Supporting metadata for Association of B7-H4, PD-L1 and tumor infiltrating lymphocytes with outcomes in breast cancer

Dataset 1:

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.

The Human Protein Atlas: https://www.proteinatlas.org/ENSG00000134258-VTCN1/cell

Dataset 2:

QIF image data are available on request (see QIF data record below).

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.

Cohort characteristics: age, ER, PR and HER2 positive or negative and cancer stage.

Sample size for expression data: 561 from Yale cohort and 444 from University of Michigan cohort.

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).

Multiplexed automated quantitative immunofluorescence (QIF) was used to measure B7-H4 and PD-L1 protein levels via H&E stained preparations in over 1,000 breast cancer cases from the Yale and UM cohorts.

Analysis was performed on associations between the marker levels, major clinico-pathological variables and survival.

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.

Dataset 2:

QIF images are stored long term in Rimm lab systems:

https://medicine.yale.edu/lab/rimm/contact/?organizationId=114109

With exception of confidential patient information, scientific data can be accessed and can be reused if needed