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Tumor Microenvironment Analysis

The Background of Tumor Microenvironment

Tumor microenvironment (TME) is the environment around a tumor that is composed of extracellular matrix (ECM), stromal cells ( fibroblasts, mesenchymal stromal cells, pericytes, occasionally adipocytes, blood, and lymphatic vascular networks), and immune cells (T and B lymphocytes, natural killer cells, and Tumor-associated macrophages). The recent clinical success of immune checkpoint inhibitors (ICIs) in treating several different types of cancer has raised the interest of TME at the genetic and phenotypic levels. Understanding the interaction between tumor cells and their microenvironment furthers our knowledge of the molecular mechanisms involved in tumor formation and facilitates immune-oncology drug development.

Key Advantages
  • Comprehensive analytical validation from FFPE: RNA isolation to library construction to sequencing.
  • Unsurpassed data quality with higher percentage of Q30, higher percentage of clean data and higher proportion of reads mapping to mRNA compared to poly(A) RNA-Seq.
  • Extensive experience with hundreds of clinical FFPE samples analyzed.
  • Comprehensive data analysis using widely accepted mainstream software and mature in-house pipelines. Our professional bioinformatics team offers standard, advanced, and customized analysis tailored to your needs.

Tumor Microenvironment Analysis by RNA-seq in Novogene

Novogene is a leading provider of genomic services and solutions with cutting-edge NGS platforms and bioinformatics expertise. Novogene, using RNA sequencing (RNA-seq), can provide a highly comprehensive tumor microenvironment analysis at a highly competitive price. Novogene can also provide insight into the genome-wide transcriptome heterogeneity at a single-cell resolution.

Analysis Contents

Tumor immunoassay using transcriptome data can be used to score and evaluate the tumor microenvironment of the sample, and to study its relationship with prognostic survival and immunotherapy response alone or in combination with other indicators. In addition, it can refine the composition of tumor microenvironment, draw the map of tumor microenvironment, which can help depicting the mechanism of immune regulation.

  • Evaluation of tumor purity
  • Tumor gene signature analysis
  • Tumor microenvironment-related cell analysis
  • TCR analysis​

Novogene Data

A paper[1] about breast cancer recently published in Cancer Epidemiology Biomarkers & Prevention by West China Hospital, Sichuan University and Novogene, Smith et. al included 76 patients with TNBC diagnosed between 2008 to 2016 in West China Hospital and 158 patients with TNBC from The Cancer Genome Atlas. On the basis of transcriptome data, we calculated the overall Immune-Score and type-specific enrichment scores for 34 types of immune cells, using xCell, a gene signature–based method. This findings suggest that plasma cells and CD4þTcm in the tumor microenvironment may play a role in the subsequent progression of TNBC. This study provides evidence of the role of immune cells in TNBC progression that may have clinicalutility. Download now