bims-fragic 2025-11-23 papers

Issue of 2025–11–23
four papers selected by
Laura Mannarino, Humanitas Research

Mol Oncol. 2025 Nov 21.

Liquid biopsy epigenetics: establishing a molecular profile based on cell-free DNA.

Christoffer Trier Maansson, Anders Lade Nielsen, Boe Sandahl Sorensen.

Liquid biopsies containing circulating tumor DNA (ctDNA) are important biomarkers across several forms of cancer. The detection of mutations in cell-free DNA (cfDNA) indicates the presence of ctDNA. However, unsatisfactory ctDNA mutation sensitivities, issues with sequencing errors, and clonal hematopoiesis variants have limited the clinical utility of mutation-based ctDNA assays. Recently, a new avenue of cfDNA assays has been developed, focusing on cfDNA epigenetics. Here, we outline the recent advancements in cfDNA epigenetics, focusing on cfDNA methylation, fragmentomics, and post-translational modifications (PTMs) of circulating nucleosomes. We present various methylation strategies concerning ctDNA detection and tissue of origin (TOO) analyses. cfDNA fragmentomics focuses on cfDNA fragment lengths, fragment end motifs, and nucleosome positioning to infer gene expression and estimate the ctDNA fraction. Lastly, we discuss the development of cell-free chromatin immunoprecipitation of circulating nucleosomes with PTMs. This method has been implemented to detect tumor gene expression, TOO, and treatment resistance. Combining the epigenetic features of cfDNA will expand the utility of liquid biopsies to give a more comprehensive insight into tumor biology, treatment response, and resistance.

Keywords: cell‐free ChIP; cell‐free DNA; epigenetics; fragmentomics; liquid biopsy; methylation

DOI: https://doi.org/10.1002/1878-0261.70145

Nat Commun. 2025 Nov 21.

Cross-dataset pan-cancer detection by correlating cell-free DNA fragment coverage with open chromatin sites across cell types.

The fragmentation patterns of whole genome sequenced cell-free DNA are promising features for tumor-agnostic cancer detection. However, systematic biases challenge their cross-cohort generalization. We introduce LIONHEART, an open source cancer detection method specifically optimized to generalize across datasets. The method correlates bias-corrected cfDNA fragment coverage across the genome with the locations of accessible chromatin regions from 898 cell and tissue type features. We use these correlations to detect changes in the cell-free DNA cell type composition caused by cancer. We test LIONHEART on nine datasets and fourteen cancer types (1106 non-cancer controls, 1449 cancers) obtained from different studies and show that it can distinguish cancer samples from non-cancer controls across cohorts with ROC AUC scores ranging from 0.62-0.95 (mean = 0.83, std = 0.12). We further validate the method on an external dataset, achieving a ROC AUC of 0.917.

DOI: https://doi.org/10.1038/s41467-025-66503-3

Sci Rep. 2025 Nov 19. 15(1): 40892

RECAP-seq: restriction enzyme-based CpG-methylated fragment amplification for early cancer detection.

Dongju Shin, Taehoon Kim, Jaywon Lee, Hwang-Phill Kim, Tae-You Kim, Duhee Bang.

Aberrant DNA methylation drives cancer development, yet current screening methods require substantial resources for targeted enrichment across multiple CpG-rich regions. Early cancer detection in cell-free DNA (cfDNA) presents additional challenges due to low circulating tumor DNA fractions (0.01-10%) that dilute cancer-specific signals. To address these limitations, we developed Restriction Enzyme-based CpG-methylated fragment AmPlification sequencing (RECAP-seq) to selectively enrich hypermethylated fragments from existing Enzymatic Methyl-seq (EM-seq) libraries. RECAP-seq combines EM-seq library preparation with BstUI restriction enzyme digestion to target CGCG motifs, achieving preferential enrichment of CpG islands. With spike-in experiments using cell line mixtures, RECAP-seq successfully distinguished samples as low as 0.001%. The method identified 7,091 hypermethylated markers, including ALX4 which showed progressive increases with colorectal cancer stage. Clinical validation using cfDNA from 35 healthy donors and 47 colorectal cancer patients demonstrated robust detection with an area under the curve (AUC) of 0.932, achieving 78.7% sensitivity at 95% specificity.

Keywords: Cell-free DNA; Colorectal cancer; DNA methylation; DNA restriction enzymes; Detection; Enrichment

DOI: https://doi.org/10.1038/s41598-025-24708-y

NPJ Precis Oncol. 2025 Nov 17. 9(1): 352

Early detection of urological tumors based on genomic characteristics of cell-free DNA fragments: a multi-center study.

Huiyong Zhang, Caihong Huang, Chunmeng Wei, Rongbin Zhou, Chengbang Wang, Wenhao Lu, Zuheng Wang, Xiao Li, Shaohua Chen, Dianyu Wang, Jin Ji, Yuexiang Li, Rirong Yang, Junyi Chen, Yanling Hu, Fubo Wang.

Cell-free DNA (cfDNA) has shown potential in distinguishing cancer patients from healthy individuals. This study investigates cfDNA fragmentomics-fragmentation patterns, end motifs (EDMs), and breakpoint motifs (BPMs)-to develop an early detection method for bladder urothelial carcinoma (BLCA), prostate adenocarcinoma (PRAD), and clear cell renal cell carcinoma (ccRCC). Using low-coverage whole genome sequencing (lcWGS) on plasma samples from 758 participants (including BLCA, PRAD, ccRCC, benign prostatic hyperplasia patients, and healthy controls), we analyzed cfDNA features. Machine learning models (logistic regression, support vector machine, random forest, XGBoost, Stacking) distinguished urological tumors from non-tumor cases with AUCs of 96% (BLCA), 99% (ccRCC), 92% (PRAD), and 89% (pan-cancer). Key discriminators included 6-bp EDMs and BPMs. A proposed two-tier screening strategy combining pan-cancer and cancer-specific features offers a cost-effective, non-invasive approach for early detection with strong clinical potential.

DOI: https://doi.org/10.1038/s41698-025-01130-1