bims-dinmec Biomed News
on DNA methylation in cancer
Issue of 2025–07–27
five papers selected by
Lorena Ancona, Humanitas Research



  1. Nat Commun. 2025 Jul 18. 16(1): 6645
      Pancreatic cancer is known for its lethal condition, with most cases being diagnosed at advanced stage. Recently, liquid biopsy has emerged as a promising tool in cancer detection. Here we develop both an early detection model and a prognostic model for pancreatic cancer using cell-free DNA (cfDNA) end motif, fragmentation, nucleosome footprint (NF), and copy number alteration (CNA) features from plasma cfDNA. A total of 975 individuals were enrolled in our study. We developed an integrated model that demonstrated superior performance in distinguishing patients with early-stage pancreatic cancer from non-cancer controls. Moreover, we find that cfDNA features are associated with prognostic outcomes among pancreatic cancer patients. In this study, a cfDNA-based liquid biopsy signature is established for the early detection and prognostic prediction of pancreatic cancer. CfDNA may become a valuable tool for enhancing early diagnosis and prognosis assessment in this challenging disease.
    DOI:  https://doi.org/10.1038/s41467-025-61890-z
  2. Epigenomes. 2025 Jul 14. pii: 25. [Epub ahead of print]9(3):
      Background/Objectives: Advances in nanopore sequencing have opened new avenues for studying DNA methylation at single-base resolution, yet their application in epigenetic ageing research remains underdeveloped. Methods: We present a novel framework that leverages the unique capabilities of nanopore sequencing to profile and interpret age-associated methylation patterns in native DNA. Results: Unlike conventional array-based approaches, long reads sequencing captures full CpG context, accommodates diverse and repetitive genomic regions, removes bisulfite conversion steps, and is compatible to the latest reference genome. Conclusions: This work establishes nanopore sequencing as a powerful tool for next-generation epigenetic ageing studies, offering a scalable and biologically rich platform for anti-ageing interventions monitoring and longitudinal ageing studies.
    Keywords:  DNA methylation; ageing related CpGs; epigenetic clock; nanopore adaptive sampling; nanopore epigenetic clock
    DOI:  https://doi.org/10.3390/epigenomes9030025
  3. Cell Commun Signal. 2025 Jul 22. 23(1): 350
      Long interspersed nucleotide element 1 (LINE1), the most abundant repetitive element in the human genome, plays a crucial role in genomic instability. Aberrant LINE1 activation, primarily regulated by DNA methylation, is a hallmark of cancer. Non-small cell lung cancer (NSCLC), the most prevalent form of lung cancer worldwide, continues to pose significant challenges due to the invasiveness, high cost, and susceptibility to false positives of current diagnostic methods, as well as the emergence of treatment resistance. This review highlights the potential of LINE1 methylation as a biomarker for NSCLC, offering novel insights into its role in diagnosis, prognosis, and therapeutic strategies. Recent studies uncovered that LINE1 hypomethylation was strongly associated with poor overall survival, suggesting its utility as both a prognostic marker and a therapeutic target. However, further research is required to elucidate its precise regulatory mechanisms in LINE1 retrotransposition and to evaluate its potential as a non-invasive biomarker for improving NSCLC management.
    Keywords:  DNA methylation; LINE1 hypomethylation; Long interspersed nucleotide element1 (LINE1); Non-small cell lung cancer (NSCLC); Retrotransposition
    DOI:  https://doi.org/10.1186/s12964-025-02343-4
  4. JAMA. 2025 Jul 21.
       Importance: Ovarian cancer is the eighth most common cause of cancer and cancer death in women worldwide. In 2022, ovarian cancer was diagnosed in approximately 324 398 individuals, and 206 839 died of ovarian cancer worldwide. In 2025, it is estimated that 20 890 US women will be diagnosed with ovarian cancer and 12 730 patients will die of ovarian cancer.
    Observations: Approximately 90% of ovarian cancers are epithelial malignancies, of which 70% to 80% are high-grade serous ovarian cancers. Less common epithelial subtypes include endometrioid, clear cell, low-grade serous, mucinous, and carcinosarcoma. The median age at diagnosis of ovarian cancer is 63 years. Risk factors include older age, family history of breast or ovarian cancer, endometriosis, and nulliparity. Hereditary factors are associated with 25% of cases, predominantly linked to BRCA1/2 gene variants. At diagnosis, approximately 95% of patients experience nonspecific symptoms, such as abdominal pain, bloating, and urinary urgency and frequency, and about 80% have advanced-stage disease (stage III-IV), including extrapelvic disease, ascites, and abdominal masses. Diagnostic and staging evaluation includes pelvic ultrasound; computed tomography of the chest, abdomen, and pelvis; and serum tumor markers such as carbohydrate antigen 125, carbohydrate antigen 19-9, and carcinoembryonic antigen. First-line treatment for early-stage ovarian cancer, defined as limited to the ovary or fallopian tube (stage I) or confined to the pelvis (stage II), is surgery (hysterectomy, bilateral salpingo-oophorectomy, omentectomy, and lymphadenectomy), followed by adjuvant chemotherapy (carboplatin and paclitaxel). With treatment, early-stage ovarian cancer has a 5-year overall survival of 70% to 95%. Advanced-stage ovarian cancer may be treated with primary cytoreductive surgery (removal of all visible cancer in the abdominal cavity) and adjuvant chemotherapy (carboplatin and paclitaxel) or with neoadjuvant chemotherapy followed by cytoreductive surgery and adjuvant chemotherapy. Most patients with advanced-stage ovarian cancer receive maintenance therapy with bevacizumab (a monoclonal antibody that blocks angiogenesis) and/or poly-adenosine diphosphate ribose polymerase (PARP) inhibitors. With treatment, the 5-year overall survival rate for advanced-stage ovarian cancer is 10% to 40%. However, individuals with BRCA-related gene variants have a 5-year overall survival rate of approximately 70% with PARP inhibitor treatment. Despite an initial remission rate of 80%, approximately 75% of patients with advanced-stage disease have ovarian cancer relapse within 2 years.
    Conclusions and Relevance: Approximately 21 000 women are diagnosed with ovarian cancer annually in the US, and approximately 80% have advanced-stage ovarian cancer at diagnosis. First-line treatment of early-stage ovarian cancer is surgery and adjuvant platinum-based chemotherapy. Treatment of advanced-stage ovarian cancer includes cytoreductive surgery, platinum-based chemotherapy, and targeted maintenance therapies such as bevacizumab and/or PARP inhibitors.
    DOI:  https://doi.org/10.1001/jama.2025.9495
  5. Front Cell Dev Biol. 2025 ;13 1630231
       Background: Repetitive elements account for a large proportion of the human genome and undergo alterations during early tumorigenesis. However, the exclusive fragmentation pattern of DNA-derived cell-free repetitive elements (cfREs) remains unclear.
    Methods: This study enrolled 32 healthy volunteers and 112 patients with five types of cancer. A novel repetitive fragmentomics approach was proposed to profile cfREs using low-pass whole genome sequencing (WGS). Five innovative repetitive fragmentomic features were designed: fragment ratio, fragment length, fragment distribution, fragment complexity, and fragment expansion. A machine learning-based multimodal model was developed using these features.
    Results: The multimodal model achieved high prediction performance for early tumor detection, even at ultra-low sequencing depths (0.1×, AUC = 0.9824). Alu and short tandem repeat (STR) were identified as the primary cfREs after filtering out low-efficiency subfamilies. Characterization of cfREs within tumor-specific regulatory regions enabled accurate tissue-of-origin (TOO) prediction (0.1×, accuracy = 0.8286) and identified aberrantly transcribed tumor driver genes.
    Conclusion: This study highlights the abundance of repetitive DNA in plasma. The innovative fragmentomics approach provides a sensitive, robust, and cost-effective method for early tumor detection and localization.
    Keywords:  cell-free DNA; early tumor detection; low-pass whole genome sequencing; repetitive element; tissue of origin
    DOI:  https://doi.org/10.3389/fcell.2025.1630231