Abstract 744: Cancer immunotherapy biomarker profiling assay
Authors: Alex Chenchik, Leonid Iakoubov, Mikhail Makhanov, Costa Frangou
Journal: Cancer Research (2016)

Abstract Selecting patients predisposed to respond to existing and novel immunotherapy treatments requires the development of novel prognostic and predictive biomarkers. Recent reports have identified several gene expression signatures specific for immunity status and immune contexture in solid tumor microenvironments, and these enable predictions of efficacy of a number of chemo- and immunotherapeutics. Robust methods for molecular characterizations of the immune mechanism in the tumor microenvironment are essential to meet the imminent need for diagnostic approaches that identify patient populations responsive to the growing number of immunotherapeutic treatments. Toward this goal, we developed the Cancer ImmuneNet 2500 (CIN2500) assay for profiling cellular composition in the tumor microenvironment and discovery of novel prognostic and predictive immune response biomarkers. The CIN2500 panel provides signatures for approximately 400 immunity-related genes from 16 predictive and prognostic core genes that have been validated in recent chemo- and immunotherapy clinical trials across several tumor types, including melanoma, colorectal, breast, and lung cancers. In addition, using computational analysis of an immunotherapy network model, we predicted and included in the assay approximately 300 key nodes in pathways specific for antigen presentation and recognition, inhibition, activation and motility of immune cells, and adhesion and apoptosis of cancer cells. The CIN2500 panel also includes a comprehensive set of 1,700 genes specific for detection and quantitative profiling in the tumor microenvironment of different types of activated immune cells of adaptive and innate immunity, and stromal, fibroblast, cancer, endothelial and adipose cell types. The CIN2500 assay quantitatively profiles the expression levels of approximately 2,500 key cancer genes from 10-100ng of total RNA using multiplex RT-PCR amplification followed by Next-Generation Sequencing (NGS). Built-in standards for each gene target enable sample-to-sample calibration of the NGS data and provide a reference to adjust for background noise that often depends on the quality of samples. Control studies have shown that the CIN2500 assay quantifiably measures 4 orders of magnitude variation in the expression levels of 2,500 immune-related genes from as few as 100 cells in whole lysate, and profiles from frozen biopsies, surgically-removed tumor samples, PBMCs, and FFPE clinical samples show a comparable range and sensitivity. We will present profiling data from infiltrating immune cells and key intact and deficient immune mechanisms in the tumor microenvironment of breast cancer samples to demonstrate the performance and utility of the CIN2500 assay. Citation Format: Alex Chenchik, Leonid Iakoubov, Mikhail Makhanov, Costa Frangou. Cancer immunotherapy biomarker profiling assay. [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 744.