Using RNA Sequencing to Characterize the Tumor Microenvironment

Area of Science:

• Immunogenomics
• Transcriptomics
• Bioinformatics

Background:

• RNA sequencing (RNA-seq) is vital for studying tumor and microenvironment transcriptomes.
• Analytical methods can infer gene expression linked to immune cell presence.
• RNA-seq is feasible across various tissue types and preservation methods.

Purpose of the Study:

• To present a comprehensive workflow for RNA sequencing (RNA-seq) in immunogenomics.
• To detail the process from bulk tissue to actionable immunogenomic data.
• To outline key steps including RNA extraction, library preparation, sequencing, and initial analysis.

Main Methods:

• RNA extraction from diverse tissue types (FFPE, fresh-frozen, fresh).
• Selection of appropriate RNA sequencing library preparation methods.
• Sequencing, data alignment, and quality assurance.
• Downstream bioinformatics analyses for immunogenomic feature extraction.

Main Results:

• A standardized workflow for processing RNA samples for immunogenomic analysis.
• Identification of methods for optimizing RNA-seq based on tissue and RNA characteristics.
• Successful extraction of immunogenomic features through a defined bioinformatics pipeline.

Conclusions:

• The described RNA-seq workflow enables robust immunogenomic data generation.
• This approach facilitates the inference of gene expression patterns related to immune cell populations.
• The methodology provides a foundation for further systems biology investigations in immunogenomics.