Fig. 5: TNF-α disrupts CLA subtype identity and anti-tumor immunity.

a Heatmap of CLA and BL PDAC identity genes, in previously published²¹ RNA-seq data of CAPAN1 cells treated with TNF-α or vehicle control (VC) for 18 h. Cell color indicates z score. n = 3 biological replicates. b–f Virtually microdissected RNA-seq data of orthotopically transplanted CAPAN1 tumors in NMRI-Foxn1^nu/nu mice treated with TNF-α or VC for 3 weeks. n = 3 tumors; one stroma-specific transcriptome was excluded from the analysis. b Deconvolution of bulk RNA-seq to generate tumor (human) and stromal (murine) cell-specific transcriptomes (Methods). Tumor cell-specific transcriptome. Gene set enrichment analysis (GSEA) for Hallmark signatures of the Molecular signature database (MSigDB) (c) and PDAC subtype signatures (d), for TNF-α versus VC. Normalized enrichment score (NES) and FDR q-value are indicated. e As in (c), for stroma-specific transcriptome. f MCPcounter analysis in stroma-specific transcriptome. Cell color indicates z score. g Relative MCPcounter scores for the indicated lineages in n = 652 patients of the TCGA, QCMG, Puleo, and Zhou cohort, separated into quartiles based on the JUNB repression signature score (as in Fig. 2k, l). MCPcounter scores were min–max normalized and standardized to the mean of the lower JUNB repression signature score group. Mean ± s.d. shown. h As in (g), but applying CIBERSORTx for deconvolution. Mean ± s.d. for CIBERSORTx percentages shown. i IF for JUNB in orthotopically transplanted CAPAN1 tumors treated with TNF-α or VC, with cell detection for nuclear JUNB⁺ cells. Scale bar 50 μm. j Quantification of i, for per-animal average nuclear JUNB intensity with mean ± s.d. shown. n = 5 animals. k As in (i), for ECAD and GATA6 staining and cell detection for nuclear GATA6⁺ cells. l Quantification of k for per-animal average ECAD intensity per FOV with mean ± s.d. shown. m As in (l), for nuclear GATA6 intensity. l, m, VC, n = 7 animals; TNF-α, n = 8 animals. n As in (i), for CD163 IHC staining. Arrows indicate positive cells. Scale bar: overview, 100 μm; insert, 25 μm. o Quantification of (n) for per-animal percentage of CD163⁺ cells with mean ± s.d. shown. n = 7 animals. g, h, j, l, m, o Two-tailed Student’s t-test with Welch’s correction. Source data are provided as a Source Data file.