Strenuous physical exercise causes a massive elevation in the concentration of circulating cell-free DNA (cfDNA), which correlates with effort intensity and duration. The cellular sources and physiological drivers of this phenomenon are unknown. Using methylation patterns of cfDNA and associated histones, we show that cfDNA in exercise originates mostly in extramedullary polymorphonuclear neutrophils. Strikingly, cardiomyocyte cfDNA concentration increases after a marathon, consistent with elevated troponin levels and indicating low-level, delayed cardiac cell death. Physical impact, low oxygen levels, and elevated core body temperature contribute to neutrophil cfDNA release, while muscle contraction, increased heart rate, β-adrenergic signaling, or steroid treatment fail to cause elevation of cfDNA. Physical training reduces neutrophil cfDNA release after a standard exercise, revealing an inverse relationship between exercise-induced cfDNA release and training level. We speculate that the release of cfDNA from neutrophils in exercise relates to the activation of neutrophils in the context of exercise-induced muscle damage.

Abstract Background: Liver metastasis is a major cause of mortality in small cell lung cancer (SCLC), but the organ-specific cues that enable metastatic colonization are poorly understood. We hypothesized that the hepatic microenvironment promotes a stem-like, high-plasticity state required for metastatic outgrowth. Methods: We analyzed patient-derived SCLC liver metastases using RNA-seq, ATAC-seq, and metabolomics, combined with spatial transcriptomics and orthotopic liver colonization models. Regional hypoxia, HIF1α signaling, and metabolic flux were assessed by protein quantification and 13C-glucose tracing. Functional studies included pharmacological ACLY inhibition (SB204990) and CRISPR-mediated ACLY knockout in vivo. Results: Across patient specimens and in vivo models, metastatic SCLC cells in the liver adopted a distinct stem-like transcriptional state, marked by activation of regenerative programs and chromatin accessibility at stemness loci (HNF1A, HNF4A, SOX9, ATF3). Spatial profiling revealed that tumor cells adjacent to hepatocytes experienced localized hypoxia, resulting in HIF1α stabilization and the transcriptional induction of ACLY, a key enzyme that generates nuclear acetyl-CoA. ATP-citrate lyase (ACLY)-dependent generation of nuclear acetyl-CoA, driving histone hyperacetylation and chromatin remodeling at liver-lineage transcription factors HNF1A, HNF4A, and SOX9. Liver-metastatic cells undergo glycolytic reprogramming, a metabolic shift that parallels hepatocyte regeneration during liver injury, providing acetyl-CoA and biosynthetic precursors to support epigenetic remodeling and lineage adaptation. Similar progenitor-like hepatic plasticity is observed across other epithelial cancers with liver tropism, including breast, colon, and non-small cell lung cancers, indicating a conserved mode of metastatic adaptation. ALY activity mediated histone hyperacetylation and epigenetic remodeling required for the stem-like state. ACLY was functionally essential. Pharmacologic ACLY inhibition blocked the induction of stem-like programs, reduced histone acetylation, and growth rate of liver metastatic cells. CRISPR-ACLY knockout prevented the acquisition of the reprogrammed phenotype. Similar hepatic niche-induced stemness signatures were observed in liver metastases from breast, colon, and NSCLC, suggesting a conserved mechanism across epithelial cancers. Conclusions: The liver microenvironment actively promotes metastatic competency by inducing a HIF1α-ACLY-acetyl-CoA-driven stem-like state in disseminated tumor cells. ACLY inhibition disrupts this metabolic-epigenetic reprogramming and markedly suppresses liver metastatic outgrowth, highlighting ACLY as a tractable therapeutic target for liver metastasis. Citation Format: Ajit Kumar SHARMA, Nobuyuki Takahashi, Sophie Zhuang, Amira Kazi, Michael Nirula, Abhinav Joshi, Yingying Cao, Rajesh Kumar, Kanak Parmar, Christopher Schultz, Parth Anil Desai, Samantha Nichols, Linda Sciuto, Yue Huang, Chiori Tabe, Yang Zhang, Sanghvi Neel, Nishanth Ulhas Nair, Christopher A Febres Aldana, Nir Friedman, Simone Difilippantonio, Thorkell Andresson, Eytan Ruppin, Stephen M. Hewitt, Anish Thomas. Hepatic niche driven metabolic-epigenetic reprogramming mediates metastatic colonization through liver progenitor like plasticity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6127.

Metastatic progression requires cancer cells to adapt to the unique constraints of distant organ microenvironments, yet the mechanisms that drive organ-specific adaptations remain poorly understood. Here, we show that the liver actively rewrites metastatic cancer cell identity, driving tumor cells toward a hepatobiliary progenitor-like state. Through integrated transcriptomic, proteomic, metabolomic, and epigenomic analyses of patient-derived rapid-autopsy samples and experimental models, we identify this state as selectively enriched in liver metastases. It is characterized by co-activation of hepatic and biliary/progenitor regulators HNF4A and SOX9 and is observed across multiple epithelial cancers, indicating a conserved response to the hepatic niche. Mechanistically, hepatocyte-derived TGF-β and hypoxia converge to activate a HIF-1α-ACLY axis, increasing nuclear acetyl-coenzyme A availability and histone acetylation at hepatic lineage regulatory elements to drive hepatobiliary reprogramming. This coordinated niche-response program can be captured transcriptionally and is associated with inferior overall survival. Disruption of this pathway suppresses hepatic reprogramming and impairs liver metastatic fitness. These findings identify the liver as an active determinant of metastatic cell fate, linking microenvironmental signaling to metabolic and chromatin remodeling programs that enable lineage plasticity. More broadly, they reveal organ-specific reprogramming as a fundamental principle of metastasis and a therapeutic vulnerability in liver metastases.

ecDNA heterogeneity in SCLC, related to Figure 4

ecDNA in SCLC, related to Figure 1

e16580 Background: Non-muscle invasive bladder cancer (NMIBC) presents a significant clinical challenge due to its high recurrence rate. Recently, a deeper understanding of tumor epigenetics has provided new opportunities for cancer detection and treatment. While significant efforts have been made to understand NMIBC biology, the molecular and epigenetic mechanisms driving its progression remain elusive. Methods: We used multiomics analysis including expression, DNA methylation, and cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) assays to uncover the molecular and epigenetic landscape of NMIBC from human tissue samples and urine. Results: High-throughput sequencing revealed more than 6,000 differentially methylated regions (DMRs) within regulatory elements, many of which were linked to cancer-related pathways and exhibited distinct signatures in cancer tissues compared to healthy controls. Next, we distinguished high and low-grade tumors based on unique DNA methylation profiles. These patterns correlated with transcription level of genes associated with cell cycle regulators, consistent with the higher proliferative capacity of high-grade tumors. Moreover, Among the DMRs, we also identified genes involved in T cell regulation. Supporting this, we demonstrated reduced CD8+ T cells infiltration in high-grade tumors, further highlighting immune dysregulation in the more aggressive disease. We extended our investigation to urine samples, performing cfChIP-seq on samples from healthy donors and NMIBC patients. By using the H3K4me3 promoter histone mark on cfDNA we could detect cell origin. Utilizing this assay, we were able to identify changes in the urine of NMIBC patients, owing to cf-nucleosome contributions from both the tumor and immune cells. Additionally, we stratified the cancer cohort by tumor grade and found enrichment in the number of differentially marked genes in high-grade tumors. Conclusions: Our detection of unique epigenetic signatures offer opportunities for biomarker development, enabling early detection through non-invasive urine based diagnostic approach. This could grade tumor more accurately and tailor personalized patient care and monitoring.

Amplified genes identified from cell-free ChIP-seq of patient plasma samples.

Fusion landscape and ecDNA RLF-MYCL fusions, related to Figure 3.

Understanding the full spectrum of tissues affected by SARS-CoV-2 is crucial for deciphering the heterogeneous clinical course of COVID-19. We analyzed DNA methylation and histone modifications in circulating chromatin to assess cell type-specific turnover in patients ranging from asymptomatic to severe cases, in relation to clinical outcomes. Severe COVID-19 was marked by a massive elevation of circulating cell-free DNA (cfDNA) from lung epithelium, cardiomyocytes, vascular endothelium, and erythroblasts, indicating increased cell death or turnover. The immune response was reflected by elevated B-cell and monocyte/macrophage cfDNA and an interferon response before cfDNA release. Strikingly, monocyte/macrophage cfDNA (but not monocyte counts), as well as lung epithelial and endothelial cfDNA, predicted clinical deterioration and duration of hospitalization. Asymptomatic patients had elevated immune cfDNA but no evidence of pulmonary or cardiac damage. Surprisingly, these patients showed elevated endothelial and erythroblast cfDNA, suggesting subclinical vascular and erythrocyte turnover are universal features of COVID-19, independent of disease severity. Epigenetic liquid biopsies provide a noninvasive means of monitoring COVID-19 patients and reveal subclinical vascular damage and red blood cell turnover.

Expression and copy-number status of recurrently highly amplified genes in patient and cell line samples. The tables summarize copy-number signal and AmpliconArchitect curation, expression of key genes and results of the multivariate analysis.

Enhancer-enhancer interaction analysis derived from H3K27ac HiChIP in the NCI-H889 and NCI-H524 cell lines. Interaction strength of proximal enhancers was calculated from the “.hic” files generated by the JuiceBox suite.