Tumor-infiltrating immune cells are highly relevant for prognosis and 
identification of immunotherapy targets in hepatocellular carcinoma (HCC). The 
recently developed CIBERSORT method allows immune cell profiling by 
deconvolution of gene expression microarray data. By applying CIBERSORT, we 
assessed the relative proportions of immune cells in 41 healthy human livers, 
305 HCC samples and 82 HCC adjacent tissues. The obtained immune cell profiles 
provided enumeration and activation status of 22 immune cell subtypes. Mast 
cells were evaluated by immunohistochemistry in ten HCC patients. Activated mast 
cells, monocytes and plasma cells were decreased in HCC, while resting mast 
cells, total and naïve B cells, CD4+ memory resting and CD8+ T cells were 
increased when compared to healthy livers. Previously described S1, S2 and S3 
molecular HCC subclasses demonstrated increased M1-polarized macrophages in the 
S3 subclass with good prognosis. Strong total immune cell infiltration into HCC 
correlated with total B cells, memory B cells, T follicular helper cells and M1 
macrophages, whereas weak infiltration was linked to resting NK cells, 
neutrophils and resting mast cells. Immunohistochemical analysis of patient 
samples confirmed the reduced frequency of mast cells in human HCC tumor tissue 
as compared to tumor adjacent tissue. Our data demonstrate that deconvolution of 
gene expression data by CIBERSORT provides valuable information about immune 
cell composition of HCC patients.