Multiplex immunofluorescence data and metadata supporting the article: Proteomics of REPLICANT Perfusate Detects Changes in the Metastatic Lymph Node Microenvironment

In breast cancer (BC), detecting low volumes of axillary lymph node (ALN) metastasis pre-operatively is difficult and novel biomarkers are needed. In this study, the authors compared reactive (tumour-free; n = 5) and macrometastatic (containing tumour deposits &gt;2mm; n = 4) ALNs by combining whole section multiplex immunofluorescence with Tandem Mass Tag (TMT)-labelled Liquid Chromatography - Tandem Mass Spectrometry (LC-MS/MS) of the circulating perfusate.<br> <b>Data access: </b>The mass-spectrometry based proteomics data generated during the study, are publicly available in the PRIDE repository: https://identifiers.org/pride.project:PXD022722. The multiplex immunofluorescence data generated during this study, are available in the figshare repository, as part of this data record. The TCGA data analysed during the study, are available in the cBioPortal for Cancer Genomics: https://identifiers.org/cbioportal:brca_tcga. All other data supporting the findings of this study, are available as part of the supplementary files that accompany the article.<br> <b>Study approval and patient consent: </b>Patients consented for use of their tissue in the current study. The study protocol was approved by King's Health Partners Biobank (Research Ethics Committee No: 18/EE/0025).<br> <b>Study aims and methodology</b>: Lymph seems to contain higher concentrations of circulating biomarkers, particularly in the early stages of metastasis. Proteomic studies have shown that lymph reflects the pathophysiology of the tissue from which it derives, and has recently been shown to be relevant to melanoma biomarker discovery and stage prediction. To date, no such studies have been performed on lymphatic exudate from BC patients undergoing an axillary lymph node dissection (ALND) however. In this study, the authors characterised the proteome of the circulating fluid collected from perfused ALNs (perfusate) using Tandem Mass Tag (TMT) labelled mass spectrometry (MS)-based shotgun proteomics. ALNs were harvested from 10 BC patients and perfused <i>ex vivo </i>at 37˚C as described previously (Research Ethics Committee No: 18/EE/0025). The following are described in more detail in the related article: patient cohort and ALN harvest, perfusate collection, multiplex immunofluorescence (MIF), proteomic analysis, neutrophil quantification, The Cancer Genome Atlas (TCGA) BC proteomics analysis and statistical analysis. <b>Data supporting the figures, tables, supplementary figures and supplementary tables in the related article: </b><b><br></b> Data supporting figure 1 and supplementary figure 1: <b>REPLICANT Metastatic Lymph Node Multiplex IF.xlsx</b> and <b>REPLICANT Reactive Lymph Nodes Multiplex IF.xlsx</b>, both in .xlsx file format. The files are part of this figshare data record. The data files contain cell density counts from REPLICANT reactive (tumour-free) lymph nodes and metastatic lymph nodes, generated algorithmically from multiplex immunofluorescence (Vectra). Data supporting figures 2 and 3; and table 1: Proteomics data publicly available in the PRIDE repository: https://identifiers.org/pride.project:PXD022722. Data supporting figure 4 and supplementary figure 2: TCGA data publicly available at cBioPortal for Cancer Genomics: https://identifiers.org/cbioportal:brca_tcga. Data supporting figure 5: Supplementary Tables 4 and 5.xlxs. The data are available as part of the supplementary files that accompany the article. Data supporting figure 6: Supplementary Table 6.xlxs. The data are available as part of the supplementary files that accompany the article. Data supporting supplementary table 1: Proteomics data publicly available in the PRIDE repository: https://identifiers.org/pride.project:PXD022722. Data supporting supplementary table 2: TCGA data publicly available at cBioPortal for Cancer Genomics: https://identifiers.org/cbioportal:brca_tcga. Data supporting supplementary table 3: Proteomics data publicly available in the PRIDE repository: https://identifiers.org/pride.project:PXD022722 and supplementary files of article https://doi.org/10.1002/pmic.200800303. Data supporting supplementary table 4: Proteomics data publicly available in the PRIDE repository: https://identifiers.org/pride.project:PXD022722 and supplementary files of article https://doi.org/10.1002/path.3959. Data supporting supplementary table 5: Proteomics data publicly available in the PRIDE repository: https://identifiers.org/pride.project:PXD022722 and supplementary files of article https://doi.org/10.1016/j.neo.2017.10.009. Data supporting supplementary table 6: Proteomics data publicly available in the PRIDE repository: https://identifiers.org/pride.project:PXD022722, and Supplementary Tables 4 and 5.xlxs.<br>