SurfaceGenie: a web-based application for prioritizing cell-type specific marker candidates

Waas, Matthew; Snarrenberg, Shana Terai; Littrell, Jack; Lipinski, Rachel A. Jones; Hansen, Polly A.; Corbett, John A.; Gundry, Rebekah L.

doi:10.1101/575969

Cited by 10 publications

(15 citation statements)

References 44 publications

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“…There are multiple sources of information to consider for evidence of surface or extracellular localization. Here we utilized transmembrane (TM) predictions, 30,36 signal peptide (SP) predictions, 31,39 and the Surface Prediction Consensus (SPC) 47 score. To highlight the complementarity of these measures and justification for inclusion in this resource, we performed set analysis of the human proteome using the UpSetR 48 web application.…”

Section: Proteome-wide Comparison Of Prediction Strategiesmentioning

confidence: 99%

CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies

Waas

Littrell

Gundry

2020

J. Am. Soc. Mass Spectrom.

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Cell surface transmembrane, extracellular, and secreted proteins are high value targets for immunophenotyping, drug development, and studies related to intercellular communication in health and disease. As the number of specific and validated affinity reagents that target this subproteome are limited, mass spectrometry (MS)-based approaches will continue to play a critical role in enabling discovery and quantitation of these molecules. Given the technical considerations that make MS-based cell surface proteome studies uniquely challenging, it can be difficult to select an appropriate experimental approach. To this end, we have integrated multiple prediction strategies and annotations into a single online resource, Compiled Interactive Resource for Extracellular and Surface Studies (CIRFESS). CIRFESS enables rapid interrogation of the human proteome to reveal the cell surface proteome theoretically detectable by current approaches and highlights where current prediction strategies provide concordant and discordant information. We applied CIRFESS to identify the percentage of various subsets of the proteome which are expected to be captured by targeted enrichment strategies, including two established methods and one that is possible but not yet demonstrated. These results will inform the selection of available proteomic strategies and development of new strategies to enhance coverage of the cell surface and extracellular proteome. CIRFESS is available at www.cellsurfer.net/cirfess. .

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Section: Proteome-wide Comparison Of Prediction Strategiesmentioning

confidence: 99%

CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies

Waas

Littrell

Gundry

2020

J. Am. Soc. Mass Spectrom.

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“…Pearson's correlation test was performed to evaluate the inter-run reproducibility of individual LC-MS analyses. Proteins with known or expected cell-surface localization were selected using GenieScore, an algorithm for the prediction of surface localization (41). The Exocarta database (www.exocarta.org) was used to compare the proteins identified with those already found in exosomes.…”

Section: Liquid Chromatography (Lc) Ms/ms (Lc-ms/ms) Lc-ms/msmentioning

confidence: 99%

Exosomes released by imatinib‑resistant K562 cells contain specific membrane markers, IFITM3, CD146 and CD36 and increase the survival of imatinib‑sensitive cells in the presence of imatinib

Hrdinova

Toman

Dresler³

et al. 2020

Int J Oncol

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Chronic myeloid leukemia (CML) is a malignant hematopoietic disorder distinguished by the presence of a BCR-ABL1 fused oncogene with constitutive kinase activity. Targeted CML therapy by specific tyrosine kinase inhibitors (TKIs) leads to a marked improvement in the survival of the patients and their quality of life. However, the development of resistance to TKIs remains a critical issue for a subset of patients. The most common cause of resistance are numerous point mutations in the BCR-ABL1 gene, followed by less common mutations and multiple mutation-independent mechanisms. Recently, exosomes, which are extracellular vesicles excreted from normal and tumor cells, have been associated with drug resistance and cancer progression. The aim of the present study was to characterize the exosomes released by imatinib-resistant K562 (K562 IR ) cells. The K562 IR -derived exosomes were internalized by imatinib-sensitive K562 cells, which thereby increased their survival in the presence of 2 µM imatinib. The exosomal cargo was subsequently analyzed to identify resistance-associated markers using a deep label-free quantification proteomic analysis. There were >3,000 exosomal proteins identified of which, 35 were found to be differentially expressed. From this, a total of 3, namely the membrane proteins, interferon-induced transmembrane protein 3, CD146 and CD36, were markedly upregulated in the exosomes derived from the K562 IR cells, and exhibited surface localization. The upregulation of these proteins was verified in the K562 IR exosomes, and also in the K562 IR cells. Using flow cytometric analysis, it was possible to further demonstrate the potential of CD146 as a cell surface marker associated with imatinib resistance in K562 cells. Taken together, these results suggested that exosomes and their respective candidate surface proteins could be potential diagnostic markers of TKI drug resistance in CML therapy.

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“…To identify novel TNBC-associated proteins, we integrated our TNBC N -glycoproteomics data with publicly available resources ( Figure 2A ). Specifically, we filtered for proteins that were enriched in TNBC compared to NCs ( Figure 2B ) and were predicted to have a cell surface localization by SurfaceGenie (Waas et al, 2020b). We next ranked the shortlisted proteins based on their detection in normal tissue by Human Protein Atlas (Uhlén et al, 2015) to prioritize surface proteins with limited overall expression in normal tissue ( Figure 2C ).…”

Section: Resultsmentioning

confidence: 99%

“…For differential expression analysis between TNBC and NC, fold change was calculated based on averaged protein intensities for each condition and a Student’s t-test followed by a Benjamini-Hochberg correction was used. The quantified data set was searched against the bioinformatics tool SurfaceGenie (Waas et al, 2020b) to identify cell surface proteins with high confidence. Normal tissue expression was evaluated by downloading normal tissue protein staining data from Human Protein Atlas (Uhlén et al, 2015) version 20.1.…”

Section: Star Methodsmentioning

confidence: 99%

“…Additional limitations that we are keen to interrogate in the future are direct detection in patient tissues using immunohistochemistry and more detailed analysis of signaling pathways downstream of PLXNB3 using our CRISPR edited cell line models. glycoproteins was restricted to include only cell surface proteins (Waas et al, 2020b) and were subsequently ranked based on lack of detection in normal tissue according to Human Protein Atlas (Uhlén et al, 2015). PLXNB3 was the top-ranking candidate that had not previously been investigated in the context of breast cancer and hence, was selected for functional interrogation.…”

Section: Limitations Of the Studymentioning

confidence: 99%

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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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SurfaceGenie: a web-based application for prioritizing cell-type specific marker candidates

Cited by 10 publications

References 44 publications

CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies

CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies

Exosomes released by imatinib‑resistant K562 cells contain specific membrane markers, IFITM3, CD146 and CD36 and increase the survival of imatinib‑sensitive cells in the presence of imatinib

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

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