Supporting metadata for expression data from Association of B7-H4, PD-L1 and tumor infiltrating lymphocytes with outcomes in breast cancer
Creators: name: Altan, Mehmet
name: Kidwell, Kelley M.
name: Pelekanou, Vasiliki
name: Carvajal-Hausdorf, Daniel E.
name: Schalper, Kurt A.
name: I.Toki, Maria
name: Thomas, Dafydd G.
name: Sabel, Michael S.
name: Hayes, Daniel F.
name: Rimm, David L.
Publisher: name: figshare
Year: 2018
Subjects: subject: Cancer
subject: 30406 Proteins and Peptides
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences

description: This data record is for protein expression data from a study investigating the relationship between protein expression of B7-H4 (co-inhibitory molecule) in breast cancer and Programmed death-ligand 1: PD-L1, Tumor Infiltrating Lymphocytes (TILs) and clinico-pathological variables in 2 independent populations.<br>The study uses multiplexed automated QIF to measure the levels of B7-H4 and PD-L1 protein and determined TILs through pathologist assessment of H&amp;E stained preparations in over a thousand breast cancer cases.<br>See https://doi.org/10.6084/m9.figshare.7352834 for QIF image data.<br><b>Data identifiers:</b>Per database searches the low RNA levels were noted in MCF7 cell lines, thus this cell line has been used for the experiments, the results for mRNA expression in commercially available cell lines can be seen in links below. <br>Expression Atlas European Bioinformatics Institute EMBL-EBI - https://www.ebi.ac.uk/gxa/search?geneQuery=[{"value":"VTCN1"}]&amp;organism=&amp;conditionQuery=[]&amp;bs={"bos taurus":["ORGANISM_PART"],"chlorocebus sabaeus":["ORGANISM_PART"],"danio rerio":["DEVELOPMENTAL_STAGE"],"equus caballus":["ORGANISM_PART"],"macaca mulatta":["ORGANISM_PART"],"monodelphis domestica":["ORGANISM_PART"],"mus musculus":["ORGANISM_PART"],"ovis aries":["ORGANISM_PART"],"papio anubis":["ORGANISM_PART"],"rattus norvegicus":["ORGANISM_PART"],"sus scrofa":["ORGANISM_PART"],"xenopus tropicalis":["ORGANISM_PART"],"homo sapiens":["CELL_LINE"]}#baseline<br><br>The Human Protein Atlas https://www.proteinatlas.org/ENSG00000134258-VTCN1/cell<b><br></b><b>Format of data and number of files: </b>EBI Expression Atlas: 13 <b>.tsv</b> text filesThe Human Protein Atlas: 1 <b>.tsv</b> text file<br><b>Software needed to access data:</b>Survival analysis of continuous marker scores for the Yale combined cohorts was performed using the X-tile software (Yale University, New Haven, CT, USA) for disease-specific survival differences. This analysis exported to GraphPad Prism 7.01 software for Kaplan Meier overall survival curve presentations. SAS (Statistical Analysis System) v 9.4 was used for analysis of the Michigan cohort, while graph pad prism and SAS v9.4 is commercially availalble X-tile can be downloaded openly from https://medicine.yale.edu/lab/rimm/research/software.aspx<br><b>Sample and cohort size:</b>Cohorts: Yale University N=654. University of Michigan N=473.Yale University cohorts were retrospectively derived from stage I-III breast cancer collections of patients who underwent surgical tumor resection and were followed at Yale University from 1976-2010. Two of the Yale University cohorts (Cohorts A and B) have been previously described and a third cohort (Cohort C) consists of tissues collected from patients with stage I–III triple negative breast cancer (TNBC). Cohort D consists of a set of 473 breast cases treated at the University of Michigan Comprehensive Cancer Center (UMCCC, derived from all patients who had definitive surgery for invasive breast cancer at UMCCC between 2004-2005, and for whom breast cancer tissue blocks were therefore available, and who underwent subsequent therapy and follow-up at UMCCC.<br><b>Cohort characteristics:</b> age, ER, PR and HER2 positive or negative and cancer stage. (For detailed cohort characteristics see the Supplementary tables 2 and 3 of the related publication.)<br><br><b>Sample size for expression data: </b>561 from Yale cohort and 444 from University of Michigan cohort.<br><b>Study design summary:</b><br>The related study is a retrospective analysis of samples from four retrospective collections of breast cancer: three from Yale University (Cohort A, B and C) and one from University of Michigan (UM) represented in tissue microarrays (TMAs).<br>Multiplexed automated quantitative immunofluorescence (QIF) was used to measure B7-H4 and PD-L1 protein levels via H&amp;E stained preparations in over 1,000 breast cancer cases from the Yale and UM cohorts.<br>Analysis was performed on associations between the marker levels, major clinico-pathological variables and survival.<b><br></b><b>Data access: </b><br>The study used cohorts from 2 academic institution; Tissue and associated clinico-pathological information was used after approval from the Yale Human Investigation Committee (protocol #9505008219) or from the University of Michigan Institutional Review Board (IRBMED#2001-0788; HUM00042180). Patient identifiers were removed to maintain patient data confidentiality, remaining information in cohort characteristics were shared in the article and supplementary tables of the related publication.