Extended Data Fig. 3: Cdk5 does not affect Pd-l1 in human or experimental BrM but negatively regulates APP and MHC-I gene expression in BrM both in vitro and in vivo.
A. Mean fluorescence intensity of Pd-l1 on the surface of indicated cells. One-way ANOVA with Dunnett’s post-hoc test. B. Immunoblotting for Pd-l1 in the indicated cell lines transfected with control or Cdk5 shRNA. C. mRNA expression of Cd274 in GFP+ single cells sorted from mice bearing BrM from GFP+ EO771.Br3.shCtl (N = 2,676 cells) or EO771.Br3.shCdk5 cells (N = 2,606 cells). Error bars indicate maximum and minimum values, box bounds indicate 1rd and 3rd quartiles, centre values indicate median, dots indicate outliers. Two-sided Wilcoxon rank-sum test. D. Two-sided Spearman's correlation analysis of the expression of CD274 and CDK5 in BrM patients from GSE164150, GSE52604 and Varešlija et al. human datasets. N = 47, 35, and 21 patients, respectively. Each dot represents a patient. E. Expression of indicated APP genes in GFP+ single cells sorted from mice bearing BrM from GFP+ EO771.Br3.shCtl (N = 2,676 cells) or EO771.Br3.shCdk5 cells (N = 2,606 cells). Each dot indicates a cell, violin shape indicates data distribution, red dot indicates the mean, bounds of the box indicate 1st and 3rd quartiles, whiskers indicate the range. Two-sided Wilcoxon rank-sum test. F. Two-sided Spearman's correlation analysis of the expression of human CDK5 and human HLA-A/B/C expression in mouse BrM lesions from MDA-MB-231.Br cells (GSE19184). Each dot represents a biological replicate. G. Two-sided Spearman's correlation analysis of the expression of CDK5 and HLA-A/B/C in single cancer cells from human breast cancer BrM lesions (GSE186344). Tables below display a cross-correlation (Spearman's) between HLA-A/B/C genes. Only samples with R2>0.5 for all cross-correlations were considered as passed the quality check. For A, results are shown as means ± SEM. N.S., not significant. QC – quality check, BrM – brain metastasis, Corr – correlation.
