Abstract B46: Gene expression in colorectal liver metastases: Distinct immune signatures and opportunities for immune modulating therapy
Authors: Nygaard Vigdis , Dagenborg Vegar Johansen , Yaqub Sheraz , Fretland Åsmund Avdem , Østrup Olga , Siwal-Pandit Laxmi , Grzyb Krzysztof , Børresen-Dale Anne-Lise , Mælandsmo Gunhild Mari , Ree Anne Hansen , Edwin Bjørn , Flatmark Kjersti 
Published: June 2021

Abstract
Colorectal cancer (CRC) is one of the most common cancers and a leading cause of cancer death in the Western world. Up to 50% of CRC patients develop metastatic disease and the liver is the most common site. The recently identified consensus molecular subtypes (CMS1-4) based on analyses of primary CRC have prognostic and therapeutic implications, but it is unclear whether these molecular subtypes are valid for metastatic disease. The tumor microenvironment plays a major role in the dynamic shaping of the tumor phenotype and the clinical impact of the immune contexture within given CMS subgroups is emerging. In this study we performed gene expression profiling of a CLM cohort for patient stratification. Surgically resected CLMs (n=44) were analyzed by genome-wide transcription profiling. Clustering approaches were applied to define subgroups. Differential gene expression analyses were performed to reveal altered expression patterns in subgroups selected by clinicopathologic parameters. Functional annotation of gene signatures was conducted. Validation in public data sets and by proteomic analyses (RPPA) is ongoing. Quantification of T-cell subsets by immunohistochemistry was scored. The CMS classifier tool revealed the cohort to be highly enriched for CMS2 and thus of limited stratification utility. In contrast, intrinsic subgroups were revealed by alternative computational approaches. Distinct immune profiles were associated with the subgroups identified. Unsupervised clustering based on high-variance genes identified a 55-gene cluster that split the cohort near evenly. Functional annotation of the 55 genes identified one subgroup to display dysregulated cholesterol/lipid homeostasis with reciprocal links to immune regulatory genes. Supervised clustering using EMT/mesenchymal signatures identified a mesenchymal subgroup (20% of the samples). Functional annotation suggested coexistence of immunosuppression with the mesenchymal phenotype. Elevated expression of immune checkpoint molecules including TIM-3, and M2 macrophage markers correlated with the EMT/mesenchymal signature. The subgroup showed relative high density of T-cell subset infiltration (CD3, CD4, CD8, FOXP3). In differential gene expression analysis, CLMs exposed to neoadjuvant chemotherapy showed activation of interferon gamma (IFNG) signaling and genes linked to immunogenic cell death. Co-expression of immune regulatory genes suggested counterbalance of the immune responses triggered by IFNG. Immune-related gene expression signatures were associated with the CLM subgroups identified. These observations underline the integration and importance of the immune interactome in CLM. The coordinated expression of immunosuppressive factors suggests not only a rationale for immune therapy, but also that development of immune-modulating strategies may be required to increase efficacy of current therapy for selected CLM patients.
Citation Format: Vigdis Nygaard, Vegar Johansen Dagenborg, Sheraz Yaqub, Åsmund Avdem Fretland, Olga Østrup, Laxmi Siwal-Pandit, Krzysztof Grzyb, Anne-Lise Børresen-Dale, Gunhild Mari Mælandsmo, Anne Hansen Ree, Bjørn Edwin, Kjersti Flatmark. Gene expression in colorectal liver metastases: Distinct immune signatures and opportunities for immune modulating therapy [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B46.