Supplementary Figure 1: LINK-A is correlated with immune suppressive microenvironment.

(a) Expression of LINK-A across 20 cancer types (median ± quantile). The boxes show the median ± 1 quartile, with whiskers extending to the most extreme data point within 1.5 interquartile ranges from the box boundaries. LINK-A expression across 20 cancer types (n=6309). The sample size for each cancer type is as follows: Bladder urothelial carcinoma [BLCA] (n = 252), Breast invasive carcinoma [BRCA] (n = 837), Cervical squamous cell carcinoma and endocervical adenocarcinoma [CESC] (n = 196), Colon adenocarcinoma [COAD] (n = 157), Glioblastoma multiforme [GBM] (n = 154), Head and neck squamous cell carcinoma [HNSC] (n = 426), Kidney chromophobe [KICH] (n = 66), Kidney renal clear cell carcinoma [KIRC] (n = 448), Kidney renal papillary cell carcinoma [KIRP] (n = 198), Brain lower grade glioma [LGG] (n = 486), Liver hepatocellular carcinoma [LIHC] (n = 200), Lung adenocarcinoma [LUAD] (n = 488), Lung squamous cell carcinoma [LUSC] (n = 220), Ovarian serous cystadenocarcinoma [OV] (n = 412), Prostate adenocarcinoma [PRAD] (n = 374), Rectum adenocarcinoma [READ] (n = 71), Skin cutaneous melanoma [SKCM] (n = 226), Stomach adenocarcinoma [STAD] (n = 285), Thyroid carcinoma [THCA] (n = 497), Uterine corpus endometrial carcinoma [UCEC] (n = 316). (b) Pearson correlation of LINK-A expression and the GZMB/CD8A ratio in 20 cancer types. The sample size of supplementary is the same as fig. 1a. (c) LINK-A expression basal-like breast cancer patients with lowest 25% versus patients with highest 25% GSVA score of different immune cells. GSVA score high group (25% upper, n = 35) and GSVA score low group (25% bottom, n =35) of different immune cell populations in TNBC breast cancer. P values were determined by unpaired two-tailed Student’s t test. (d) Measurement of staining intensity of CD8 of human TNBC tissues upon Pembrolizumab treatment (n=12 tissues) (*p < 0.5). Results are mean ± s.d. of n = 6, 6 tissues. P values were determined by unpaired two-tailed Student’s t test. (e-i) Pearson correlation of immunoblotting intensities of TAP2 (e), TPSN (f), CALR (g), MHC I (h) or B2M (i) and LINK-A copy numbers of human TNBC tissues upon Pembrolizuman treatment (n = 12 tissues). (j) Localization of LINK-A by DNA FISH (green) in the primary Tg(LINK-A) mammary gland epithelial cells or MMTV-Tg(LINK-A) tumor cells. Nuclei are counterstained with DAPI (blue). Scale bar: 20 µm. Three independent experiments were performed and yielded similar results. (k,l) Copy number of GAPDH (left) or LINK-A (right) of adjacent normal breast tissues, non-TNBC or TNBC tissues (k) or Tg(LINK-A) mammary gland or MMTV-Tg(LINK-A) breast tumor (l). n = 16, 112 and 33 human tissues (k) or 15 and 15 animals (l) (n.s., p > 0.05, ***p < 0.001). Results are mean ± s.e.m. P values were determined by one-way ANOVA (k) or unpaired two-tailed Student’s t test (l). (m) Comparison of LINK-A copy number in MMTV-Tg(LINK-A) breast tumor and human TNBC tissues (n = 15 animals and 33 tissues respectively)(n.s., p > 0.05). Results are mean ± s.e.m. P values were determined by unpaired two-tailed Student’s t test.