Tuesday, October 9, 2018
Tumor microenvironment plays an important role in regulating the pathogenesis of malignant diseases and circumventing the anti-tumor immune response in the immune-quiescent (“cold”) tumors. New technologies for dissecting the tumor microenvironment are emerging, including bioinformatics platform for analysing the “omics” data of the tumor microenvironment. Ongoing efforts to characterize the tumor microenvironment to stratify patients for immunotherapy, and find biomarkers of response often use methods that are limited by 1) availability of adequate tumor tissue from needle biopsy material; 2) restricted set of cell surface and phenotypic markers to analyze the cellular composition with limited tissue availability, and 3) loss of tissue integrity during processing for downstream analysis.
Recently, single-cell transcriptomics has enabled studies to analyze the heterogeneity in a population of cells from a tissue and define gene expression signatures in the tumor microenvironment, but the quality of data generated is still governed by the sample collection method and quality of RNA ( determined by the presence of viable cells). Alternatively, genomic methods that use deconvolution to assess relative enrichment of different cells types can be utilized to understand the composition of the tumor microenvironment, but that approach can also be limited in utility by biases introduced by dependencies in the cell type. Taken together, a robust method of studying the tumor microenvironment to identify the molecular signature is still needed. To this end, MedGenome has developed OncoPeptTUME, a genomic solution that utilizes its highly cell-type specific proprietary minimal gene expression signature for 8 different immune cells. The expression of genes for a given signature was transformed to produce a cell-type specific immune score that was used to quantitate the relative proportion of cell types present in the complex tumor microenvironment. In this white-paper we highlight a) how the proprietary gene expression signatures were generated and validated, b) robustness of our gene signatures compared to other existing methods in identifying cell types of interest c) utility of the OncoPeptTUME in defining immunogenicity ( via immune score assignments) of tumors and predicting prognosis and long-term survival benefits based on the immune signatures of the tumors.
During this webcast the speaker will:
- Discuss why it is important to dissect the tumor microenvironment.
- Discuss what are the current technologies for characterizing the tumor microenvironment and their limitations.
- Present an example of dissecting the tumor microenvironment of pancreatic cancer by using MedGenome’s OncopeptTUME platform and also discuss the future directions.
Dr. Lei Zheng M.D., Ph.D
Associate Professor of Oncology and Surgery
Johns Hopkins University School of Medicine
Dr. Ankita Das