Gene expression differs between MCL cells in PB and LN due to activation of signaling pathways in the LN. (A) Heat map of 130 genes that were differentially expressed in purified MCL cells obtained from PB (PBT, n = 17) and LN (LNT, n = 4) in 18 patients (>2-fold change, FDR < 0.2). Gene expression data were median-centered. Relative expression is indicated by the color scale. (B and C) GSEA identified a large number of upregulated gene sets in LNT compared with PBT. Accordingly, 166 relevant gene sets were selected having FDR ≤ 0.01, NES ≥1.80, and ≥10 “leading edge genes” (the genes of a given gene set most significantly differentially expressed in the experimental data), then grouped into 4 categories based on their functional similarities (supplemental Table 3). Two of these 4 categories are displayed: (B) “Signaling and interaction with the microenvironment” and (C) “Proliferation/malignancy”. Within each subcategory, the “signature score” of the gene set with the highest NES was calculated and displayed. This signature score was computed as the average of the mRNA expression level of the leading edge genes of a given gene set. The signature scores were compared between PBT and LNT samples using unpaired Student t test. AKT, protein kinase B; APRIL, a proliferation inducing ligand; BAFF, B-cell activating factor; E2F, E2F transcription factor; ERK, extracellular signal regulated kinase; GSK3, glycogen synthase kinase 3; IL, interleukin; LNT, purified tumor cells from LN; MAPK, mitogen-activated protein kinase; mTOR, mammalian target of rapamycin; MYC, v-myc avian myelocytomatosis viral oncogene homolog; PBT, purified tumor cells from PB; PG, prostaglandin; PI3K, phosphatidylinositol 3-kinase; Rb, retinoblastoma; TGFβ, transforming growth factor-β. ***P < .001; **P < .01.