DOI: 10.5061/dryad.m905qfvfc
title: Data from: Dynamics of the CD9 interactome during bacterial infection of epithelial cells by proximity labelling proteomics

description: Bacterial species utilise different receptors at the cell membrane to
 adhere to cells. Previously, we demonstrated that interference with CD9, a
 human tetraspanin, reduces adherence of multiple species of bacteria to
 cells. CD9 is not a receptor but organises numerous commandeered host
 proteins at the cell membrane; however, the full interactome has not yet
 been delineated. Using a CD9 proximity labelling model, a first for CD9,
 we observed a diverse interactome, with 710 enriched proteins in
 uninfected cells. Proximal proteins were associated with various cellular
 processes, including extracellular matrix (ECM)–receptor interactions and
 tight junctions. Several known bacterial receptors were also detected,
 including CD44, CD46, and CD147. The interactome was dynamic during
 infection with two distinct bacterial species, Neisseria meningitidis and
 Staphylococcus aureus. In total, 12 human proteins were enriched during
 meningococcal infection, compared to one during staphylococcal infection,
 demonstrating different host factor requirements during CD9-mediated
 bacterial adherence. CD44 or CD147 knockdown reduced staphylococcal and
 meningococcal adherence, respectively, but not vice versa. However, in
 combination with CD9 interference, no additive effects were observed,
 demonstrating association of these proteins during infection. We have
 developed a tool that measures changes within the CD9 interactome,
 demonstrated CD9 as a universal organiser of bacterial ‘adhesion
 platforms’, and shown efficacy of a disrupting CD9-derived peptide.
description: # Data from: Dynamics of the CD9 interactome during bacterial infection of
 epithelial cells by proximity labelling proteomics Dataset DOI:
 [10.5061/dryad.m905qfvfc](10.5061/dryad.m905qfvfc) ## Description of the
 data and file structure **Data S2. Cell compartment and cellular pathway
 analysis of identified proteins.** Data files contain analysis of
 significantly enriched proteins identified by mass spectrometry at 30, 60
 and 240 minutes. Data files supplied by SubcellulaRVis demonstrates the
 cellular compartment analysis of the enriched proteins. Data files
 supplied by WebGestalt provide the KEGG pathway analysis of the
 significantly enriched proteins. ### Files and variables ####
 File: CellVis_Enrichment_30_mins.csv **Description:** Cellular compartment
 analysis from SubcellulaRVis after 30 mins. #### File:
 CellVis_Enrichment_60_mins.csv **Description:** Cellular compartment
 analysis from SubcellulaRVis after 60 mins. #### File:
 CellVis_Enrichment_240_mins.csv **Description:** Cellular compartment
 analysis from SubcellulaRVis after 240 mins. * Compartment: The cellular
 localization category based on Gene Ontology (GO) Cellular Component
 terms. * p: p value associated with the enrichment of genes within the GO
 annotated pathway * FDR: False discovery rate associated with genes
 enriched within the GO annotated pathway * Significant: Whether the
 compartment passes the statistical significance threshold * n: The number
 of genes from input list that are associated with that cellular
 compartment * Genes: The list of genes from dataset that map to that
 compartment #### File: Supplementary_Data_2.zip (hosted on Zenodo)
 **Description:** Files are organised in to analysis of datasets from 30,
 60 and 240 minutes. Each directory contains: i) a .html file containing
 the KEGG pathway analysis from WebGestalt ii) various .txt and .png files
 which are used to build the .html file **Description of .txt files and
 .png files within zipped directories:**
 `enriched_geneset_wsc_topsets_wg_result.txt`* - describes the top GO sets
 observed through a weighted set cover analysis of the dataset.
 `enrichment_results_wg_result.txt`* - describes the top GO sets observed
 with no redundancy reduction.  Column 1 - geneSet - GO annotated pathway,
 hsa* Column 2 - description - description of GO annotated pathway Column 3
 - link - hyperlink to the GO annotated pathway Column 4 - size - number of
 genes associated with the GO annotated pathway Column 5 - overlap - number
 of genes from the analysed dataset which overlap with the GO annotated
 pathway Column 6 - expect - number of genes expected to overlap with the
 GO annotated dataset Column 7 - enrichmentRatio - ratio of expected
 enriched genes. The number of overlapping genes divided by the number of
 expected genes  Column 8 - pValue - p value associated with the enrichment
 of genes within the GO annotated pathway Column 9 - FDR - False discovery
 rate associated with genes enriched within the GO annotated pathway Column
 10 - overlapId - Entrez Gene ID associated with enriched genes from the
 analysed dataset associated with the GO annotated pathway Column 11 -
 userId - Gene names associated with the enriched genes from the analysed
 dataset associated with the GO annotated pathway
 `goslim_summary_wg_result.png`* - demonstrates bar charts produced by GO
 Slim analysis showing Biological process categories, Cellular component
 categories and Molecular Function categories
 `goslim_summary_wg_result_bp.txt`* - tabular form of the GO Slim analysis
 showing biological process analysis Column 1 - GO biological process
 annotation Column 2 - description of GO biological process Column 3 -
 number of genes associated `goslim_summary_wg_result_cc.txt`* - tabular
 form of the GO Slim analysis showing cellular compartment analysis Column
 1 - GO cellular compartment annotation Column 2 - description of GO
 biological process Column 3 - number of genes associated
 `goslim_summary_wg_result_mf.txt`** - *tabular form of the GO Slim
 analysis showing molecular function analysis Column 1 - GO molecular
 function annotation Column 2 - description of GO biological process Column
 3 - number of genes associated `interestingID_mappingTable_wg_result.txt`*
 - table showing mapped function of analysed genes Column 1 - userId -
 GeneID provided by the user Column 2 - geneSymbol - recognised gene symbol
 Column 3 - geneName - full gene name Column 4 - entrezgene - number
 associated with the gene in the Entrez database Column 5 - gLink -
 Hyperlink associated with the gene within the NCBI database
 `interestingID_unmappedList_wg_result.txt`* - list of unmapped genes from
 the analysed dataset, lists user inputted gene names not recognised in the
 database ## Code/software Files will require to be unzipped using any
 compression software. .html files can be opened with any web browser, .csv
 files can be opened with Microsoft Excel. ## Access information Data was
 analysed from the following sources: * SubcellulaRVis
 ([https://shiny.its.manchester.ac.uk/subcellularvis/](https://shiny.its.manchester.ac.uk/subcellularvis/)) * WebGestalt ([https://www.webgestalt.org/](https://www.webgestalt.org/))