Figure 3. Conventional Th subset marker expression in TIL.
(A–C) Th subset marker genes were quantified in the patient confirmation set by (A and B) qRT-PCR and (C) flow cytometry. (A) Mean ΔCt values (relative to the Th-specific endogen CASC3) are inversely proportional to the relative intensity of gene expression; CD4+ TIL (n = 6) are compared with D-PB (n = 6). (B) CD4+ TIL from extensively infiltrated tumors (n = 6) are compared with minimally infiltrated tumors (n = 12). “n = <18” indicates that the number of minimally infiltrated tumors assessed was as noted. (C) Protein expression was assessed by flow cytometry (Supplemental Figure 2). (D–F) Microarray data from the patient discovery set and (G) qRT-pCR data of memory versus total CD4+ T cells from healthy donor cells are shown for comparison with (D) CD4+ T cells isolated from the first tissue (i.e., TIL) relative to the second tissue (i.e., P-PB), (E) CD4+ T cells isolated from ER– relative to ER+ tumors, (F) CD4+ T cells isolated from extensively infiltrated tumors relative to minimally infiltrated tumors, and (G) D-PB CD4+CD45RO+ memory T cells (n = 3) compared with total CD4+ T cells (n = 3). (H) Microarray data of D-PB memory CD4+ T cells after S or tumor SN treatment (Figure 6 and Supplemental Table 6). Fold change or ratio values are shown as blue (downregulated) and orange (upregulated); P values (2-tailed Student’s t test with unequal variance) in green are significant (P < 0.05); n.d., not determined (for qRT-PCR data no data = n.d.); nc, no change (for microarray data empty cells = nc). For gene symbols, “v” indicates transcript variant.