Inferring gene expression from cell-free DNA fragmentation profiles. Academic Article uri icon

Overview

abstract

  • Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.

publication date

  • March 31, 2022

Research

keywords

  • Cell-Free Nucleic Acids
  • Neoplasms

Identity

PubMed Central ID

  • PMC9337986

Scopus Document Identifier

  • 85127432644

Digital Object Identifier (DOI)

  • 10.1038/s41587-022-01222-4

PubMed ID

  • 35361996

Additional Document Info

volume

  • 40

issue

  • 4