Abstract 7180: DNA methylation profiling of peripheral blood mononuclear cells from small-cell lung cancer patients treated with hypomethylating agent plus carboplatin
Authors: Elnaz Abbasi Farid, Zhen Fu, Collin M. Coon, Shadia I. Jalal, Kenneth P. Nephew
Journal: Cancer Research (2025)

Abstract Small-cell lung cancer (SCLC), representing 15% of lung cancers, is one of the deadliest malignancies, with a 5-year survival rate under 7%. Despite initial sensitivity to platinum-based chemotherapy, rapid recurrence and treatment resistance remain hallmarks. Epigenetic modifications, particularly DNA methylation, play a critical role in tumor heterogeneity and resistance. Guadecitabine, a hypomethylating agent (HMA), has shown potential when combined with carboplatin. Building on these findings, we conducted a phase II single-arm trial to evaluate this combination as a second-line treatment for extensive-stage SCLC (ES-SCLC). Peripheral blood mononuclear cells (PBMCs) serve as a minimally invasive source to study systemic epigenetic changes, reflecting tumor-specific modifications. To investigate therapy-associated methylation changes, we analyzed PBMCs from 31 patients on NCT0391345 clinical trial testing guadecitabine and carboplatin: 20 paired pre- and post-treatment samples, 6 pre-treatment samples, and 5 post-treatment samples. DNA was extracted using the DNeasy Blood and Tissue Kit, quantified with NanoDrop™ and Qubit spectrophotometry, bisulfite-converted, and analyzed using the Infinium HumanMethylationEPIC v2.0 platform. Data were processed with SeSAMe to generate β-value matrices. Differentially Methylated Positions (DMPs) were identified using a β-value cutoff of 0.2 and an adjusted P &amp;lt; 0.05. Functional analysis of significant DMPs was conducted via Ingenuity Pathway Analysis (IPA).Guadecitabine treatment induced 334 hypomethylated and 9 hypermethylated CpG loci, with pathway analysis revealing significant changes in SCLC and NF-kappa B signaling. Key pathways included Rho GTPase signaling (metastasis), pulmonary fibrosis signaling (lung remodeling), p75 NTR signaling (cell survival), and several other signaling pathways (ID1, MYC mediated apoptosis, immunogenic cell death). Deconvolution analysis showed decreased B cells, NK cells, monocytes, eosinophils, and a trend toward reduced CD4+ and CD8+ T cells post-treatment. Conversely, neutrophils significantly increased, suggesting an inflammatory shift in the tumor microenvironment. These findings demonstrate that guadecitabine treatment induces significant CpG methylation changes in PBMCs, impacting genes and pathways critical to cellular signaling, tissue remodeling, and survival mechanisms. The identification of key pathways, including those involved in metastasis, lung remodeling, and tumor cell survival, highlights the potential role of HMAs in modulating epigenetic and biological processes relevant to SCLC progression and therapy. Citation Format: Elnaz Abbasi Farid, Zhen Fu, Collin M. Coon, Shadia I. Jalal, Kenneth P. Nephew. DNA methylation profiling of peripheral blood mononuclear cells from small-cell lung cancer patients treated with hypomethylating agent plus carboplatin [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7180.