CIRFESS: An interactive resource for querying the set of theoretically detectable peptides for cell surface and extracellular enrichment proteomic studies

Waas, Matthew; Littrell, Jack; Gundry, Rebekah L.

doi:10.1101/2020.01.22.916148

Cited by 3 publications

(5 citation statements)

References 58 publications

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“…Our webtool, Veneer, provides an automated, standardized solution for classification, annotation and accurate reporting of data generated by μCSC and related workflows. Whereas most cell surface proteins are potentially glycosylated 9,49 , μCSC is biased to detecting N-glycosylated peptides that contain available and accessible vicinal-diol groups on corresponding glycans and for which the glycosite resides in a tryptic peptide of suitable m/z for MS detection 14,47 . Thus, relevant non-glycosylated proteins (for example, TMEM65 (ref.…”

Section: Discussionmentioning

confidence: 99%

“…We identified LSMEM2 as a high-priority cardiomyocyte-restricted candidate because we have only observed it previously on the surface of human pluripotent stem-cell-derived cardiomyocytes (hPSC-CMs) 17,18 . It was inferred from the detection of one extracellular glycopeptide unique to LSMEM2 among the human proteome 9 (Fig. 4c).…”

Section: Lsmem2 Is a Cardiomyocyte-restricted Cell Surface Proteinmentioning

confidence: 98%

“…The N-glycosite information is valuable for determining the orientation of uncharacterized transmembrane proteins necessary to inform downstream antibody development. In the 'Prioritize module', CIRFESS 9 provides a quality control measure to match predicted versus experimentally identified N-glycosylated extracellular peptides. SurfaceGenie 10 rapidly prioritizes candidate cell-type-specific markers.…”

Section: Cellsurfer Platformmentioning

confidence: 99%

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Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts

et al. 2023

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Cardiac cell surface proteins are drug targets and useful biomarkers for discriminating among cellular phenotypes and disease states. Here we developed an analytical platform, CellSurfer, that enables quantitative cell surface proteome (surfaceome) profiling of cells present in limited quantities, and we apply it to isolated primary human heart cells. We report experimental evidence of surface localization and extracellular domains for 1,144 N-glycoproteins, including cell-type-restricted and region-restricted glycoproteins. We identified a surface protein specific for healthy cardiomyocytes, LSMEM2, and validated an anti-LSMEM2 monoclonal antibody for flow cytometry and imaging. Surfaceome comparisons among pluripotent stem cell derivatives and their primary counterparts highlighted important differences with direct implications for drug screening and disease modeling. Finally, 20% of cell surface proteins, including LSMEM2, were differentially abundant between failing and non-failing cardiomyocytes. These results represent a rich resource to advance development of cell type and organ-specific targets for drug delivery, disease modeling, immunophenotyping and in vivo imaging

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Section: Discussionmentioning

confidence: 99%

Section: Lsmem2 Is a Cardiomyocyte-restricted Cell Surface Proteinmentioning

confidence: 98%

Section: Cellsurfer Platformmentioning

confidence: 99%

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Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts

et al. 2023

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“…8 Notably, >80% of cell surface proteins are predicted to be N-glycosylated. 9,10 Glycosylation is essential for protein function, such as cell adhesion, receptor−ligand interaction, and proper protein folding, 11 and is often enhanced or altered in cancer. 12 Moreover, N-glycan residues represent a useful "handle" for capturing and enriching cell surface proteins before subsequent proteomic analysis, and such enrichment protocols have been successfully used to interrogate the surfaceome of cancer cells 13−19 and normal nonmalignant cells.…”

Section: ■ Introductionmentioning

confidence: 99%

Glycoproteomics Identifies Plexin-B3 as a Targetable Cell Surface Protein Required for the Growth and Invasion of Triple-Negative Breast Cancer Cells

et al. 2022

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Driven by the lack of targeted therapies, triple-negative breast cancers (TNBCs) have the worst overall survival of all breast cancer subtypes. Considering that cell surface proteins are favorable drug targets and are predominantly glycosylated, glycoproteome profiling has significant potential to facilitate the identification of much-needed drug targets for TNBCs. Here, we performed N -glycoproteomics on six TNBCs and five normal control (NC) cell lines using hydrazide-based enrichment. Quantitative proteomics and integrative data mining led to the discovery of Plexin-B3 (PLXNB3), a previously undescribed TNBC-enriched cell surface protein. Furthermore, siRNA knockdown and CRISPR-Cas9 editing of in vitro and in vivo models show that PLXNB3 is required for TNBC cell line growth, invasion, and migration. Altogether, we provide insights into N -glycoproteome remodeling associated with TNBCs and functional evaluation of an extracted target, which indicate the surface protein PLXNB3 as a potential therapeutic target for TNBCs.

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“…Thus, in-depth analysis of the cell surface proteome (i.e., surfaceome) requires enrichment strategies (Kuhlmann et al, 2018). Notably, >80% of cell surface proteins are predicted to be N -glycosylated (Apweiler, 1999; Waas et al, 2020a).…”

Section: Introductionmentioning

confidence: 99%

Glycoproteomics Identifies Plexin-B3 as Targetable Cell Surface Protein Required for Growth and Invasion of Triple Negative Breast Cancer Cells

Kuhlmann

Govindarajan

Mejia-Guerrero

et al. 2022

Preprint

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SummaryDriven by the lack of targeted therapies, triple negative breast cancers (TNBC) have the worst overall survival of all breast cancer subtypes. Considering cell surface proteins are favorable drug targets and are predominantly glycosylated, glycoproteome profiling has significant potential to facilitate the identification of much-needed drug targets for TNBC. Here, we performed N-glycoproteomics on six TNBC and five normal control (NC) cell lines using hydrazide-based enrichment. Quantitative proteomics and integrative data mining led to the discovery of Plexin-B3 (PLXNB3), a previously undescribed TNBC-enriched cell surface protein. Furthermore, siRNA knock-down and CRISPR-Cas9 editing of in vitro and in vivo models show that PLXNB3 is required for TNBC cell line growth, invasion, and migration. Altogether, we provide insight into N-glycoproteome remodeling associated with TNBC and functional evaluation of an extracted target, which indicate the surface protein PLXNB3 as a potential therapeutic target for TNBC.HighlightsIn-depth N-glycoproteomic profiles of six TNBC and five NC cell line modelsIdentification of PLXNB3 as a novel TNBC-enriched cell surface proteinPLXNB3 affects growth, invasion, and migration in TNBC modelsPLXNB3 inhibition represents a targeted treatment option for TNBC

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CIRFESS: An interactive resource for querying the set of theoretically detectable peptides for cell surface and extracellular enrichment proteomic studies

Cited by 3 publications

References 58 publications

Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts

Surfaceome mapping of primary human heart cells with CellSurfer uncovers cardiomyocyte surface protein LSMEM2 and proteome dynamics in failing hearts

Glycoproteomics Identifies Plexin-B3 as a Targetable Cell Surface Protein Required for the Growth and Invasion of Triple-Negative Breast Cancer Cells

Glycoproteomics Identifies Plexin-B3 as Targetable Cell Surface Protein Required for Growth and Invasion of Triple Negative Breast Cancer Cells

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