Why study the TME with NGS?
The tumor microenvironment (TME) is a complex network of cells, molecules and blood vessels that shapes tumor growth, progression and response to therapy. A key part of this system is the tumor immune microenvironment (TIME), where interactions between tumor cells and immune cells can influence immune activation, suppression and tumor immune evasion. This makes immune cell profiling, including analysis of tumor-infiltrating lymphocytes (TILs), especially important in immuno-oncology research.
Intratumoral heterogeneity within the TME remains a major challenge in tumor profiling and understanding cancer biology. Because the TME is highly dynamic and heterogeneous, its analysis requires sensitive technologies that can resolve its diverse cellular and molecular components. Next-generation sequencing (NGS) provides the depth and resolution needed to capture genomic and transcriptomic complexity and uncover the molecular interactions shaping the TME.
RNA sequencing approaches for TME analysis
RNA-seq provides powerful insights into the cellular and molecular complexity of the TME. By profiling gene expression, researchers can investigate interactions between tumor, immune and stromal cells, identify biomarkers associated with disease progression or treatment response, and gain a deeper understanding of the biological processes that shape the TME.
Depending on the research question, bulk RNA-seq enables tissue-wide transcriptome profiling across large sample cohorts, while single-cell RNA-seq resolves the cellular diversity and functional states that underlie these tissue-level signals. Together, these complementary approaches provide a comprehensive view of the TME across multiple levels of biological resolution.
Select the right RNA-seq solution for your research question
Whole transcriptome analysis
Characterize tissue-wide gene expression with bulk RNA-seq or resolve cellular heterogeneity and transcriptional states with single-cell RNA-seq.
miRNA profiling
Profile known and novel microRNAs to investigate gene regulation, discover biomarkers and understand disease mechanisms.
Featured articles, webinars and posters
QIAseq FastSelect has really been phenomenal with the RNA sequencing in my project. The RNA was degraded and almost unusable, but QIAseq FastSelect really removes the ribosomal RNA in these degraded samples and has improved our sequencing libraries.
Brandon Mistretta, Doctoral Student, Department of Biology and Biochemistry, University of Houston
TCR profiling in the TME
T cell receptor (TCR) profiling reveals how T cells recognize and respond to tumors. Researchers can characterize immune repertoires across cohorts with bulk TCR sequencing or combine TCR profiling with single-cell sequencing to link individual clonotypes to gene expression and functional states.
When combined with bulk or single-cell RNA-seq, TCR profiling provides a more comprehensive view of the tumor microenvironment by integrating immune repertoire information with transcriptomic data. This integrated approach helps researchers investigate immune repertoire diversity, monitor clonal expansion, identify biomarkers of immunotherapy response and gain deeper insights into the mechanisms underlying anti-tumor immunity, treatment resistance and immune-oncology research.
Select the right TCR-seq solution for your research question
Characterize adaptive immune repertoires with bulk TCR sequencing or combine TCR clonotypes with single-cell transcriptomics to understand T-cell function and tumor immunity.
Featured resources, guides and webinars
Sample preparation
Successful tumor microenvironment studies begin with high-quality samples. Reliable extraction of high-quality RNA from fresh, frozen and FFPE tissue supports robust bulk sequencing workflows, while optimized preparation of single-cell suspensions or nuclei enables accurate single-cell analysis. QIAGEN and Parse Biosciences provide complementary solutions spanning sample preparation, sequencing and downstream analysis to help researchers generate reliable data across a wide range of TME applications.
Preparing challenging samples for TME analysis
Data analysis and pathway mapping
Integrated bioinformatics workflows help transform sequencing data into biological insights. Analyze transcriptomic and immune repertoire data to identify clonotypes, characterize immune cell populations, map molecular pathways and predict upstream regulators, enabling a deeper understanding of tumor biology, anti-tumor immunity and tumor–immune interactions.
Bioinformatics solutions
Transform sequencing data into biological insights with integrated bioinformatics solutions for pathway analysis, interactive visualization and single-cell data interpretation.
Featured bioinformatics resources
Research case studies
See how researchers are applying RNA-seq, TCR profiling and bioinformatics to investigate the TME across a range of cancer research applications.
Build your TME workflow
Explore integrated solutions for every stage of tumor microenvironment sequencing workflows, from RNA isolation and library preparation to immune profiling and bioinformatics analysis.