In this study, we compared the four most common strategies for the enrichment of lysosomes using data-independent acquisition. We performed centrifugation at 20,000 × g to generate an organelle-enriched pellet, two-step sucrose density gradient centrifugation, enrichment by superparamagnetic iron oxide nanoparticles (SPIONs), and immunoprecipitation using a 3xHA tagged version of the lysosomal membrane protein TMEM192. Our results show that SPIONs and TMEM192 immunoprecipitation outperform the other approaches with enrichment factors of up to 118-fold for certain proteins relative to whole cell lysates. Furthermore, we achieved an increase in identified lysosomal proteins and a higher reproducibility in protein intensities for label-free quantification in comparison to the other strategies

Systematic Comparison of Strategies for the Enrichment of Lysosomes by Data Independent Acquisition

In mammalian cells, the lysosome is the main organelle for the degradation of macromolecules and the recycling of their building blocks. Correct lysosomal function is essential, and mutations in every known lysosomal hydrolase result in so-called lysosomal storage disorders, a group of rare and often fatal inherited diseases. Furthermore, it is becoming more and more apparent that lysosomes play also decisive roles in other diseases, such as cancer and common neurodegenerative disorders. This leads to an increasing interest in the proteomic analysis of lysosomes for which enrichment is a prerequisite. In this study, we compared the four most common strategies for the enrichment of lysosomes using data-independent acquisition. We performed centrifugation at 20,000 × g to generate an organelle-enriched pellet, two-step sucrose density gradient centrifugation, enrichment by superparamagnetic iron oxide nanoparticles (SPIONs), and immunoprecipitation using a 3xHA tagged version of the lysosomal membrane protein TMEM192. Our results show that SPIONs and TMEM192 immunoprecipitation outperform the other approaches with enrichment factors of up to 118-fold for certain proteins relative to whole cell lysates. Furthermore, we achieved an increase in identified lysosomal proteins and a higher reproducibility in protein intensities for label-free quantification in comparison to the other strategies

Systematic Comparison of Strategies for the Enrichment of Lysosomes by Data Independent Acquisition

In mammalian cells, the lysosome is the main organelle for the degradation of macromolecules and the recycling of their building blocks. Correct lysosomal function is essential, and mutations in every known lysosomal hydrolase result in so-called lysosomal storage disorders, a group of rare and often fatal inherited diseases. Furthermore, it is becoming more and more apparent that lysosomes play also decisive roles in other diseases, such as cancer and common neurodegenerative disorders. This leads to an increasing interest in the proteomic analysis of lysosomes for which enrichment is a prerequisite. In this study, we compared the four most common strategies for the enrichment of lysosomes using data-independent acquisition. We performed centrifugation at 20,000 × g to generate an organelle-enriched pellet, two-step sucrose density gradient centrifugation, enrichment by superparamagnetic iron oxide nanoparticles (SPIONs), and immunoprecipitation using a 3xHA tagged version of the lysosomal membrane protein TMEM192. Our results show that SPIONs and TMEM192 immunoprecipitation outperform the other approaches with enrichment factors of up to 118-fold for certain proteins relative to whole cell lysates. Furthermore, we achieved an increase in identified lysosomal proteins and a higher reproducibility in protein intensities for label-free quantification in comparison to the other strategies

Systematic Comparison of Strategies for the Enrichment of Lysosomes by Data Independent Acquisition

In mammalian cells, the lysosome is the main organelle for the degradation of macromolecules and the recycling of their building blocks. Correct lysosomal function is essential, and mutations in every known lysosomal hydrolase result in so-called lysosomal storage disorders, a group of rare and often fatal inherited diseases. Furthermore, it is becoming more and more apparent that lysosomes play also decisive roles in other diseases, such as cancer and common neurodegenerative disorders. This leads to an increasing interest in the proteomic analysis of lysosomes for which enrichment is a prerequisite. In this study, we compared the four most common strategies for the enrichment of lysosomes using data-independent acquisition. We performed centrifugation at 20,000 × g to generate an organelle-enriched pellet, two-step sucrose density gradient centrifugation, enrichment by superparamagnetic iron oxide nanoparticles (SPIONs), and immunoprecipitation using a 3xHA tagged version of the lysosomal membrane protein TMEM192. Our results show that SPIONs and TMEM192 immunoprecipitation outperform the other approaches with enrichment factors of up to 118-fold for certain proteins relative to whole cell lysates. Furthermore, we achieved an increase in identified lysosomal proteins and a higher reproducibility in protein intensities for label-free quantification in comparison to the other strategies

Adhesion molecules expression analysis.

<p>(A) Relative mRNA levels of VCAM-1, ICAM-1, e-selectin and p-selectin in aortic arches from p55^+/+LDLR^−/− (n = 10) and p55^−/−LDLR^−/− (n = 8) mice. Values are represented relative to expression in p55^+/+LDLR^−/− arches. (B) Immunohistochemical staining of VCAM-1 expression on sections from aortic valve areas indicating a less intense endothelial staining in p55^−/−LDLR^−/− mice. Original magnification×200. (C) Staining quantification. * p = 0.01 by Student's t-test. Error bars indicate SEM.</p

General characterization of AngII infused mice.

<p>(A) Body weight (B) plasma cholesterol and (C) plasma triglyceride levels in p55^+/+LDLR^−/− and p55^−/−LDLR^−/− mice before (n = 13–14 mice/group) and after 5 weeks of high fat feeding (4 weeks of AngII infusion; n = 8–12 mice/group). (D) Plasma levels of pro-inflammatory cytokines and chemokines (n = 7–9 mice/group) after 5 weeks of high fat feeding (4 weeks of AngII infusion). * p<0.05 by Student's t-test. Error bars indicate SEM.</p

Atherosclerosis quantification.

<p>(A) Atherosclerotic lesion area in the aortic sinuses of p55^+/+LDLR^−/− (squares, n = 18) and p55^−/−LDLR^−/− (triangles, n = 16) mice. Each symbol represents one animal; bars represent means. * p = 0.02 by Student's t-test. (B) Representative lesions from p55^+/+LDLR^−/− and p55^−/−LDLR^−/− mice are shown. Original magnification×40. (C) Lesion classification according to severity. (D) Gene expression analysis in p55^+/+LDLR^−/− (n = 10) and p55^−/−LDLR^−/− (n = 8) aortic arches. Values are represented relative to expression in p55^+/+LDLR^−/− arches. * p = 0.03 by Student's t-test. Error bars indicate SEM.</p

Cytokine and chemokine expression analysis.

<p>(A) Relative mRNA levels of IκBα, TNF, IL-6, IL-10 and (B) MCP-1, MIP-1α, MIP-1β, RANTES in aortic arches from p55^+/+LDLR^−/− (n = 10) and p55^−/−LDLR^−/− (n = 8) mice. Values are represented relative to expression in p55^+/+LDLR^−/− arches. (C) Plasma levels of pro-inflammatory cytokines and chemokines (n = 12–15 mice/group) after 8 weeks of high fat feeding. Error bars indicate SEM.</p