Fig. 2
Similarities and differences in gene expression by immune cells infiltrating inflamed tissues vs melanoma metastases. A, LCM of immune cells infiltrating regions of normal tissue inflammation and cancer in a post-mortem liver specimen. Yellow circles, dissected areas containing inflammatory infiltrates in the non-cancerous portion of the liver (specimen I-5); green circles, dissected areas containing tumor infiltrating immune cells in a metastatic melanoma deposit (specimen T-4). H&E, hematoxylin and eosin staining. Black bars, 100 µm. B, Unsupervised hierarchical clustering of PTPRC-normalized Ct values reveals similarities in expression of many genes across all samples. Expression of 122 candidate genes was evaluated with multiplex qRT-PCR. PTPRC-normalized Cts (Ctgene – CtPTPRC) were clustered and visualized by heat map using Java TreeView. Pink or green colors indicate genes expressed abundantly or poorly, respectively, in the samples. Clustering reveals a high degree of similarity between a lymph node metastasis and a normal lymph node specimen, but does not differentiate the 6 remaining specimens including 2 melanoma metastases and 4 non-cancerous inflamed tissues. C, Volcano plot reveals groups of genes with related functions upregulated in 4 inflamed normal tissues vs 3 tumor specimens. PTPRC-normalized Ct values were used to calculate fold changes of gene expression. Red dots in the upper left region of the plot indicate genes significantly upregulated (fold change magnitude ≥ 2.0, and Welch’s t-test 2-sided p-value ≤ 0.10) in inflamed normal tissues. Genes related to immunosuppressive cell types and cytokines are indicated by magenta boxes, Tregs by blue boxes, COX-2/PGE2 pathway by green boxes, and lymphocyte activation by peach boxes. Black dots in the lower half of the plot indicate genes without differential expression. No genes were upregulated in tumor samples. Genes that were undetectable in any specimen (IL4, IL17A, IL22, and IL23A) were omitted