bims-tumhet Biomed News
on Tumor heterogeneity
Issue of 2025–06–22
fourteen papers selected by
Sergio Marchini, Humanitas Research



  1. Eur J Cancer. 2025 Jun 03. pii: S0959-8049(25)00316-8. [Epub ahead of print]225 115534
       IMPORTANCE AND BACKGROUND: In high-grade serous ovarian cancer (HGSOC) bevacizumab (bev)/olaparib (ola) maintenance was approved for patients with homologous recombination DNA repair deficiency (HRD+) tumors. Although different methods exist to score genomic instability, DNA quality, tumor cell content, and costs may impair our ability to identify patients that will benefit from treatment.
    PATIENTS AND METHOD: We analyzed BRCA1 and RAD51C methylation as an HRD determination tool in patients newly diagnosed of HGSOC (n = 519) based on data from the PAOLA-1/ENGOT-ov25 trial phase III prospective trial. Methylation was analyzed using quantitative methylation specific PCR, correlated to HRD scores, PFS and OS.
    RESULTS: 67 (12.9 %) were BRCA1 and 25 (4.8 %) were RAD51C methylated. Of the 81 samples with a failed HRD score, 13 were methylated. Methylated samples were HRD+ (mean score [95 % CI]; 65.9 [62.7-69.1] and 53.3 [48.0-58.6]) and almost mutually exclusive of BRCA1&2 mutations. A significant PFS1 benefit independently of methylation ratios was observed in patients with methylated tumors with bev-ola maintenance compared to bev alone (HR=0.49, 95 % CI 0.29-0.83, P = 0.008). An OS benefit was shown for patients defined as "all-HRD" (including methylation) (HR=0.59, 95 % CI 0.41-0.86, P = 0.007).
    CONCLUSIONS: This study confirms the feasibility and clinical value of BRCA1/RAD51C methylation for predicting response to ola-bev maintenance in newly diagnosed HGSOC. Assessment of methylation in parallel to mutation testing allowed the identification of nearly 85 % of HRD+ samples at low costs. This study suggests that methylation testing could be easily implemented to optimize the selection of patients that benefit from olaparib+bevacizumab maintenance.
    Keywords:  BRCA1; Methylation; Ovary cancer; PARPi; RAD51C
    DOI:  https://doi.org/10.1016/j.ejca.2025.115534
  2. Nat Rev Clin Oncol. 2025 Jun 13.
      Cancer screening is an essential public health intervention for diagnosing cancers at an early stage that can enable earlier treatment - ideally with curative intent - and thus lead to improved outcomes. Over the past decade, liquid biopsy-based tests have emerged as a promising, minimally invasive and broadly applicable screening approach by combining multi-cancer early detection (MCED) with tumour tissue-of-origin identification. Large-scale randomized clinical trials evaluating liquid biopsy-based MCED approaches are now under way, although whether the diagnostic performance of this first generation of MCED tests is sufficient to translate into clinical benefits remains to be determined. In this Review, we discuss the promises and pitfalls of current MCED tests and highlight possible trajectories for the field of early cancer detection.
    DOI:  https://doi.org/10.1038/s41571-025-01033-x
  3. Genome Biol. 2025 Jun 20. 26(1): 176
       BACKGROUND: Spatial transcriptomics technologies are revolutionizing our understanding of intra-tumor heterogeneity and the tumor microenvironment by revealing single-cell molecular profiles within their spatial tissue context. The rapid development of spatial transcriptomics methods, each with unique characteristics, makes it challenging to select the most suitable technology for specific research objectives. Here, we compare four imaging-based approaches-RNAscope HiPlex, Molecular Cartography, Merscope, and Xenium-alongside Visium, a sequencing-based method. These technologies were employed to study cryosections of medulloblastoma with extensive nodularity (MBEN), a tumor chosen for its distinct microanatomical features.
    RESULTS: Our analysis reveals that automated imaging-based spatial transcriptomics methods are well-suited to delineate the intricate MBEN microanatomy and capture cell-type-specific transcriptome profiles. We devise approaches to compare the sensitivity and specificity of different methods, along with their unique attributes, to guide method selection based on the research objective. Furthermore, we demonstrate how reimaging slides after the spatial transcriptomics analysis can significantly improve cell segmentation accuracy and integrate additional transcript and protein readouts, expanding the analytical possibilities and depth of insight.
    CONCLUSIONS: This study underscores important distinctions between spatial transcriptomics technologies and offers a framework for evaluating their performance. Our findings support informed decisions regarding methods and outline strategies to improve the resolution and scope of spatial transcriptomic analyses, ultimately advancing spatial transcriptomics applications in solid tumor research.
    Keywords:  MERFISH; Medulloblastoma; Merscope; Molecular Cartography; RNAscope; Spatial transcriptomics; Visium; Xenium
    DOI:  https://doi.org/10.1186/s13059-025-03624-4
  4. Int J Gynecol Cancer. 2025 May 15. pii: S1048-891X(25)01061-8. [Epub ahead of print] 101941
       OBJECTIVE: We aimed to study whether the detection of circulating tumor DNA (ctDNA) may predict the risk of early relapse for patients with localized endometrial carcinoma.
    METHODS: Patients who underwent surgical resection at Cochin University Hospital (2021-2023) for International Federation of Gynecology and Obstetrics 2018 stage I to III endometrial carcinoma were prospectively included in a prospective biocollection cohort study. All patients had a plasma sample before surgery (EDTA collection tubes, 4-5 mL). After extraction and bisulfite-conversion of cell-free DNA, ctDNA was evaluated using a droplet-digital polymerase chain reaction assay targeting universally-hypermethylated positions in endometrial carcinoma (OXT, ZSCAN12 genes), and defined as significantly detected above the limit of detection. Patients were classified as high-risk based on 2022 European Society for Medical Oncology/European Society of Gynaecological Oncology/European Society of Pathology guidelines, or preoperative features (non-endometrioid histology, p53-abnormal tumors, or stage III). Events of interest were tumor progression or relapse (event-free survival). Adjusted-HR (aHR) was estimated using Cox regression.
    RESULTS: Among 128 patients included with median follow-up of 26 months (interquartile range; 15-35), ctDNA was detected in 18 patients (14%). Patients with ctDNA had a 1-year event-free rate of 67% (95% CI [48% to 92%]), vs 91% [82% to 100%] among patients without ctDNA. The ctDNA was detected in 10 (29%) patients among those with preoperative high-risk features (N = 34, 1-year event-free rate = 60% [36%-100%]). ctDNA was associated with event-free survival independently of stage (aHR = 4.26 [1.68-10.8]), 2022 guidelines high-risk (aHR = 3.72 [1.57-8.87]), or preoperative high-risk features (aHR = 3.98 [1.65-9.60]).
    CONCLUSIONS: Elevated ctDNA before surgery identifies a very high-risk subgroup of newly diagnosed endometrial carcinoma, suggestive of occult metastasis. Further studies are warranted to validate this finding and investigate the window of opportunity for neoadjuvant approaches.
    Keywords:  Circulating Tumor DNA; DNA Methylation; Endometrial Carcinoma; Molecular Characterization; Personalized Medicine
    DOI:  https://doi.org/10.1016/j.ijgc.2025.101941
  5. Nat Commun. 2025 Jun 17. 16(1): 5310
      Post-transplant complications reduce allograft and recipient survival. Current approaches for detecting allograft injury non-invasively are limited and do not differentiate between cellular mechanisms. Here, we monitor cellular damages after liver transplants from cell-free DNA (cfDNA) fragments released from dying cells into the circulation. We analyzed 130 blood samples collected from 44 patients at different time points after transplant. Sequence-based methylation of cfDNA fragments were mapped to an atlas of cell-type-specific DNA methylation patterns derived from 476 methylomes of purified cells. For liver cell types, DNA methylation patterns and multi-omic data integration show distinct enrichment in open chromatin and functionally important regulatory regions. We find that multi-tissue cellular damages post-transplant recover in patients without allograft injury during the first post-operative week. However, sustained elevation of hepatocyte and biliary epithelial cfDNA within the first month indicates early-onset allograft injury. Further, cfDNA composition differentiates amongst causes of allograft injury indicating the potential for non-invasive monitoring and intervention.
    DOI:  https://doi.org/10.1038/s41467-025-60507-9
  6. JAMA Oncol. 2025 Jun 18.
       Importance: Immune checkpoint inhibitors (ICIs) have dramatically transformed the therapeutic landscape of deficient mismatch repair/microsatellite unstable-high (dMMR/MSI-H) metastatic colorectal cancer (mCRC); however, ICI use is challenged by primary resistance and timing of discontinuation. Whether circulating tumor DNA (ctDNA) may be predictive of progression-free survival (PFS) and overall survival (OS) in this treatment context remains unknown.
    Objective: To assess the prognostic and predictive role of ctDNA, detected by tumor-specific methylation markers, in patients with dMMR/MSI-H mCRC treated with ICIs.
    Design, Setting, and Participants: This prespecified secondary analysis of the SAMCO-PRODIGE 54 randomized clinical trial evaluated ctDNA in patients with dMMR/MSI-H mCRC treated with avelumab or standard chemotherapy, with or without a targeted agent in the second-line setting, to assess its prognostic role. Plasma samples were obtained prospectively for ctDNA analysis, and digital droplet polymerase chain reaction amplification of bisulfite-converted cell-free DNA (cfDNA) for WIF1 and NPY genes was used to quantify ctDNA levels. These samples were collected from April 2018 to April 2021 at 49 sites in France at baseline (V1) and 1-month posttreatment initiation (V2) during. Data analyses were performed from October 1 to November 1, 2024.
    Intervention: Avelumab or standard chemotherapy with or without targeted agents.
    Main Outcomes and Measures: PFS and OS according to baseline ctDNA positivity or concentration, and early ctDNA variation (ΔctDNA = [V1-V2] ÷ V1).
    Results: The predictive analysis included 99 patients (mean [SD] age, 66 [13] years; 51 female [51.5%]) with plasma samples available for ctDNA assessment at V1, of which 74 had samples available also at V2 for Change in ctDNA assessment. In the 99 patients with available V1 plasma samples, baseline ctDNA positivity or concentration were not associated with clinical outcomes. Change in ctDNA (cutoff at median value) was significantly associated with both PFS (hazard ratio [HR], 2.98; 95% CI, 1.77-5.01; P < .001) and OS (HR, 3.61; 95% CI, 1.81-7.17; P < .001). This association was evident in patients treated with avelumab (PFS HR, 4.22; 95% CI, 1.77-10.1; P = .001; OS HR, 17.40; 95% CI, 3.82-79.70; P < .001) than in those receiving chemotherapy (PFS HR, 2.09; 95% CI, 1.03-4.21; P = .04; OS HR, 1.51; 95% CI, 0.61-3.72; P = .38). Avelumab (vs chemotherapy) improved PFS in favorable ctDNA responders (HR, 0.33; 95% CI, 0.14-0.77; log-rank P = .008) but not in poor responders (HR, 1.32; 95% CI, 0.67-2.62; log-rank P = .42) Combined ctDNA response and RECIST, version 1.1, assessment accurately predicted long-term OS. In the multivariable analysis, lack of ctDNA response was associated with an increased risk of disease progression and death in the avelumab group (HR, 7.27; 95% CI, 2.23-23.7; P = .001) but not in the chemotherapy group (HR, 1.61; 95% CI, 0.66-3.93; P = .30).
    Conclusions: The findings of this secondary analysis of an RCT found that change in ctDNA at 1-month posttreatment can predict long-term outcomes in patients with dMMR/MSI-H mCRC treated with ICIs.
    Trial Registration: ClinicalTrials.gov Identifier: NCT03186326.
    DOI:  https://doi.org/10.1001/jamaoncol.2025.1646
  7. Cancer Cell. 2025 Jun 10. pii: S1535-6108(25)00223-5. [Epub ahead of print]
      Hypermutation induced by mismatch repair (MMR) inactivation leads to immune surveillance in colorectal cancer (CRC) and in several other malignancies. We investigated the impact of a rationally designed chemotherapy combination on the generation of hypermutation and immunogenicity in otherwise immune-refractory CRC and breast cancer mouse models. Combinatorial treatment with cisplatin (CDDP) and temozolomide (TMZ) induces an adaptive downregulation of MMR, resulting in chemotherapy-dependent hypermutability and increase in predicted neoantigens. This combination specifically alters the immune fitness of the tumors, ultimately leading to CD8+ T cell-mediated immune surveillance, immunoediting of chemotherapy-induced neoantigens, and durable immunological memory. Treatment with CDDP and TMZ also remodels the innate immune microenvironment and induces long-lasting responses and complete rejections when combined with anti-PD-1 therapy in mice. The same effects are not observed using the clinically approved combination of 5-fluorouracil, oxaliplatin, and irinotecan (FOLFOXIRI). Treatment-induced hypermutation can enhance anti-tumor immune responses, offering additional avenues for cancer treatment.
    Keywords:  chemotherapy; cisplatin; colorectal cancer; cytotoxic chemotherapy; immune checkpoint blockade; immune rewiring; immune surveillance; mismatch repair modulation; neoantigens; temozolomide
    DOI:  https://doi.org/10.1016/j.ccell.2025.05.014
  8. J Liq Biopsy. 2025 Jun;8 100301
      Circulating tumor DNA (ctDNA) testing has transformed precision oncology by enabling the non-invasive detection of actionable mutations. To facilitate broader clinical adoption and improve testing accuracy, standardized quality criteria must be clearly defined and universally implemented. The International Society of Liquid Biopsy (ISLB) established the Quality Control and Accreditation Committee to develop consensus-based minimal standards for ctDNA analysis in oncology. Ensuring reliable and reproducible ctDNA testing necessitates standardization across the pre-analytical, analytical, and post-analytical phases. Key considerations include appropriate blood collection, efficient cfDNA isolation and purification, thorough assay validation, and precise data interpretation. The ISLB is committed to leading collaborative efforts among laboratories, regulatory bodies, and professional organizations to advance standardization and ensure high-quality ctDNA testing worldwide. Through initiatives led by the Quality Control and Accreditation Committee, educational programs, and multidisciplinary stakeholder workshops, ISLB provides a structured framework to promote standardization and foster innovation. By addressing current challenges and advocating for robust quality standards, ctDNA testing can reach its full potential in advancing personalized cancer care, enabling more precise and timely interventions for patients. This manuscript provides the first global initiative for quality control in liquid biopsy, presenting the ISLB perspective on minimal requirements for ctDNA testing in solid tumors.
    Keywords:  Circulating tumor DNA (ctDNA); Liquid biopsy; Precision oncology; Quality assurance; Standardization
    DOI:  https://doi.org/10.1016/j.jlb.2025.100301
  9. J Mol Diagn. 2025 Jun 13. pii: S1525-1578(25)00136-9. [Epub ahead of print]
      Homologous recombination deficiency (HRD) is a genomic feature present in some malignant neoplasms and is attributed to the failure of the homologous recombination repair pathway. Tumors with an HRD-positive status may have a distinct prognosis and/or response to therapies, including poly (ADP-ribose) polymerase inhibitors. The Association for Molecular Pathology assembled an expert panel to examine current practice and perform a scoping review of the medical literature pertaining to the molecular detection of HRD in the clinical setting. The expert panel examined the following topics: components of existing and proposed HRD and genomic instability biomarkers (including mutational signatures, loss of heterozygosity, mutations in homologous recombination repair-associated genes, and epigenetic silencing of RAD51C, BRCA1, or BRCA2); technical considerations for identifying genomic scars from tumor and germline next-generation sequencing results; guidelines on interpretation and caveats when reporting assessments of genomic instability and HRD scores; and the clinical significance of HRD. The panel formulated a set of expert consensus opinion recommendations regarding HRD assay design and validation to guide laboratories in developing HRD tests to ensure high-quality and reproducible results.
    DOI:  https://doi.org/10.1016/j.jmoldx.2025.05.003
  10. Eur J Cancer. 2025 Jun 09. pii: S0959-8049(25)00354-5. [Epub ahead of print]225 115572
      Immune checkpoint blockade (ICB) have revolutionized medical oncology, with the occurrence of cures in situations regarded as palliative. However, most patients develop resistance and the selection of responders remains difficult. The search for predictive biomarkers for immunotherapy has revealed that tertiary lymphoid structures (TLS) in the tumor microenvironment (TME) may be indicative of treatment effectiveness, since they may reflect the presence of an immune infiltrate with an anti-tumor effect. A better understanding of TLS neogenesis would help to establish anti-tumor strategies. For this purpose, this review outlines therapeutic modalities that could increase the immunogenicity and antigenicity of tumor cells, in particular immunogenic cell death (ICD), to turn "cold" tumors in "hot" tumors through interventions that promote the development of TLS. Second, the review describes the therapeutic strategies to enhance immune response against tumors, especially the resources to induce TLS, to strengthen cytotoxic T response / decrease Tregs and to promote the homing of immune cells. Future strategies should focus on a synergistic tactic combining both the enhancement of cancer cell immunogenicity and the stimulation of the immune system. PROVENANCE AND PEER REVIEW: Review commissioned by Aurelien Marabelle; externally peer reviewed.
    Keywords:  Immunology; Immunotherapy; Terrtiary lymphoid structure; Tumor micro environment
    DOI:  https://doi.org/10.1016/j.ejca.2025.115572
  11. Breast Cancer Res. 2025 Jun 16. 27(1): 108
       BACKGROUND: Plasma cell-free DNA (cfDNA) methylation is emerging as a non-invasive marker for various cancers. We aimed to identify specific methylation markers for diagnosis, differentiation from benign tumors, and prognosis of breast cancer (BC), which are essential for clinical decision-making yet seldom examined together.
    METHODS: BC-specific methylation markers were identified using an in-house 850K dataset combined with large-scale publicly available 450 or 850K datasets. Multiplex digital droplet PCR (mddPCR) assays were developed to detect methylation in cfDNA from 201 BC patients, 83 healthy donors, and 71 individuals harboring benign tumors. Diagnostic and prognostic performance were evaluated using logistic and Cox regression models, respectively. The basic mechanism of a selected gene was explored through in vitro experiments.
    RESULTS: We identified 21 BC-specific methylated CpG sites that distinguished BC from tumor-adjacent tissues with high diagnostic accuracy. In the cfDNA cohort, three mddPCR assays targeting eight markers achieved an area under the curve (AUC) of 0.856 (95% CI = 0.814-0.898) for distinguishing BC from healthy controls, and 0.742 (95% CI = 0.684-0.801) for differentiating BC from benign tumors. Notably, combining these methylation markers with mammography and ultrasound improved diagnostic performance, resulting in an AUC of 0.898 (95% CI = 0.858-0.938) for differentiating BC from benign tumors. In the TCGA-BC dataset, prognostic model based on six sites was associated with poor overall survival prognosis (hazard ratio = 2.826, 95%CI: 1.841-4.338, p < 0.0001). In vitro experiments elucidated that FAM126A overexpression regulates BC cells malignant phenotypes.
    CONCLUSIONS: Our study demonstrated potential values of methylation-based markers in the detection and prognosis of BC.
    Keywords:  Breast cancer; Cell-free DNA; Diagnosis; Methylation; Multiplex droplet digital PCR; Prognosis
    DOI:  https://doi.org/10.1186/s13058-025-02066-x
  12. Oral Oncol. 2025 Jun 13. pii: S1368-8375(25)00246-5. [Epub ahead of print]167 107417
      Head and neck cancer (HNC) is the sixth most prevalent cancer worldwide with a poor prognosis when diagnosed at advanced clinical stages. The main risk factors are tobacco consumption and alcohol abuse. However, the incidence of oropharyngeal cancer (OPC) is increasing due to human papillomavirus (HPV) infection. Current diagnostic techniques for both HPV-positive and HPV-negative HNC often involve invasive, costly, and time intensive procedures. Alternatively, liquid biopsies have emerged as a minimally invasive technique which may lessen the burden of cancer diagnoses on both patients and healthcare resources. This technique analyzes biological components released by tumors into the bloodstream, such as circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), exosomes, tumor proteins, and methylation changes, allowing for specific cancer detection and surveillance. This article reviewed the status and clinical applications of ctDNA and CTCs in the diagnosis and treatment of HPV-positive HNC. In addition, a systematic review following PRISMA 2020 Checklist (PROSPERO ID: 560498) was conducted to investigate whether liquid biopsies could be leveraged to assess the role of the immune system on treatment outcomes and the overall survival of HNC patients. Two public databases (Medline and Embase) were searched using relevant MeSH (Medical Subject Headings) terms and keywords. After multiple rounds of screening, eight studies published between 2017 and 2024 involving 814 cancer patients from three different countries were retained for data extraction. The data demonstrated that the immune microenvironment of HNC patients could be characterized via liquid biopsy, however, future validation is required. Furthermore, through the detection of HPV ctDNA, liquid biopsy technology has shown promise in diagnostics, as a predictor of patient prognoses and treatment responses, and as a tool to monitor disease progression in HPV-positive HNC.
    Keywords:  Diagnostic biomarkers; HPV-associated head and neck cancer; Head and neck cancer; Human papillomavirus; Immune microenvironment; Liquid biopsy; Oropharyngeal cancer; Prognostic biomarkers; circulating tumor DNA (ctDNA); circulating tumor cells (CTCs)
    DOI:  https://doi.org/10.1016/j.oraloncology.2025.107417
  13. Oncologist. 2025 Jun 04. pii: oyaf141. [Epub ahead of print]30(6):
      The homologous recombination (HR) system repairs DNA double-strand breaks produced by the DNA damage response, which is a complex signaling pathway consisting of the key proteins BRCA1/2 and other DNA repair proteins, such as the ATM, PALB2, BARD1, RAD51, and Fanconi anemia proteins. Mutations and epigenetic alterations in HR-related genes may lead to homologous recombination deficiency (HRD), resulting in genomic instability and contributing to the development of certain solid tumors. The biological significance and molecular mechanism of BRCA1/2 mutation-related HRD are well understood, but the relationships of other HR-related genes and their variant forms with HRD have not been sufficiently studied. These genes exhibit multiple forms of variation, including one or more HR genes, germline or somatic mutations, monoallelic or biallelic variants, and not all variants present HRD. Therefore, HRD is usually defined as HR-related gene variation, but recent studies have shown that defining it as the combined score of loss of heterozygosity, LST and TAI, known as the HRD score, can more accurately assess genomic instability. In patients with HRD, platinum-based therapy and poly ADP-ribose polymerase enzyme inhibitor (PARPi) have been shown to perform well in ovarian, breast, and prostate cancers. For gastrointestinal cancer (GI cancer), HRD has been relatively well studied in pancreatic cancer, but its role in other cancers has rarely been reported. Herein, we review the pathogenesis and predictive value of HRD, including the use of platinum drugs, PARPi, and immunotherapy, in digestive system tumors.
    Keywords:  HR-related genes; gastrointestinal cancer (GI cancer); homologous recombination deficiency (HRD); platinum sensitivity; poly ADP-ribose polymerase enzyme inhibitor (PARPi)
    DOI:  https://doi.org/10.1093/oncolo/oyaf141