Plasma nucleosome profiling reports on tumor burden and molecular subtypes in small cell lung cancer

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Abstract

BACKGROUND Small-cell lung cancer (SCLC) is an aggressive malignancy with a poor prognosis and marked transcriptional heterogeneity that may drive distinct therapeutic vulnerabilities. Clinical translation of molecular subtyping has been limited by restricted access to tumor biopsies, particularly at relapse.METHODS We applied chromatin immunoprecipitation of cell-free nucleosomes carrying active histone modifications followed by sequencing (cfChIP-seq) to 441 plasma samples from individuals with advanced SCLC, other neuroendocrine carcinomas, or non-SCLC cancers, as well as from healthy controls. Plasma cfChIP-seq profiles were integrated with matched tumor transcriptomes from 73 samples, including 41 time-matched pairs.RESULTS cfChIP-seq captured the epigenetic and transcriptional landscape of tumor-derived cell-free DNA (cfDNA), including SCLC tissue- and cell-of-origin signatures. A quantitative cfChIP-seq–derived SCLC score tracked radiographic tumor burden and was associated with prognosis. Signals at promoters of lineage-defining transcription factor genes, including ASCL1, NEUROD1, POU2F3, and ATOH1, correlated strongly with matched tumor RNA expression and supported noninvasive inference of SCLC transcriptional subtypes directly from plasma.CONCLUSION Plasma cfChIP-seq provides a practical liquid biopsy platform for real-time assessment of tumor burden, tumor state, and molecular subtype in SCLC. These findings support further development of cfChIP-seq for precision monitoring and subtype-informed therapeutic stratification in SCLC.TRIAL REGISTRATION ClinicalTrials.gov NCT02484404, NCT02487095, NCT02769962, NCT03554473, NCT03896503, and NCT02146170.FUNDING Center for Cancer Research; Intramural Program of the NCI (ZIA BC 011793); European Research Council (ERC) (Adg no. 101019560 “cfChIP”).

Authors

Gavriel Fialkoff, Nobuyuki Takahashi, Israa Sharkia, Jenia Gutin, Nadav Hermoni, Michael Nirula, Rajesh Kumar, Lorinc Pongor, Samantha Nichols, Linda Sciuto, Kanak Parmar, Parth Desai, Priya Suresh, Melissa Abel, Rajaa El Meskini, Myriam Maoz, Yakir Rottenberg, Shoshan Nevo, Hovav Nechushtan, Tamar Peretz, Diana Roame, Ayala Hubert, Jonathan E. Cohen, Azzam Salah, Mark Temper, Albert Grinshpun, Zoe Weaver-Ohler, Arun Rajan, William Douglas Figg Sr., Aviad Zick, Ronen Sadeh, Nir Friedman, Anish Thomas