{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:45:10Z","timestamp":1785422710085,"version":"3.56.0"},"reference-count":40,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T00:00:00Z","timestamp":1774656000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Van Andel Research Institute\u2014Stand Up To Cancer Epigenetics Dream Team"},{"id":[{"id":"https:\/\/ror.org\/00wm07d60","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Institutes of Health, National Cancer Institute","doi-asserted-by":"publisher","award":["P30CA082709-25"],"award-info":[{"award-number":["P30CA082709-25"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"award":["P30CA082709-25"],"award-info":[{"award-number":["P30CA082709-25"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Merck and Astex, Inc."}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pharmaceuticals"],"abstract":"<jats:p>Background\/Objectives: Epigenetic modifications, particularly DNA methylation, contribute to tumor progression and therapy resistance. Guadecitabine, a hypomethylating agent (HMA), has shown promising clinical activity when combined with carboplatin in preclinical models. We evaluated the combination of guadecitabine with carboplatin as a second-line treatment for extensive-stage small-cell lung cancer (SCLC; NCT03913455), one of the deadliest malignancies. Here, we report methylome changes in peripheral blood mononuclear cells (PBMCs) collected at baseline and during treatment from patients on the trial. Methods: PMBC DNA was analyzed using Infinium HumanMethylationEPIC v1.0 bead chips. Data were processed, and differentially methylated positions (DMPs) were identified and analyzed for pathway enrichment using bioinformatic approaches, and immune deconvolution analyses were conducted to investigate the impact on immune cell composition. Results: Direct comparison of PBMCs between cycle 2 day 5 (C2D5; post-treatment) vs. cycle 1 day 1 (C1D1; pre-treatment) revealed a greater number of hypomethylated DMPs (380 DMPs in C2D5 vs. C1D1 PBMCs; p &lt; 0.05, |\u03b2| &gt; 20%). Moreover, when first compared with normal PBMCs from cancer-free controls, the number of hypomethylated DMPs was even greater in C2D5 than in C1D1 (1771 vs. 237 DMPs, respectively; p &lt; 0.05, |\u03b2| &gt; 20%). Long interspersed nucleotide elements-1 (LINE-1) were significantly hypomethylated in PBMCs after HMA treatment (C2D5 vs. C1D1). Pathway analysis of hypomethylated DMPs revealed significant alterations in key signaling pathways, including NF-\u03baB, Rho GTPase, and pulmonary fibrosis in C1D1 vs. C2D5. Normal PBMCs to C1D1 PBMCs revealed changes in IL-3 signaling, Fc\u03b3 receptor-mediated phagocytosis, and molecular mechanisms of cancer. Deconvolution analysis revealed a greater percentage of monocytes in C1D1 vs. normal PBMCs; after HMA treatment, percentages of monocytes and B cells decreased, while the eosinophil percentage increased in C1D1 vs. C2D5. Conclusions: HMA treatment has a global impact on PBMC methylomes in cancer patients. DNA methylation changes were associated with biological pathways related to PBMC function, and shifts in distinct immune cell populations were observed.<\/jats:p>","DOI":"10.3390\/ph19040542","type":"journal-article","created":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T13:41:03Z","timestamp":1774878063000},"page":"542","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Effects of the Hypomethylating Agent Guadecitabine on Peripheral Blood Mononuclear Cell Methylomes and Immune Cell Populations in Small-Cell Lung Cancer Patients"],"prefix":"10.3390","volume":"19","author":[{"given":"Elnaz Abbasi","family":"Farid","sequence":"first","affiliation":[{"name":"Medical Sciences Program, School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shu","family":"Zhang","sequence":"additional","affiliation":[{"name":"Medical Sciences Program, School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Fu","sequence":"additional","affiliation":[{"name":"Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, MI 49505, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Collin M.","family":"Coon","sequence":"additional","affiliation":[{"name":"Medical Sciences Program, School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2169-5035","authenticated-orcid":false,"given":"Daniela","family":"Matei","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shadia I.","family":"Jalal","sequence":"additional","affiliation":[{"name":"Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA"},{"name":"Department of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2192-1346","authenticated-orcid":false,"given":"Kenneth P.","family":"Nephew","sequence":"additional","affiliation":[{"name":"Medical Sciences Program, School of Medicine-Bloomington, Indiana University, Bloomington, IN 47405, USA"},{"name":"Indiana University Melvin and Bren Simon Comprehensive Cancer Center, Indianapolis, IN 46202, USA"},{"name":"Department of Anatomy, Cell Biology and Physiology, School of Medicine, Indiana University, Indianapolis, IN 46202, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,3,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1038\/s41571-019-0316-z","article-title":"Immunotherapeutic approaches for small-cell lung cancer","volume":"17","author":"Iams","year":"2020","journal-title":"Nat. Rev. Clin. Oncol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41572-020-00235-0","article-title":"Small-cell lung cancer","volume":"7","author":"Rudin","year":"2021","journal-title":"Nat. Rev. Dis. Primers"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"69","DOI":"10.21037\/tlcr.2018.01.16","article-title":"Current standards for clinical management of small cell lung cancer","volume":"7","author":"Farago","year":"2018","journal-title":"Transl. Lung Cancer Res."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1016\/j.neo.2017.07.007","article-title":"What\u2019s new in SCLC? A review","volume":"19","author":"Oronsky","year":"2017","journal-title":"Neoplasia"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"101821","DOI":"10.1016\/j.tranon.2023.101821","article-title":"Epigenetic modifications: Key players in cancer heterogeneity and drug resistance","volume":"39","author":"Sadida","year":"2024","journal-title":"Transl. Oncol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Wu, J., Feng, J., Zhang, Q., He, Y., Xu, C., Wang, C., and Li, W. (2023). Epigenetic regulation of stem cells in lung cancer oncogenesis and therapy resistance. Front. Genet., 14.","DOI":"10.3389\/fgene.2023.1120815"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Martinez-Useros, J., Martin-Galan, M., Florez-Cespedes, M., and Garcia-Foncillas, J. (2021). Epigenetics of most aggressive solid tumors: Pathways, targets and treatments. Cancers, 13.","DOI":"10.3390\/cancers13133209"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"113016","DOI":"10.1016\/j.celrep.2023.113016","article-title":"Neuroendocrine lineage commitment of small cell lung cancers can be leveraged into p53-independent non-cytotoxic therapy","volume":"42","author":"Biswas","year":"2023","journal-title":"Cell Rep."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5777","DOI":"10.1158\/1078-0432.CCR-06-0669","article-title":"Phase I study of decitabine-mediated gene expression in patients with cancers involving the lungs, esophagus, or pleura","volume":"12","author":"Schrump","year":"2006","journal-title":"Clin. Cancer Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1186\/s13148-025-01992-z","article-title":"Peripheral blood mononuclear cell DNA methylation biomarkers for prognostic stratification in Chinese lung adenocarcinoma: A genome-wide epigenetic profiling study","volume":"17","author":"Li","year":"2025","journal-title":"Clin. Epigenet."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s13148-017-0436-1","article-title":"The signature of liver cancer in immune cells DNA methylation","volume":"10","author":"Zhang","year":"2018","journal-title":"Clin. Epigenet."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1186\/s13148-022-01382-9","article-title":"Gene body methylation in cancer: Molecular mechanisms and clinical applications","volume":"14","author":"Wang","year":"2022","journal-title":"Clin. Epigenet."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"4724","DOI":"10.1038\/s41467-023-40389-5","article-title":"A multiplex blood-based assay targeting DNA methylation in PBMCs enables early detection of breast cancer","volume":"14","author":"Wang","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"3636","DOI":"10.1158\/0008-5472.CAN-22-3402","article-title":"DNA Methylation-Based Testing in Peripheral Blood Mononuclear Cells Enables Accurate and Early Detection of Colorectal Cancer","volume":"83","author":"Xie","year":"2023","journal-title":"Cancer Res."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1016\/j.cllc.2023.03.003","article-title":"A Brief Report of a Phase II trial Evaluating Efficacy and Safety of Hypomethylating Agent Guadecitabine in Combination with Carboplatin in Extensive Stage Small Cell Lung Cancer","volume":"24","author":"Wei","year":"2023","journal-title":"Clin. Lung Cancer"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.2741\/3782","article-title":"NF-kappaB in lung cancer, a carcinogenesis mediator and a prevention and therapy target","volume":"16","author":"Chen","year":"2011","journal-title":"Front. Biosci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1186\/s13148-020-00876-8","article-title":"Epigenome-wide DNA methylation analysis of small cell lung cancer cell lines suggests potential chemotherapy targets","volume":"12","author":"Krushkal","year":"2020","journal-title":"Clin. Epigenet."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"384","DOI":"10.2188\/jea.JE20120003","article-title":"DNA methylation in peripheral blood: A potential biomarker for cancer molecular epidemiology","volume":"22","author":"Li","year":"2012","journal-title":"J. Epidemiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"166583","DOI":"10.1016\/j.bbadis.2022.166583","article-title":"Blood-based DNA methylation signatures in cancer: A systematic review","volume":"1869","author":"Li","year":"2023","journal-title":"Biochim. Biophys. Acta BBA Mol. Basis Dis."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/s12943-022-01543-7","article-title":"Liquid biopsy: A step closer to transform diagnosis, prognosis and future of cancer treatments","volume":"21","author":"Lone","year":"2022","journal-title":"Mol. Cancer"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1007\/s11010-021-04265-4","article-title":"Global DNA methylation profile at LINE-1 repeats and promoter methylation of genes involved in DNA damage response and repair pathways in human peripheral blood mononuclear cells in response to \u03b3-radiation","volume":"477","author":"Priya","year":"2022","journal-title":"Mol. Cell. Biochem."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"2197","DOI":"10.1158\/0008-5472.CAN-11-3909","article-title":"Epigenetic resensitization to platinum in ovarian cancer","volume":"72","author":"Matei","year":"2012","journal-title":"Cancer Res."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1158\/1078-0432.CCR-17-3055","article-title":"A Phase I Clinical Trial of Guadecitabine and Carboplatin in Platinum-Resistant, Recurrent Ovarian Cancer: Clinical, Pharmacokinetic, and Pharmacodynamic Analyses","volume":"24","author":"Matei","year":"2018","journal-title":"Clin. Cancer Res."},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Zhang, X., Zhang, R., and Yu, J. (2020). New understanding of the relevant role of LINE-1 retrotransposition in human disease and immune modulation. Front. Cell Dev. Biol., 8.","DOI":"10.3389\/fcell.2020.00657"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2213","DOI":"10.1158\/1078-0432.CCR-16-1754","article-title":"Platinum-Based Chemotherapy Induces Methylation Changes in Blood DNA Associated with Overall Survival in Patients with Ovarian Cancer","volume":"23","author":"Flanagan","year":"2017","journal-title":"Clin. Cancer Res."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Mosaddeghzadeh, N., and Ahmadian, M.R. (2021). The RHO family GTPases: Mechanisms of regulation and signaling. Cells, 10.","DOI":"10.3390\/cells10071831"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"455","DOI":"10.1152\/physrev.00045.2020","article-title":"Rho GTPase signaling in cancer progression and dissemination","volume":"102","author":"Samain","year":"2022","journal-title":"Physiol. Rev."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.lfs.2018.03.032","article-title":"Idiopathic pulmonary fibrosis (IPF) signaling pathways and protective roles of melatonin","volume":"201","author":"Hosseinzadeh","year":"2018","journal-title":"Life Sci."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"6840","DOI":"10.1038\/ncomms7840","article-title":"Id1 suppresses anti-tumour immune responses and promotes tumour progression by impairing myeloid cell maturation","volume":"6","author":"Papaspyridonos","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e001388","DOI":"10.1136\/jitc-2020-001388","article-title":"MYC oncogene is associated with suppression of tumor immunity and targeting Myc induces tumor cell immunogenicity for therapeutic whole cell vaccination","volume":"9","author":"Wu","year":"2021","journal-title":"J. Immunother. Cancer"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Wang, J., Zhang, W., Li, H., Wang, Y., Qi, J., and Nie, J. (2025). Cell-free DNA methylation and fragmentomics-based liquid biopsy for accurate esophageal cancer detection. BMC Cancer, 25.","DOI":"10.1186\/s12885-025-15150-4"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1613","DOI":"10.1038\/s42003-025-09017-4","article-title":"5-hydroxymethylcytosine analysis reveals stable epigenomic changes in tumor tissue that enable cancer detection in cell-free DNA","volume":"8","author":"Xue","year":"2025","journal-title":"Commun. Biol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"189497","DOI":"10.1016\/j.bbcan.2025.189497","article-title":"Decoding the epigenetic landscape: ctDNA methylation as a game-changer in hepatocellular carcinoma management","volume":"1880","author":"Yang","year":"2025","journal-title":"Biochim. Biophys. Acta BBA Rev. Cancer"},{"key":"ref_34","first-page":"e123","article-title":"SeSAMe: Reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions","volume":"46","author":"Zhou","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"ref_35","unstructured":"Zhou, W., and Shen, H. (2026, March 24). R Package, 1.24.0 ed; sesameData: Supporting Data for SeSAMe Package (v1.24.0). Available online: https:\/\/bioconductor.org\/packages\/release\/data\/experiment\/html\/sesameData.html."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"2185742","DOI":"10.1080\/15592294.2023.2185742","article-title":"Validation of the new EPIC DNA methylation microarray (900K EPIC v2) for high-throughput profiling of the human DNA methylome","volume":"18","author":"Esteller","year":"2023","journal-title":"Epigenetics"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1038\/s41592-018-0213-x","article-title":"Identification of differentially methylated cell types in epigenome-wide association studies","volume":"15","author":"Zheng","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"757","DOI":"10.2217\/epi-2016-0153","article-title":"Cell-type deconvolution in epigenome-wide association studies: A review and recommendations","volume":"9","author":"Teschendorff","year":"2017","journal-title":"Epigenomics"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"378","DOI":"10.32614\/RJ-2017-066","article-title":"glmmTMB Balances Speed and Flexibility Among Packages for Zero-inflated Generalized Linear Mixed Modeling","volume":"9","author":"Brooks","year":"2017","journal-title":"R J."},{"key":"ref_40","unstructured":"Lenth, R.V. (2026, March 24). R Package, 1.10.7-100003 ed; Estimated Marginal Means, aka Least-Squares Means. Available online: https:\/\/cran.r-project.org\/web\/packages\/emmeans\/index.html."}],"container-title":["Pharmaceuticals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1424-8247\/19\/4\/542\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T15:55:21Z","timestamp":1775058921000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1424-8247\/19\/4\/542"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,3,28]]},"references-count":40,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4]]}},"alternative-id":["ph19040542"],"URL":"https:\/\/doi.org\/10.3390\/ph19040542","relation":{},"ISSN":["1424-8247"],"issn-type":[{"value":"1424-8247","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,3,28]]}}}