43An immune active cancer phenotype typified by a T helper 1 (Th-1) immune response has 44 been associated with increased responsiveness to immunotherapy and favorable prognosis 45 in some but not all cancer types. The reason of this differential prognostic connotation remains 46 unknown. Through a multi-modal Pan-cancer analysis among 31 different histologies (9,282 47 patients), we demonstrated that the favorable prognostic connotation conferred by the 48 presence of a Th-1 immune response was abolished in tumors displaying specific tumor-cell 49 intrinsic attributes such as high TGF-ß signaling and low proliferation capacity. This 50 observation was validated in the context of immune-checkpoint inhibition. WNT-ß catenin, 51 barrier molecules, Notch, hedgehog, mismatch repair, telomerase activity, and AMPK 52 signaling were the pathways most coherently associated with an immune silent phenotype 53 together with mutations of driver genes including IDH1/2, FOXA2, HDAC3, PSIP1, MAP3K1, 54 KRAS, NRAS, EGFR, FGFR3, WNT5A, and IRF7. Our findings could be used to prioritize 55 hierarchically relevant targets for combination therapies and to refine stratification algorithms. 56 57 Keywords 58 -Pan-cancer 59 -Immunologic Constant of Rejection 60 -Prognosis 61 -Mutational load 62 -Neoantigen load 63 -Aneuploidy 64 -Tumor intrinsic pathway enrichment 65 -Cancer Immunotherapy phenotypes (Hendrickx et al., 2017). In particular, we reported that transcriptional 104 dysregulation of the MAPK pathways sustained by genetic alterations (i.e., MAP3K1 and 105 MAP2K4 mutations) are enriched in immune silent tumors (Hendrickx et al., 2017). We also 106 observed that the ICR signature refines and improves the prognostic value of conventional 107 prognostic signatures adopted in breast cancer (Bertucci et al., 2018). Here, we propose a 108 systematic analysis of the entire TCGA cohort encompassing 31 different histologies. Using a 109 pan-cancer approach, we identified novel relationships between tumor genetic programs and 110 immune orientation. After having demonstrated differential associations between ICR 111 classification and overall survival across cancer types, we systemically analyzed in which 112 (molecular) contexts ICR has prognostic value and in which ones it does not. Combination of 113 immune orientation with tumor intrinsic attributes that interact with its prognostic significance 114 could refine tumor immunologic classifications. This approach was validated in the context of 115 immune-checkpoint inhibition allowing better predictive precision.