MOESM1 of Immune gene expression profiling reveals heterogeneity in luminal breast tumors

Additional file 1: Figure S1. Schematic representation of the strategy for the quantification of TILs in H&E stained images. Figure S2. Expression levels of immune-related genes in the three luminal immune subtypes and non-luminal (HER2-enriched and basal-like) tumors in HKBC. Figure S3. MCP-counter scores and CIBERSORT relative fractions of a subset of immune cell subpopulations in the three luminal immune subtypes and non-luminal (HER2-enriched and basal-like, separately) tumors in HKBC. Figure S4. MCP-counter scores of eight immune cell subpopulations in the three luminal immune subtypes and non-luminal (HER2-enriched and basal-like) tumors with the adjustment of tumor purity in HKBC. Figure S5. Replication of luminal immune subtypes in TCGA and KBC datasets: a) MCP-counter scores for eight immune cell subpopulations; b) Relative fractions of immune cell subpopulations by CIBERSORT (cell populations with extremely low fractions were not shown); c) High-TIL tumors showed upregulation of genes in immune activation and regulation activities than tumors in the other two luminal immune subtypes; d) High-ISG tumors expressed higher levels of ISG genes than tumors in the other two luminal immune subtypes. Figure S6. Genomic features associated with luminal immune subtypes in HKBC (HER2-enriched and basal-like, separately): a) ESR1/ESR2 ratios; b) number of mutations. Figure S7. Replication of genomic features associated with luminal immune subtypes in TCGA and KBC datasets: a) ESR1/ESR2 ratios; b) age at diagnosis; c) 10-year overall survival. Figure S8. Expression of APOBEC3B in normal and tumor tissue in relation to the polymorphic germline APOBEC3B deletion represented by rs12628403-C allele in HKBC. Figure S9. MCP-counter scores of eight immune cell subpopulations in adjacent normal breast tissue in the three luminal immune subgroups and non-luminal (HER2-enriched and basal-like) patients of HKBC.