Abstract Background The immune system plays a pivotal role in the development and progression of colorectal cancer (CRC). Tumor immune rejection has been previously linked to activation of the interferon stimulated genes (ISG) pathway including STAT1, IRF5 and IRF1. Here, we tested the associations of ISG pathway genes with cytotoxic T cell (CTL) infiltration, granzymeB and perforin secretion, tumor expression of intercellular adhesion molecule 1 (ICAM-1), and clinicopathological factors. Further, we investigated the poorly understood regulation of STAT1 and IRF1 by miR-34a and miR-93 using sequential in situ hybridization (ISH) /immunohistochemistry and digital image analysis. Methods Resection specimens from 244 CRC patients with full clinicopathological data were included in this study. ngTMA (next generation tissue microarray) slides containing 8 punches of tumor and normal tissue from each case were immunostained for proteins of interest. The expression of the miRNAs was visualized on consecutive slides by ISH. Precise correlation analysis of miRNA expression and the target proteins was performed using digital image analysis. Results Active interferon signaling in the tumor microenvironment negatively correlated with the presence of distant metastasis (STAT1: p = 0.013, OR = 0.98, 95%CI = 0.96-0.99; IRF1: p = 0.014, OR = 0.96, 95%CI = 0.940.99; IRF5: p = 0.009, OR = 0.96, HR = 0.93-0.99). High miR-34a and miR-93 expression corresponded to a 22.5 fold decrease of STAT1 and IRF1 (p = 0.006, OR = 0.39, 95%CI = 0.20-0.77; p = 0.058, OR: 0.48 95%CI = 0.231.02). Finally, a combined score was generated from the three protein markers, representing an immune activated and a “quiescent” phenotype. The activated phenotype was associated with elevated CD8+ CTL infiltration (p = 0.007, HR = 2.07, 95%CI = 1.22-3.52), an increase in granzymeB (p<0.001, HR = 3.22, 95%CI = 1.70-6.08), perforin (p = 0.020, OR = 1.90, 95%CI = 1.10-3.26) and ICAM-1 expression (p = 0.006, OR = 0.2.17, 95%CI = 1.263.85). Patients with immune activated CRC had a considerably reduced risk of developing distant metastases (p = 0.001, OR = 0.034, 95%CI = 0.006-0.183). Conclusion Here, we describe a combined marker phenotype that can help to differentiate between patients with an activated and “quiescent” immune phenotype of CRC. The score is based on a quantitative assessment of STAT1, IRF1 and IRF5 expression by digital image analysis. Increased tumor infiltrating CTLs, granzymeB, perforin and tumor ICAM-1 expression, as well as a lower risk of distant metastases characterize the immune activated phenotype. Targeted inhibition of miR34a and miR-93 may be a promising strategy to activate the anti-tumoral immune response and will be validated in future experimental studies. Citation Format: Lena Sokol, Viktor H. Koelzer, Stefan P. Zahnd, Lucine Christe, Inti Zlobec, Alessandro Lugli. A signature of rejection in colorectal cancer: immune markers and their epigenetic regulation. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4135.