BACKGROUND: Most patients with early stage triple negative breast cancer (TNBC) 
receive adjuvant chemotherapy. Activation of the immune system is associated 
with tumor response and may help identify TNBC with favorable outcome.
METHODS: Gene expression data were obtained from the GEO Dataset 
GDS2250/GSE3744. Affymetrix CEL files were downloaded and analyzed with 
Affymetrix Transcriptome Analysis Console 3.0. Functional genomics was 
implemented with David Bioinformatics Resources 6.8. Data contained at Oncomine 
were used to identify genes upregulated in basal-like cancer compared to normal 
breast tissue. Data contained at cBioportal were used to assess for molecular 
alterations. The KMPlotter online tool, METABRIC and GSE25066 datasets were used 
to associate gene signatures with clinical outcome.
RESULTS: 1564 upregulated genes were identified as differentially expressed 
between normal and basal-like tumors. Of these, 16 genes associated with immune 
function were linked with clinical outcome. HLA-C, HLA-F, HLA-G and TIGIT were 
associated with both improved relapse-free survival (RFS) and overall survival 
(OS). The combination of HLA-F/TIGIT and HLA-C/HLA-F/TIGIT showed the most 
favorable outcome (HR for RFS 0.44, p<0.001; HR for OS 0.22, p<0.001; and HR for 
RFS 0.46, p<0.001; HR for OS 0.15, p<0.001; respectively). The association of 
HLA-C/HLA-F with outcome was confirmed using the METABRIC and GSE25066 datasets. 
No copy number alterations of these genes were identified.
CONCLUSION: We describe a gene signature associated with immune function and 
favorable outcome in basal-like breast cancer. Incorporation of this signature 
in prospective studies may help to stratify risk of early stage TNBC.