Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes

Heeke, Simon; Rocha, Pedro P.; Arriola Aperribay, Edurne; Heymach, John V.

doi:http://dx.doi.org/10.1016/j.ccell.2024.01.001

Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes

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Heeke S, Gay CM, Estecio MR, Tran H, Morris BB, Zhang B, et al. Tumor- and circulating-free DNA methylation identifies clinically relevant small cell lung cancer subtypes. Cancer Cell. 2024 Feb 12;42(2):225-37.e5. DOI: 10.1016/j.ccell.2024.01.001

Abstract

Small cell lung cancer (SCLC) is an aggressive malignancy composed of distinct transcriptional subtypes, but implementing subtyping in the clinic has remained challenging, particularly due to limited tissue availability. Given the known epigenetic regulation of critical SCLC transcriptional programs, we hypothesized that subtype-specific patterns of DNA methylation could be detected in tumor or blood from SCLC patients. Using genomic-wide reduced-representation bisulfite sequencing (RRBS) in two cohorts totaling 179 SCLC patients and using machine learning approaches, we report a highly accurate DNA methylation-based classifier (SCLC-DMC) that can distinguish SCLC subtypes. We further adjust the classifier for circulating-free DNA (cfDNA) to subtype SCLC from plasma. Using the cfDNA classifier (cfDMC), we demonstrate that SCLC phenotypes can evolve during disease progression, highlighting the need for longitudinal tracking of SCLC during clinical treatment. These data establish that tumor and cfDNA methylation can be used to identify SCLC subtypes and might guide precision SCLC therapy.