bims-tumhet Biomed News
on Tumor heterogeneity
Issue of 2025–08–10
eight papers selected by
Sergio Marchini, Humanitas Research



  1. Clin Epigenetics. 2025 Aug 07. 17(1): 140
       OBJECTIVES: PARP inhibitors (PARPi) have become the new standard maintenance treatment for patients with advanced homologous recombination deficiency (HRD) ovarian cancer; they are also used upon platinum-sensitive relapse. HRD in ovarian cancer is primarily assessed through BRCA genes mutations and genomic scar scores, which are key biomarkers forecasting PARPi benefit. However, the role of BRCA1 promoter methylation in guiding clinical management is unclear. Evidence is needed to improve patient selection before initiating PARPi and to minimize PARPi-related toxicities. Our study aimed to determine the clinical relevance of BRCA1 promoter methylation for patients with ovarian carcinoma.
    METHOD: The KOMET (Ovarian Cancer Methylation) study is a single-center retrospective study involving 88 ovarian cancer patients treated between January 2021 and July 2024. Methylation was assessed using Methylation specific high-resolution melting (MS-HRM). Outcomes were measured based on progression-free survival (PFS) from diagnosis and from the initiation of PARPi treatment, as well as overall survival (OS).
    RESULTS: A methylated BRCA1 promoter was detected in 17 out of 88 (19%) tumor tissues. Statistically, PFS from PARPi initiation was significantly different between the BRCA1 methylated promoter (BRCA1mp) group and the BRCA1 unmethylated promoter and HRD negative (BRCA1up HRD-) group (p value = 0.0003 log rank test; Hazard Ratio (HR), 95% CI 0.04-0.40). OS was also significantly different between these groups (p value = 0.047 log rank test; HR = 0.30, 95% CI 0.10-0.84), as was PFS from diagnosis (p value = 0.02 log rank test; HR = 0.43, 95% CI 0.21-0.89).
    CONCLUSION: BRCA1 promoter methylation in ovarian cancer is associated with a better response to PARPi and platinum salt chemotherapy than tumors without promoter methylation or classical homologous recombination deficiency. Patients with unmethylated BRCA1 promoters and HRD-negative tumors appeared to have a poorer prognosis in terms of PFS from diagnosis. BRCA1 methylation should be considered as a theragnostic biomarker for initiation of PARPi.
    DOI:  https://doi.org/10.1186/s13148-025-01917-w
  2. Eur J Cancer. 2025 Jul 30. pii: S0959-8049(25)00415-0. [Epub ahead of print]227 115633
       BACKGROUND AND AIMS: There is an urgent need for effective prognostic biomarkers to better stratify patients with advanced hepatocellular carcinoma (HCC) undergoing systemic therapy. Shallow whole-genome sequencing (sWGS) of cell-free DNA (cfDNA) is a cost-effective approach for assessing circulating tumour DNA (ctDNA), genomic alterations, and fragmentomic patterns. This study aimed to evaluate sWGS-derived biomarkers as predictors of outcomes in advanced HCC patients receiving systemic treatment.
    METHODS: Pretreatment plasma samples from 134 patients treated with either tyrosine kinase inhibitors (TKIs; n = 83) or immune checkpoint inhibitors (ICIs; n = 51) were analysed using sWGS. Tumour fraction (TF) and copy number alterations (CNAs) were derived using ichorCNA, while DNA fragmentation was assessed using the DELFI approach. Associations with progression-free survival (PFS) and overall survival (OS) were evaluated.
    RESULTS: High TF was significantly associated with shorter median PFS (3.0 vs. 10.6 months; p<0.001) and OS (7.8 vs. 21.6 months; p=0.02). High fragmentation similarly correlated with reduced PFS (4.7 vs. 10.7 months; p<0.001) and OS (13.1 vs. 22.3 months; p<0.001). In multivariate analysis within the ICI subgroup, high fragmentation and BCLC stage independently predicted shorter PFS and OS. High AFP levels, advanced BCLC stage, and larger tumours correlated with elevated TF. Frequent CNA gains were observed in chromosomal arms 1q and 8q.
    CONCLUSION: High TF and high fragmentation levels are associated with worse clinical outcomes in advanced HCC patients treated with systemic therapy, making them promising prognostic biomarkers to consider for guiding treatment decisions.
    Keywords:  Circulating cell-free DNA; Circulating tumour DNA; Hepatocellular carcinoma; Immunotherapy; Shallow whole-genome sequencing; Tumour fraction; Tyrosine kinase inhibitors
    DOI:  https://doi.org/10.1016/j.ejca.2025.115633
  3. Clin Cancer Res. 2025 Aug 08.
      A recent article evaluated the concordance rate between tumor and plasma genotyping for detecting actionable genomic alterations to guide targeted therapy. These results support the utility of liquid biopsy for enrolling patients into genomically-guided trials, especially in scenarios where tissue is unavailable or biopsy is not feasible.
    DOI:  https://doi.org/10.1158/1078-0432.CCR-25-1927
  4. Zhonghua Lao Dong Wei Sheng Zhi Ye Bing Za Zhi. 2025 Jul 20. 43(7): 547-551
      Malignant mesothelioma is a rare tumor that is highly correlated with asbestos exposure. Due to the insidious early symptoms, mesothelioma is usually diagnosed in the advanced stages of the disease. Therefore, there is an urgent need for some early detection biomarkers to assist in the diagnosis of mesothelioma. The detection of DNA methylation can be one of the new research directions. This article provides a comprehensive discussion on the research progress of DNA methylation in malignant mesothelioma, including genes that can serve as diagnostic markers for malignant mesothelioma and the current problems in clinical application. It also provides new insights for future research directions using DNA methylation as a diagnostic marker for mesothelioma.
    Keywords:  Biomarkers; DNA Methylation; Diagnosis; Diagnostic markers; Malignant mesothelioma; Mesothelioma
    DOI:  https://doi.org/10.3760/cma.j.cn121094-20240417-00170
  5. Nat Rev Dis Primers. 2025 Aug 07. 11(1): 56
      Mesothelioma is a lethal cancer caused by exposure to asbestos, which arises predominantly in the pleural lining of the thoracic cavity or, less commonly, in the peritoneum, pericardium or tunica vaginalis. The incidence of mesothelioma increased globally during the late twentieth century, correlating with the use of asbestos, and it continues to rise in some regions. Asbestos tumorigenesis involves fibre persistence that leads to DNA damage mediated by chronic inflammation. The genomic landscape of mesothelioma is predominantly characterized by tumour suppressor alterations, most frequently occurring in BAP1, CDKN2A, CDKN2B, MTAP, NF2 and TP53. Patients with mesothelioma commonly present with fatigue, dyspnoea and/or cough caused by pleural effusion, pain and reduced appetite with weight loss. Imaging, cytology, histology and immunohistochemistry are used in diagnosis and support tumour staging. Genetic tests are relevant to reveal disease predispositions. Mesotheliomas are classified on the basis of histology into three distinct subtypes: epithelioid (the most common subtype with the best prognosis), biphasic and sarcomatoid (worst prognosis). Chemotherapy has been the standard of care for the past two decades but immune checkpoint inhibition targeting PD1 and CTLA4 is now considered to be the first-line treatment, showing improvement compared with chemotherapy. Few randomized trials have investigated the role of surgery and radiotherapy and none has found a clear benefit over systemic therapies. Mesothelioma is associated with considerable negative effects on quality of life in physical and emotional domains and also substantially affects patients' families and caregivers.
    DOI:  https://doi.org/10.1038/s41572-025-00640-3
  6. Head Neck. 2025 Aug 07.
       BACKGROUND: Head and neck cancers (HNCs) are too often diagnosed at advanced stages when outcomes are poor. Additionally, robust tools for the early detection of recurrence remain elusive. These gaps drive interest in so-called liquid biopsy approaches for HNC detection, prognostication, and surveillance. Molecular heterogeneity presents challenges to liquid biopsy testing, but emerging approaches provide promising avenues toward clinical utility.
    METHODS: We review the latest developments in HNC liquid biopsies, provide perspectives on viral-associated and nonviral-associated cancers, and assess various biofluids, analytes, and molecular profiling approaches.
    RESULTS: Liquid biopsy assays targeting viral DNA from peripheral blood plasma have established clinical performance, and utility studies are ongoing, serving as a blueprint for other emerging assays.
    CONCLUSION: The use of multiple biofluid sources and analytes may improve detection sensitivity and clinical applicability. Standardization and harmonization of analysis methods will be critical for enhancing biomarker discovery and enabling reliable clinical implementation.
    Keywords:  head and neck cancer; liquid biopsy; squamous cell carcinoma
    DOI:  https://doi.org/10.1002/hed.70009