Extended Data Fig. 3: Transcriptomic analysis of TIL harvest tumors from SEL-TIL + P arm.
From: Neoantigen-specific tumor-infiltrating lymphocytes in gastrointestinal cancers: a phase 2 trial
a. Volcano plot of DEGs between TIL harvest lesions of responders (n = 8) and non-responders (n = 25). Dotted lines indicate adjusted p-values < 0.05 (Benjamini-Hochberg corrected to adjust for multiple comparisons) and absolute log2FC > 2. Highlighted genes include selected immune-related genes and those from IPA-indicated pathways (Extended Data Fig. 4a). b. Normalized enrichment scores (NES) of significantly enriched hallmark gene sets (nominal p-value < 0.05, GSEA) in TIL harvest lesions from responders (black) or non-responders (white). Gene sets with false discovery rates < 0.3 are included to correct for multiple comparisons. c. Clustering of bulk tumor RNA-seq data by patient (SEL-TIL + P) according to top and bottom 100 response-associated DEGs. Z-scaled gene expression is indicated red to blue, and clinical response to TIL is shown below cluster plots (black for RECIST response, white for non-response). Responder-enriched clusters 1 and 2 show enhanced expression of response-associated genes, while non-responder-enriched clusters 3 and 4 show heightened expression of non-response-associated genes.
