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 >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.

Data access: 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.

Study approval and
patient consent: 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).

Study aims and methodology: 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 ex vivo 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.

Data supporting the figures, tables, supplementary figures and
supplementary tables in the related article:

Data supporting figure 1 and supplementary figure 1: REPLICANT Metastatic
Lymph Node Multiplex IF.xlsx and REPLICANT Reactive Lymph Nodes Multiplex
IF.xlsx, 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.