High-risk gene expression profiles for colorectal liver metastases

Abstract

Presenter: Michael Turgeon MD | Emory University Background: Over half of patients with colorectal cancer develop liver metastases with a minority of patients considered resectable at presentation. While there has been significant progress in the development of new biologics for the treatment of colorectal liver metastases (CRLM), only a small proportion of patients harbor actionable mutations. Furthermore, gene expression patterns of liver-specific metastases remain unclear. Our aim was to identify high-risk gene expression profiles for patients with CRLM to better inform prognosis and the development of novel targeted therapies. Methods: We examined 53 formalin-fixed paraffin-embedded (FFPE) colorectal liver metastasis samples from patients who underwent complete metastasectomy from 2009-2017 at a single institution. Immune cell infiltration was confirmed with CD45 antibody staining via immunohistochemistry (IHC). Targeted mRNA expression profiling was performed with extracted RNA using the NanoString Immune Oncology (IO360) 750-gene panel. Expression counts were normalized by the geometric mean of the positive-control and the most stable housekeeping genes were selected using the geNorm algorithm followed by log2 transformation. The differential expression analysis with fold changes and p-values were calculated using the NanoString methodology. Groups of interest were dichotomized based on synchronous versus metachronous disease and risk profiles. Risk profiles were based on median and quartile overall survival (OS) cut-points. “High-risk” was considered OS below the median or 25th percentile, while “low-risk” was OS above the median, above the 75th percentile, or no death due to disease. Results: Of 53 patients, median overall survival was 58 months. Median follow-up was 36 months. Using the NanoString IO360 panel, we detected no differentially expressed genes between synchronous (n=28) and metachronous (n=25) CRLM. Considering risk profiles, four differentially expressed genes were identified comparing tumors from high-risk (n=4) versus low-risk (n=18) patients based on a median OS cut-point of 45 months. Pathway analysis indicated these gene expression signatures were associated with antigen presentation, DNA repair, and collagen synthesis. When comparing the 25th percentile (high-risk n=2) to the 75th percentile (low-risk n=16), a total of 68 down-regulated genes were detected that were primarily involved in the antigen presentation pathways. Conclusion: Patients with colorectal liver metastases with poor overall survival may have a distinct, “high-risk” gene expression profile that manifests in alterations in antigen presentation, DNA repair, and collagen synthesis pathways. The identified genes serve as promising molecular markers for prognostication and for the development of novel targeted therapies. Next steps include NanoString analysis with an expanded cohort, immunohistochemistry to validate protein expression, and modulation of gene expression in cell lines.