Predicting response to immune checkpoint blockade in NSCLC with tumour-only RNA-seq

Area of Science:

• Oncology
• Genomics
• Immunotherapy

Background:

• Targeted RNA sequencing (RNA-seq) from FFPE specimens is clinically used for gene expression and fusion detection in cancer.
• The study investigates RNA-seq's utility for measuring tumor mutational burden (TMB) and immune gene expression from FFPE samples.
• The goal is to assess if these RNA-based markers predict response to immune checkpoint blockade in non-small cell lung cancer (NSCLC) patients.

Purpose of the Study:

• To determine if targeted RNA-seq can quantify tumor mutational burden (TMB) from FFPE specimens.
• To evaluate the predictive value of RNA-seq derived TMB and immune-cell-restricted gene expression for immune checkpoint blockade response.
• To compare the diagnostic ability of RNA-seq derived TMB with DNA-based TMB.

Main Methods:

• Developed a method to determine TMB from tumor-only RNA-seq using The Cancer Genome Atlas LUAD dataset, correlating with DNA-sequencing TMB (Spearman r=0.79).
• Applied this method to targeted RNA-seq data from NSCLC patients.
• Validated RNA-seq TMB against an orthogonal assay (Spearman r=0.49).

Main Results:

• RNA-seq derived TMB was significantly higher in responders to immune checkpoint blockade (P=0.028).
• RNA-seq TMB predicted treatment response (AUC=0.640).
• Expression of immune-cell-restricted genes did not correlate with patient outcomes.

Conclusions:

• Tumor mutational burden calculated from targeted RNA sequencing demonstrates comparable diagnostic ability to TMB derived from targeted DNA sequencing.
• Targeted RNA-seq is a viable method for assessing TMB in FFPE samples for predicting immunotherapy response.