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Aredo JV, Jamali A, Zhu J, Heater N, Wakelee HA, Vaklavas C, Anagnostou V, Lu J. Liquid Biopsy Approaches for Cancer Characterization, Residual Disease Detection, and Therapy Monitoring. Am Soc Clin Oncol Educ Book 2025; 45:e481114. [PMID: 40305739 DOI: 10.1200/edbk-25-481114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2025]
Abstract
Liquid biopsy encompasses a variety of molecular approaches to detect circulating tumor DNA (ctDNA) and has become a powerful tool in the diagnosis and treatment of solid tumors. Current applications include comprehensive genomic profiling for identifying targetable mutations and therapeutic resistance mechanisms, with emerging applications in minimal residual disease detection and treatment response monitoring. Increasingly, the potential for liquid biopsy in guiding treatment decisions is under active investigation through prospective clinical trials using ctDNA-adaptive interventions in patients with early-stage and metastatic cancers. Limitations arise on the basis of the sensitivity and feasibility of individual liquid biopsy assays; nonetheless, emerging technologies set the stage for improving these shortcomings. As the global oncology community continues to ascertain the clinical value of liquid biopsy across the continuum of patient care, this minimally invasive approach heralds a significant advancement in the promise of precision oncology.
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Affiliation(s)
- Jacqueline V Aredo
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | - Amna Jamali
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins School of Medicine, Baltimore, MD
| | - Jessica Zhu
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Natalie Heater
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Heather A Wakelee
- Division of Oncology, Department of Medicine, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA
| | | | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
- The Johns Hopkins Molecular Tumor Board, Johns Hopkins School of Medicine, Baltimore, MD
- Lung Cancer Precision Medicine Center of Excellence, Johns Hopkins University School of Medicine, Baltimore, MD
- The Bloomberg∼Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Janice Lu
- Division of Hematology and Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL
- Circulating Tumor Cell (CTC) Core Facility, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Chicago, IL
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Baldini C, Porte M, Rouleau E, Touat M. Liquid biopsy in gliomas-are we there yet? Ann Oncol 2025; 36:606-608. [PMID: 40180123 DOI: 10.1016/j.annonc.2025.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Accepted: 03/27/2025] [Indexed: 04/05/2025] Open
Affiliation(s)
- C Baldini
- Drug Development Department (DITEP), Gustave Roussy, Villejuif, France; Laboratoire d'Immunomonitoring en Oncologie, Oncology Immunomonitoring Unit, INSERM US23, CNRS UMS 3655, Gustave Roussy, Université Paris-Saclay, Villejuif, Ile-de-France, France.
| | - M Porte
- Drug Development Department (DITEP), Gustave Roussy, Villejuif, France
| | - E Rouleau
- Department of Medical Biology and Pathology, Cancer Genetics Laboratory, Gustave Roussy, Villejuif, France
| | - M Touat
- Neuro-oncology Department, Sorbonne Université, Inserm, CNRS, UMR S 1127, Institut du Cerveau, Paris Brain Institute, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France
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Stahler A, Stintzing S. [Molecular testing and liquid biopsies in colorectal cancer]. RADIOLOGIE (HEIDELBERG, GERMANY) 2025; 65:410-415. [PMID: 40268765 DOI: 10.1007/s00117-025-01454-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2025]
Abstract
BACKGROUND The introduction of new DNA sequencing technologies has led to the discovery of many prognostically and predictively relevant biomarkers in tumor tissue and blood from patients with colorectal cancer. OBJECTIVES Presentation of meaningful tissue-based molecular pathological diagnostics and discussion of the clinical application of circulating tumor DNA (ctDNA) from liquid biopsies in colorectal cancer. MATERIALS AND METHODS Evaluation of existing literature and congress publications, discussion of post hoc analyses of clinical studies and expert recommendations. RESULTS In Union for International Cancer Control (UICC) stages II/III, the tissue-based evaluation of microsatellite instability (MSI-H) contributes to individual therapy optimization through advice on adjuvant chemotherapy (colon cancer, UICC II) or, if necessary, individual neo-adjuvant therapy concepts via the use of immunotherapy (colon, rectal cancer, UICC II/III). From liquid biopsies, ctDNA was associated with minimal residual disease, which influences disease-free survival. In the metastatic stage (UICC IV), tissue-based determination of RAS and BRAF V600E mutations, MSI‑H and in the near future also HER2/neu overexpression should be performed. Broader molecular diagnostics to optimize first-line therapy (molecular hyperselection) shows little additional benefit. ctDNA can be used for longitudinal monitoring of clonal tumor evolution or as an alternative to invasive diagnostics in patients. CONCLUSIONS Molecular pathological diagnostics from tissue and blood complement each other and should be used in a targeted and meaningful way according to the underlying question.
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Affiliation(s)
- Arndt Stahler
- Med. Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie (CCM), Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland.
| | - Sebastian Stintzing
- Med. Klinik m. S. Hämatologie, Onkologie und Tumorimmunologie (CCM), Charité Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Deutschland
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Kahn CL, Petersen MM, Kleif J, Mansvelders MSE, Rasmussen M, Jørgensen LN, Vilandt J, Seidelin JB, Jaensch C, Bondeven P, Gotschalck KA, Løve US, Andersen B, Christensen IJ, LaPoint LC, Therkildsen C. Circulating Tumor DNA in Addition to Fecal Immunochemical Test in a Dual-Test Colorectal Cancer Screening Approach. Clin Colorectal Cancer 2025; 24:310-319.e1. [PMID: 40204621 DOI: 10.1016/j.clcc.2025.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Revised: 02/03/2025] [Accepted: 03/07/2025] [Indexed: 04/11/2025]
Abstract
BACKGROUND Early detection is paramount when reducing incidence and mortality of colorectal cancer (CRC). Current population-based screening programs primarily use fecal immunochemical test (FIT) to allocate individuals for colonoscopy although low specificity challenges colonoscopy capacities. We aimed to assess the potential of circulating tumor (ct)DNA markers for early CRC detection in a dual-test CRC screening approach among FIT positive individuals. METHODS Plasma samples from 774 FIT positive (≥100 ng Hemoglobin/mL) individuals from the Danish CRC screening program were analyzed for hypermethylated DNA in the genes Branched Chain Amino-acid Transaminase 1 (BCAT1), Ikaros-Family Zinc Finger transcription 1 (IKZF1), and Interferon Regulator Factor 4 (IRF4). Multivariate logistic regression models were generated adding the ctDNA markers and age to the FIT value. The dual-test approach was benchmarked to FIT at specific thresholds. RESULTS The dual-test approach improved CRC detection compared to the FIT alone (AUC of 87.2 [95% CI, 82.9-91.4] vs AUC of 72.5 [95% CI, 67.0-77.9]). This was also seen when adding advanced adenomas to the outcome resulting in AUCs of 71.8 [95% CI, 67.8-75.8] for the dual-test approach compared to 65.5 [95% CI, 61.3-69.7] for the FIT model alone. Benchmarking the dual-test approach at FIT cut-offs between 100 and 600 ng Hb/mL showed a potential for either reducing the colonoscopy requirement by up to 56% or increasing CRC detection by up to 28%. CONCLUSIONS As increasing FIT cutoff will decrease CRC detection rate, application of the ctDNA panel can increase the sensitivity and specificity in a dual-test approach among asymptomatic individuals.
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Affiliation(s)
| | - Mathias M Petersen
- Gastro Unit, Hvidovre Hospital, Hvidovre, Denmark; Institute for Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Kleif
- Gastro Unit, Hvidovre Hospital, Hvidovre, Denmark; Institute for Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; Department of Surgery, Nordsjællands Hospital, Hillerød, Denmark
| | | | - Morten Rasmussen
- Institute for Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; Digestive Disease Center, Bispebjerg Hospital, Copenhagen, Denmark
| | - Lars N Jørgensen
- Institute for Clinical Medicine, University of Copenhagen, Copenhagen, Denmark; Digestive Disease Center, Bispebjerg Hospital, Copenhagen, Denmark
| | - Jesper Vilandt
- Department of Surgery, Nordsjællands Hospital, Hillerød, Denmark
| | - Jakob B Seidelin
- Gastro Unit, Section for Gastroenterology, Herlev Hospital, Herlev, Denmark
| | - Claudia Jaensch
- Endocrine Laboratory, Department of Clinical Chemistry, Amsterdam UMC, AMC & VUMC, Amsterdam, The Netherlands
| | - Peter Bondeven
- Department of Surgery, Randers Hospital, Randers, Denmark
| | - Kåre A Gotschalck
- Department of Surgery, Horsens Hospital, Horsens, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Uffe S Løve
- Department of Surgery, Viborg Hospital, Viborg, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Berit Andersen
- Department of Public Health Programmes and University Research Clinic for Cancer Screening, Randers Regional Hospital, Randers, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Gianmarco M, Carolina P, Gregorio M, Michela V, Monica P, Claire GG, Michele M, Giulia M, Roberta M, Cinzia A, Lorena B, Marcello T, Fabiana P, Roberta M. Circulating tumor DNA monitoring in advanced mutated melanoma (LIQUID-MEL). THE JOURNAL OF LIQUID BIOPSY 2025; 8:100295. [PMID: 40276578 PMCID: PMC12019447 DOI: 10.1016/j.jlb.2025.100295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2025] [Revised: 04/07/2025] [Accepted: 04/08/2025] [Indexed: 04/26/2025]
Abstract
Introduction Immune checkpoint inhibitors (ICIs) have revolutionized the treatment of metastatic melanoma, but a percentage of patients did not show benefit. Circulating tumor DNA (ctDNA) has emerged as a potential non-invasive tool for monitoring disease evolution and treatment response. The present study aimed to evaluate the clinical utility of ctDNA dynamics in patients with metastatic melanoma receiving ICIs, while exploring its role in the oncological course. Materials and methods The LIQUID-MEL study is a prospective, single-centre pilot study including patients with BRAF/NRAS-mutant metastatic melanoma. ctDNA was quantified using digital droplet PCR (ddPCR) at four different time points. Uni- and multivariable Cox regression models were used to assess the correlation between shedding and progression-free survival (PFS), and overall survival (OS). Results Overall, 23 patients were included. At baseline, ctDNA was detectable in 5/23 (21.7 %) cases. Baseline ctDNA shedding was associated with shorter PFS (3.88 months vs. 0.69 months, p=0.012). A strong numerical trend was observed also in OS (12.66 months vs. 2.53 months, p=0.287). Shedding at baseline did not demonstrate independent prognostic or predictive value in the uni- and multivariable analysis. The longitudinal analysis revealed intriguing patterns of ctDNA shedding in individual patients. Conclusion ctDNA detectability and its dynamic changes during treatment may have potential clinical utility in patients with metastatic melanoma, offering a valuable non-invasive tool for monitoring disease and treatment response. The small sample size limited the statistical power of the analysis. Further studies with larger cohorts are needed to validate its role in routine clinical practice.
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Affiliation(s)
| | - Palazzi Carolina
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Monica Gregorio
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Verzè Michela
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Pluchino Monica
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | | | - Maffezzoli Michele
- Department of Medicine and Surgery, University of Parma, Parma, Italy
- Portsmouth Hospital University NHS Trust, Portsmouth, United Kingdom
| | - Mazzaschi Giulia
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Manuguerra Roberta
- Pathology Unit, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Azzoni Cinzia
- Pathology Unit, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Bottarelli Lorena
- Pathology Unit, Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Tiseo Marcello
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
- Department of Medicine and Surgery, University of Parma, Parma, Italy
| | - Perrone Fabiana
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
| | - Minari Roberta
- Medical Oncology Unit, University Hospital of Parma, Parma, Italy
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Cabezas-Camarero S, Pérez-Alfayate R, García-Barberán V, Gandía-González ML, García-Feijóo P, López-Cade I, Lorca V, Casado-Fariñas I, Cerón MA, Paz-Cabezas M, Sotelo MJ, García Conde M, Roldán Delgado H, Sánchez Medina Y, Díaz-Millán I, Pérez-Segura P. ctDNA detection in cerebrospinal fluid and plasma and mutational concordance with the primary tumor in a multicenter prospective study of patients with glioma. Ann Oncol 2025; 36:660-672. [PMID: 39978637 DOI: 10.1016/j.annonc.2025.02.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2024] [Revised: 01/18/2025] [Accepted: 02/03/2025] [Indexed: 02/22/2025] Open
Abstract
BACKGROUND Cerebrospinal fluid (CSF) stands as an easily accessible reservoir for circulating tumor DNA (ctDNA) analysis in patients with central nervous system (CNS) tumors, although evidence is still limited. Our aim was to prospectively evaluate the feasibility of detecting ctDNA for mutational analysis in CSF and plasma in patients with glioma. METHODS This was a prospective study of patients with glioma diagnosed at four third-level hospitals in Spain. A customized next-generation sequencing (NGS) eight-gene panel (IDH1, IDH2, ATRX, TP53, PTEN, PIK3CA, EGFR, BRAF) was used in paired CSF, plasma and tumor samples. Mutation concordance occurred when the same pathogenic gene variant was detected in tumor and ctDNA. The prognostic value of ctDNA and that of its median variant allele frequency (mVAF) were analyzed. RESULTS Between February 2017 and March 2020, 37 patients with glioma were enrolled. The 32 patients with analyzable CSF samples comprised patients with new diagnosis (n = 23) and relapse (n = 9); World Health Organization fifth Edition types: IDH-mutant astrocytoma (n = 10), IDH-mutant oligodendroglioma (n = 6) and IDH-wildtype glioblastoma (n = 16); CSF-ctDNA-positive: 19/32 (59%); and CSF-ctDNA-negative: 13/32 (41%). CSF mutation numbers were 1 (10/19), 2 (7/19) and 3 (2/19). Frequencies of CSF-ctDNA-mutated genes were EGFR (8/19, 42%), PTEN (7/19, 37%), TP53 (6/19, 32%), IDH1 (5/19, 26%) and PIK3CA (4/19, 21%). Tumor-CSF mutation concordance was found in 16/19 (84%). Progression-free and overall survival were significantly shorter in ctDNA-positive patients with VAF equal to or greater than the mVAF compared with ctDNA-positive patients with VAF lower than the mVAF. No association was found between ctDNA in CSF and distance to closest CSF reservoir, tumor size or IDH status. ctDNA was detected in 2 of 14 (14%) individual plasma samples, in both cases concordant with the primary tumor. CONCLUSION CSF is a reliable reservoir for ctDNA analyses in patients with glioma. ctDNA is detectable in plasma although at a lower rate. Larger, prospective studies should be conducted to refine the potential role of liquid biopsy in this disease.
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Affiliation(s)
- S Cabezas-Camarero
- Department of Medical Oncology, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain; Department of Medical Oncology Department, IOB Institute of Oncology-Madrid, Madrid, Spain.
| | - R Pérez-Alfayate
- Department of Neurosurgery, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain
| | - V García-Barberán
- Molecular Oncology Laboratory, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain
| | - M L Gandía-González
- Department of Neurosurgery, Hospital Universitario La Paz, IdIPaz, Madrid, Spain
| | - P García-Feijóo
- Department of Neurosurgery, Hospital Universitario La Paz, IdIPaz, Madrid, Spain
| | - I López-Cade
- Experimental Therapeutics Unit, Department of Medical Oncology, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain
| | - V Lorca
- Molecular Oncology Laboratory, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain
| | - I Casado-Fariñas
- Pathology Department, Hospital Clínico Universitario San Carlos, Madrid, Spain
| | - M A Cerón
- Experimental Therapeutics Unit, Department of Medical Oncology, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain
| | - M Paz-Cabezas
- Department of Medical Oncology, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain; Molecular Oncology Laboratory, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain
| | - M J Sotelo
- Department of Medical Oncology, Aliada Cancer Center, Lima, Spain; Department of Medical Oncology, Clínica San Felipe, Lima, Spain; Department of Medical Oncology, Hospital María Auxiliadora, Lima, Perú, Spain
| | - M García Conde
- Department of Neurosurgery, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife
| | - H Roldán Delgado
- Department of Neurosurgery, Hospital Universitario de Canarias, La Laguna, Santa Cruz de Tenerife
| | - Y Sánchez Medina
- Department of Neurosurgery, Hospital Nuestra Señora de la Candelaria, Santa Cruz de Tenerife, Spain
| | - I Díaz-Millán
- Department of Medical Oncology, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain
| | - P Pérez-Segura
- Department of Medical Oncology, Hospital Clínico Universitario San Carlos, IdISSC, Madrid, Spain; Department of Medical Oncology Department, IOB Institute of Oncology-Madrid, Madrid, Spain
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Tabrizi S, Martin-Alonso C, Xiong K, Bhatia SN, Adalsteinsson VA, Love JC. Modulating cell-free DNA biology as the next frontier in liquid biopsies. Trends Cell Biol 2025; 35:459-469. [PMID: 39730275 PMCID: PMC12145268 DOI: 10.1016/j.tcb.2024.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2024] [Revised: 11/05/2024] [Accepted: 11/20/2024] [Indexed: 12/29/2024]
Abstract
Technical advances over the past two decades have enabled robust detection of cell-free DNA (cfDNA) in biological samples. Yet, higher clinical sensitivity is required to realize the full potential of liquid biopsies. This opinion article argues that to overcome current limitations, the abundance of informative cfDNA molecules - such as circulating tumor DNA (ctDNA) - collected in a sample needs to increase. To accomplish this, new methods to modulate the biological processes that govern cfDNA production, trafficking, and clearance in the body are needed, informed by a deeper understanding of cfDNA biology. Successful development of such methods could enable a major leap in the performance of liquid biopsies and vastly expand their utility across the spectrum of clinical care.
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Affiliation(s)
- Shervin Tabrizi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Radiation Oncology, Mass General Brigham, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Wyss Institute at Harvard University, Boston, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA
| | | | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Passiglia F, Pepe F, Russo G, Garbo E, Listì A, Benso F, Scimone C, Palumbo L, Pluchino M, Minari R, Bordi P, Cani M, Ungaro A, Ambrogio C, Taulli R, Capelletto E, Balbi M, Righi L, Tiseo M, Giannarelli D, Troncone G, Novello S, Malapelle U. Circulating tumor DNA dynamic variation predicts sotorasib efficacy in KRASp.G12C-mutated advanced non-small cell lung cancer. Cancer 2025; 131:e35917. [PMID: 40445863 PMCID: PMC12124469 DOI: 10.1002/cncr.35917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Revised: 04/17/2025] [Accepted: 04/21/2025] [Indexed: 06/02/2025]
Abstract
BACKGROUND The objective of this study was to investigate the correlation between circulating tumor DNA (ctDNA) KRAS G12C-mutation dynamic variations and treatment outcomes in patients with advanced non-small cell lung cancer (NSCLC) receiving sotorasib therapy in a real-world setting. METHODS Peripheral blood samples were prospectively collected from 32 patients at baseline, at cycle 3, and then at each radiologic assessment during sotorasib treatment. Both tissue and plasma samples were analyzed by using ultra-deep, customized next-generation sequencing (NGS) assays. Plasma samples from 27 of 32 patients also were analyzed by digital polymerase chain reaction analysis, and ctDNA dynamic variations were correlated with radiologic responses and patients' clinical outcomes. RESULTS A significant correlation between NGS and digital polymerase chain reaction-detected KRAS G12C variant allelic fractions (p < .001) was observed. Patients who achieved clearance of KRAS G12C-mutant ctDNA levels had a significant improvement in the objective response rate (80% vs. 8%; p < .001), median progression-free survival (7.9 vs. 2.8 months; p < .001), and median overall survival (16.8 vs. 6.4 months; p < .001) compared with those who did not achieve clearance. The clearance of ctDNA was the only prognostic factor significantly associated with both median progression-free survival (hazard ratio, 0.15; 95% confidence interval, 0.04-0.48) and median overall survival (hazard ratio, 0.09; 95% confidence interval, 0.02-0.45) in multivariable analysis. Moreover, a dynamic increase in the KRAS G12C median variant allele fraction anticipated radiologic disease progression in 70% of patients who were evaluable at the resistance time point. CONCLUSIONS This study demonstrated that early clearance of KRAS G12C-mutant ctDNA predicted the clinical benefit of sotorasib in patients with advanced NSCLC, suggesting that dynamic monitoring of ctDNA levels also may anticipate sotorasib resistance.
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Affiliation(s)
- Francesco Passiglia
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Francesco Pepe
- Department of Public HealthUniversity Federico II of NaplesNaplesItaly
| | - Gianluca Russo
- Department of Public HealthUniversity Federico II of NaplesNaplesItaly
| | - Edoardo Garbo
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Angela Listì
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Federica Benso
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Claudia Scimone
- Department of Public HealthUniversity Federico II of NaplesNaplesItaly
| | - Lucia Palumbo
- Department of Public HealthUniversity Federico II of NaplesNaplesItaly
| | - Monica Pluchino
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
| | - Roberta Minari
- Medical Oncology UnitUniversity Hospital of ParmaParmaItaly
| | - Paola Bordi
- Medical Oncology UnitUniversity Hospital of ParmaParmaItaly
| | - Massimiliano Cani
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Antonio Ungaro
- Medical Oncology UnitSan Giuseppe Moscati HospitalTarantoItaly
| | - Chiara Ambrogio
- Department of Molecular Biotechnology and Health SciencesMolecular Biotechnology CenterUniversity of TurinTurinItaly
| | - Riccardo Taulli
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Enrica Capelletto
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Maurizio Balbi
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Luisella Righi
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Marcello Tiseo
- Department of Medicine and SurgeryUniversity of ParmaParmaItaly
- Medical Oncology UnitUniversity Hospital of ParmaParmaItaly
| | - Diana Giannarelli
- IRCCS‐Facility of Epidemiology and BiostatisticsFondazione Policlinico Universitario A. GemelliRomeItaly
| | | | - Silvia Novello
- Department of OncologyUniversity of TurinS. Luigi Gonzaga Hospital‐OrbassanoTurinItaly
| | - Umberto Malapelle
- Department of Public HealthUniversity Federico II of NaplesNaplesItaly
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Rasic G, Alonso A, Collado L, Devaiah AK, Godfrey TE. Circulating Tumor DNA in the Surgical Management of Cancer: A Review of Clinical Trials to Understand Future Impact on Multidisciplinary Practice. Am Surg 2025:31348251346546. [PMID: 40418937 DOI: 10.1177/00031348251346546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2025]
Abstract
BackgroundCirculating tumor DNA (ctDNA) has been proposed as a surrogate for solid tumor tissue biopsies. Our study evaluated trends of clinical trials that assess the role of ctDNA in surgical oncology.MethodsThe ClinicalTrials.gov database was queried for clinical trial that evaluated the use of ctDNA in the management of patients who underwent curative resections for solid tumor malignancies. Studies were categorized based on the phase of operative care were ctDNA was assessed and further stratified based on surgical application. Descriptive statistics were utilized to describe trends of included trials.ResultsOf 382,298 clinical trials, our study identified 68 trials (2014-2021). The majority of these trials were phase 2 (82.4%) and actively recruiting (63.2%). The most commonly studied malignancies were breast (20.0%), colon (17.1%) and lung (14.3%) cancers. Majority of trials assessed ctDNA utility in preoperative prognostication (52.9%) and in postoperative adjuvant therapy candidacy (16.2%).DiscussionThere have been significant strides in the use of ctDNA in surgical oncology including preoperative prognostication, postoperative surveillance, and risk stratification for adjuvant therapy. In recognizing the dynamic landscape of clinical trials, multidisciplinary oncology teams can be better informed to anticipate the clinical implications of ctDNA within their practice.
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Affiliation(s)
- Gordana Rasic
- Department of Surgery, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Andrea Alonso
- Department of Surgery, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Loreski Collado
- Department of Surgery, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Anand K Devaiah
- Department of Otolaryngology - Head and Neck Surgery, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Tony E Godfrey
- Department of Surgery, Boston Medical Center, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
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Stubbe B, Stoico MP, Terp SK, Madsen PH, Lundbye-Christensen S, Hansen CP, Poulsen LØ, Rasmussen LS, Yilmaz MN, Jensen LH, Hansen TF, Pfeiffer P, Larsen AC, Krarup HB, Pedersen IS, Hasselby JP, Johansen AZ, Chen IM, Johansen JS, Thorlacius-Ussing O, Henriksen SD. Promoter hypermethylation of SFRP1 is an allele fraction-dependent prognostic biomarker in metastatic pancreatic ductal adenocarcinoma. Front Oncol 2025; 15:1568386. [PMID: 40492125 PMCID: PMC12146188 DOI: 10.3389/fonc.2025.1568386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Accepted: 05/07/2025] [Indexed: 06/11/2025] Open
Abstract
Introduction Metastatic pancreatic ductal adenocarcinoma (PDAC) is highly lethal. Promoter hypermethylation of SFRP1 (phSFRP1) in cell-free DNA is an established prognostic biomarker in PDAC. We used digital droplet PCR (ddPCR) to examine whether the prognostic impact of phSFRP1 was allele fraction (AF) dependent. Methods Prospectively collected plasma samples were analyzed blinded. Dual-strand methylation ddPCR assays were designed for SFRP1, with single-strand assay for the reference gene EPHA3. Patients were stratified into unmethylated SFRP1 (umSFRP1), low phSFRP1 AF (phSFRP1low), and high phSFRP1 AF (phSFRP1high). Survival was assessed with Kaplan-Meier curves. The 3-, 6-, and 12-month absolute risk difference (ARD) was calculated, and performance assessed with ROC analyses. Results Overall, 354 patients were included. Patients with umSFRP1 (n=137) had a mOS of 9.1 months compared to 7.2 months in phSFRP1low (n=78) and 3.4 months in phSFRP1high (n=143, P<0.01). phSFRP1high was associated with increased mortality at 3 (ARD 26%, 95%CI: 15, 37), 6 (ARD 37%, 95%CI: 26, 48), and 12 months (ARD 23%, 95%CI: 14, 33). phSFRP1low was associated with increased mortality at 12 months (ARD 13%, 95%CI: 2, 25) but not at 3 (ARD -3%, 95%CI: -13, 8) or 6 months (ARD 3%, 95%CI: -10, 17). phSFRP1 significantly improved performance in predicting mortality compared to only clinical variables (AUC: 0.70-0.71 vs. 0.54-0.57). Discussion Patients with phSFRP1high had significantly shorter survival than phSFRP1low or umSFRP1, indicating AF-dependent prognostic effects. phSFRP1low had a worse prognosis than umSFRP1 at only 12 months, indicating dynamic changes. This could help personalize the treatment of PDAC.
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Affiliation(s)
- Benjamin Stubbe
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Malene P. Stoico
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Simone K. Terp
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Poul H. Madsen
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Søren Lundbye-Christensen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Unit of Research Data and Biostatistics, Aalborg University Hospital, Aalborg, Denmark
| | - Carsten P. Hansen
- Department of Surgery, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Laurids Ø. Poulsen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Louise S. Rasmussen
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Mette N. Yilmaz
- Department of Oncology and Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Lars H. Jensen
- Department of Oncology, University Hospital of Southern Denmark, Vejle, Denmark
| | - Torben F. Hansen
- Department of Oncology, University Hospital of Southern Denmark, Vejle, Denmark
| | - Per Pfeiffer
- Department of Medical Oncology, Odense University Medical Center, University of Odense, Odense, Denmark
| | - Anders C. Larsen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Henrik B. Krarup
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Inge S. Pedersen
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Jane P. Hasselby
- Department of Pathology, Copenhagen University Hospital – Rigshospitalet, Copenhagen, Denmark
| | - Astrid Z. Johansen
- Department of Oncology, Copenhagen University Hospital – Herlev and Gentofte, Herlev, Denmark
| | - Inna M. Chen
- Department of Oncology, Copenhagen University Hospital – Herlev and Gentofte, Herlev, Denmark
| | - Julia S. Johansen
- Department of Oncology, Copenhagen University Hospital – Herlev and Gentofte, Herlev, Denmark
- Department of Medicine, Copenhagen University Hospital-Herlev and Gentofte Hospital, Herlev, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole Thorlacius-Ussing
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
| | - Stine D. Henriksen
- Department of Gastrointestinal Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
- Clinical Cancer Research Center, Aalborg University Hospital, Aalborg, Denmark
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11
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Addamo-De Nard B, Geissmann M, Akhoundova D, Pistoni C, Brezina T, Zoche M, Weber A, Hussung S, Fritsch R. A novel KRAS exon 2 drop-off digital PCR assay for mutation detection in cell-free DNA of cancer patients. Diagn Pathol 2025; 20:62. [PMID: 40413426 PMCID: PMC12103757 DOI: 10.1186/s13000-025-01637-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Accepted: 03/27/2025] [Indexed: 05/27/2025] Open
Abstract
BACKGROUND KRAS exon 2 mutations are highly prevalent in human malignancies, making them attractive targets for detection and monitoring in cell-free DNA (cfDNA) of cancer patients. Drop-off assays designed for digital polymerase chain reaction (ddPCR drop-off) span entire mutational hotspots and detect any mutated allele within the covered region, overcoming a major limitation of mutation-specific ddPCR assays. We therefore set out to develop a novel KRAS codon 12/13 ddPCR drop-off assay for the robust, highly sensitive and specific detection of KRAS exon 2 hotspot mutations in cfDNA. METHODS We designed, optimized and extensively validated a KRAS codon 12/13 ddPCR drop-off assay. We compared assay performance to a commercially available KRAS multiplex assay. For clinical validation, we analyzed plasma samples collected from patients with KRAS-mutated gastrointestinal malignancies. RESULTS Limit of detection of the newly established ddPCR drop-off assay was 0.57 copies/µL, limit of blank was 0.13 copies/µ. The inter-assay precision (r2) was 0.9096. Our newly developed KRAS ddPCR drop-off assay accurately identified single nucleotide variants in 35/36 (97.2%) of circulating tumor DNA-positive samples from the patient validation cohort. Assay cross-validation showed that the newly established KRAS codon 12/13 ddPCR drop-off assay outperformed a commercially available KRAS multiplex ddPCR assay in terms of specificity. Moreover, the newly developed assay proved to be suitable for multiplexing with mutation-specific probes. CONCLUSION We developed and clinically validated a highly accurate ddPCR drop-off assay for KRAS exon 2 hot-spot detection in cfDNA with broad applicability for clinic and research.
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Affiliation(s)
- Bianca Addamo-De Nard
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Meret Geissmann
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Dilara Akhoundova
- Department of Medical Oncology, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Clelia Pistoni
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
- University of Zurich, Zurich, Switzerland
| | - Tomas Brezina
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
| | - Martin Zoche
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Achim Weber
- Institute of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
- Institute of Molecular Cancer Research (IMCR), University of Zurich, Zurich, Switzerland
| | - Saskia Hussung
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland
- University of Zurich, Zurich, Switzerland
| | - Ralph Fritsch
- Department of Medical Oncology and Hematology, University Hospital Zurich, Zurich, Switzerland.
- University of Zurich, Zurich, Switzerland.
- Comprehensive Cancer Center Zurich, Raemistrasse 100, Zurich, 8091, Switzerland.
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12
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Alampritis G, Thoukididou SN, Ramos M, Georgiou P, Kalofonou M, Simillis C. Diagnostic value of genetic and epigenetic biomarker panels for colorectal cancer detection: a systematic review. Int J Colorectal Dis 2025; 40:125. [PMID: 40402271 PMCID: PMC12098509 DOI: 10.1007/s00384-025-04904-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/29/2025] [Indexed: 05/23/2025]
Abstract
PURPOSE Exploration of effective screening methods is imperative to improve current screening for colorectal cancer (CRC). Our aim was to systematically search the literature to identify and assess the diagnostic accuracy of both genetic and epigenetic biomarker panels for CRC detection using liquid biopsies for circulating tumour DNA (ctDNA) from stool, blood, or urine. METHODS A systematic review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) with searches in Medline, Embase, CENTRAL, and Web Of Science from inception up to March 20, 2025, using pre-defined keywords. Study quality assessment was performed using QUADAS-2 tool (Quality Assessment for Diagnostic Accuracy Studies 2). Primary and secondary outcomes were panel performance (sensitivity and specificity) for CRC, advanced precancerous lesions (APL), and staging of disease. RESULTS Forty-four studies were included. Exceptional performance for both CRC (sensitivity and specificity) and APL (sensitivity) was displayed by biomarker panels including methylated SDC2 with methylated SFRP1/2 (CRC: 91.5%/97.3%, APL: 89.2%) or methylated TFPI2 (CRC: 94.9%/98.1%, APL: 100%), and a 5-biomarker panel of mutational targets APC, Bat-26, KRAS, L-DNA, and p53 (CRC: 91.0%/93.0%, APL: 82.0%). Suboptimal APL sensitivities up to 57.0% were exhibited by Cologuard and variant panels (including KRAS, methylated BMP3, methylated NDRG4, FIT), and 47.8% for combinations including methylated SEPT9. CONCLUSIONS High-performance, candidate ctDNA biomarker panels with exceptional diagnostic accuracy for both CRC and APL have been identified. Further work should focus on the development of large-scale studies to justify their clinical implementation.
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Affiliation(s)
- Georgios Alampritis
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Colorectal Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sarah Nohelia Thoukididou
- Department of Surgery, University of Cambridge, Cambridge, UK
- Cambridge Colorectal Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Maria Ramos
- Department of Electrical and Electronic Engineering, Imperial College London, London, UK
| | - Pantelis Georgiou
- Department of Electrical and Electronic Engineering, Imperial College London, London, UK
| | - Melpomeni Kalofonou
- Department of Electrical and Electronic Engineering, Imperial College London, London, UK
| | - Constantinos Simillis
- Department of Surgery, University of Cambridge, Cambridge, UK.
- Cambridge Colorectal Unit, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
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13
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Routman DM, Van Abel KM, Price KA, Moore EJ, Patel SH, Hinni ML, Fruth B, Foster NR, Yin LX, Neben-Wittich M, Garces YI, McGee LA, Lester SC, Gamez ME, Rwigema JCM, Holtzman AL, Price DL, Janus JR, Kasperbauer JL, Chintakuntlawar AV, Garcia JJ, Foote RL, Ma DJ. ctDNA and Recurrence Risk for Adjuvant De-Escalation in HPV-Positive Oropharyngeal Carcinoma: A Secondary Analysis of the DART Phase 3 Randomized Clinical Trial. JAMA Otolaryngol Head Neck Surg 2025:2834560. [PMID: 40402484 PMCID: PMC12100506 DOI: 10.1001/jamaoto.2025.0903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 03/30/2025] [Indexed: 05/23/2025]
Abstract
Importance The De-escalated Adjuvant Radiation Therapy (DART) phase 3 randomized clinical trial (RCT) showed that in patients with human papillomavirus (HPV)-associated oropharyngeal squamous cell carcinoma, postoperative minimal residual disease (MRD), detected through circulating tumor HPV DNA (ctHPVDNA), was associated with a higher risk of disease progression. When considered along with pathologic factors, postoperative ctHPVDNA assessment may improve patient selection for adjuvant treatment de-escalation; however, more data are needed to demonstrate how it may be used in personalizing treatment intensity. Objective To determine the association of postoperative MRD status with progression-free survival (PFS) after surgery for HPV-associated oropharyngeal squamous cell carcinoma. Design, Setting, and Participants This was a secondary analysis of the DART RCT, which was conducted from October 2016 to August 2020 in multiple sites in the US. Participants from the de-escalated adjuvant radiation therapy group and the standard of care group with available blood specimen data were included. Reports from 3-month posttreatment surveillance visits were used to assess associations and outcomes. Data analyses were performed from March 2023 to March of 2025. Interventions The DART group received 30 to 36 Gy of radiation therapy in 1.5 to 1.8 Gy twice daily, plus docetaxel, 15 mg/m2, on days 1 and 8. The standard of care group received 60 Gy with or without weekly cisplatin, 40 mg/m2. Main Outcome and Measure PFS. Results The analysis included 140 patients (mean [SD] age, 59.1 [8.4] years; 12 [8.6%] females and 128 [91.4%] males; 97 [69.3%] with no smoking history); characteristics were similar to the overall DART RCT population. Of these, 17 patients (12.1%) had postoperative MRD (13 of 96 [13.5%] receiving DART and 4 of 44 [9.1%] receiving standard of care). For all patients, postoperative MRD positivity was strongly associated with worsened PFS at 24 months (MRD positivity, 69.5%; MRD negativity, 95.9%; hazard ratio [HR], 0.19; 95% CI, 0.06-0.59). MRD positivity was associated with PFS when evaluating only those patients in the DART group, where 24-month PFS was 68.4% compared to 92.6% for MRD-negative patients (HR, 0.28; 95% CI, 0.08-0.93). Three months after completion of all treatment, 8 of 117 patients (6.8%) had detectable ctHPVDNA, whereas 109 of 117 (93.2%) did not, and detection was highly associated with PFS (HR, 20.48; 95% CI, 6.91-60.67). Conclusions and Relevance This secondary analysis of the DART RCT found that patients with detectable ctHPVDNA after surgery had a higher risk of disease progression. When added to the pathologic factors considered, ctHPVDNA assessment may improve selection of patients for treatment de-escalation. In addition, the 3-month posttreatment time point, early in surveillance, may identify a sizable portion of patients with progression and may guide intervention and surveillance after surgery for HPV-associated oropharyngeal squamous cell carcinoma. Trial Registration ClinicalTrials.gov Identifier: NCT02908477.
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Affiliation(s)
- David M. Routman
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Kathryn M. Van Abel
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota
| | | | - Eric J. Moore
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota
| | - Samir H. Patel
- Department of Radiation Oncology, Mayo Clinic, Phoenix, Arizona
| | | | - Briant Fruth
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Nathan R. Foster
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota
| | - Linda X. Yin
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota
| | | | | | - Lisa A. McGee
- Department of Radiation Oncology, Mayo Clinic, Phoenix, Arizona
| | - Scott C. Lester
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | | | | | - Adam L. Holtzman
- Department of Radiation Oncology, Mayo Clinic, Jacksonville, Florida
| | - Daniel L. Price
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota
| | - Jeffrey R. Janus
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Jacksonville, Florida
| | - Jan L. Kasperbauer
- Department of Otolaryngology, Head and Neck Surgery, Mayo Clinic, Rochester, Minnesota
| | | | - Joaquin J. Garcia
- Department of Laboratory Medicine & Pathology, Mayo Clinic, Rochester, Minnesota
| | - Robert L. Foote
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Daniel J. Ma
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
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14
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Englisz A, Smycz-Kubańska M, Królewska-Daszczyńska P, Błaut M, Duszyc A, Mielczarek-Palacz A. The Application of Circulating Tumour DNA (ctDNA) in the Diagnosis, Prognosis, and Treatment Monitoring of Gynaecological and Breast Cancers (Review). Diagnostics (Basel) 2025; 15:1289. [PMID: 40428282 PMCID: PMC12109643 DOI: 10.3390/diagnostics15101289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2025] [Revised: 05/16/2025] [Accepted: 05/19/2025] [Indexed: 05/29/2025] Open
Abstract
Gynaecological cancers, including endometrial, ovarian, and cervical cancers as well as breast cancer, despite numerous studies, still constitute a challenge for modern oncology. For this reason, research aimed at the application of modern diagnostic methods that are useful in early detection, prognosis, and treatment monitoring deserves special attention, Great hopes are currently being placed on the use of liquid biopsy (LB), which examines various tumour components, including cell-free RNA (cfRNA), circulating tumour cells (CTCs), circulating tumour DNA (ctDNA), exosomes, and tumour-educated platelets (TEPs). LB has shown promise as a minimally invasive means of early diagnosis of cancers, detection of recurrence, prediction of therapy response, treatment monitoring, and drug selection. The integration of this test into clinical practice in modern oncology is challenging, but offers many benefits, including reducing the risks associated with invasive procedures, improving diagnostic and therapeutic efficacy, and improving the quality of life of oncology patients. The aim of this review is to present recent reports on the use of ctDNA in diagnosing, predicting the outcome of, and monitoring the treatment of gynaecological and breast cancers.
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Affiliation(s)
- Aleksandra Englisz
- The Doctoral School, Medical University of Silesia, 40-055 Katowice, Poland;
| | - Marta Smycz-Kubańska
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (M.S.-K.); (P.K.-D.); (M.B.); (A.D.)
| | - Patrycja Królewska-Daszczyńska
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (M.S.-K.); (P.K.-D.); (M.B.); (A.D.)
| | - Magdalena Błaut
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (M.S.-K.); (P.K.-D.); (M.B.); (A.D.)
| | - Agnieszka Duszyc
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (M.S.-K.); (P.K.-D.); (M.B.); (A.D.)
| | - Aleksandra Mielczarek-Palacz
- Department of Immunology and Serology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (M.S.-K.); (P.K.-D.); (M.B.); (A.D.)
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15
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Dennehy C, Conroy MR, Forde PM. Immunotherapy for resectable lung cancer. Cancer 2025; 131:e35849. [PMID: 40334018 PMCID: PMC12057804 DOI: 10.1002/cncr.35849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 03/20/2025] [Accepted: 03/24/2025] [Indexed: 05/09/2025]
Abstract
Lung cancer remains a significant global health challenge, demanding innovative treatment strategies. Immune checkpoint blockade has revolutionized cancer care, leading to improved survival across advanced malignancies and has now become a standard therapy for earlier stage, resectable lung cancer. This review article consolidates the current landscape and future prospects of neoadjuvant and perioperative immunotherapy in lung cancer. The authors outline key findings from clinical trials in resectable lung cancer, including early efficacy, safety profiles, and emerging impact on disease recurrence, and overall survival. Additionally, this review elucidates the challenges encountered, including patient selection criteria, optimal treatment schedules, immune-related adverse events, and impact on surgery. This comprehensive analysis amalgamates current evidence with future directions, providing a roadmap for clinicians, researchers, and stakeholders to navigate the dynamic realm of immunotherapy for surgically resectable lung cancer.
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Affiliation(s)
- Colum Dennehy
- Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Michael R. Conroy
- Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Patrick M. Forde
- Sidney Kimmel Comprehensive Cancer CenterJohns Hopkins University School of MedicineBaltimoreMarylandUSA
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16
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Riviere-Cazaux C, Graser CJ, Warrington AE, Hoplin MD, Andersen KM, Malik N, Palmer EA, Carlstrom LP, Dasari S, Munoz-Casabella A, Ikram S, Ghadimi K, Himes BT, Jusue-Torres I, Sarkaria JN, Meyer FB, Van Gompel JJ, Kizilbash SH, Sener U, Michor F, Campian JL, Parney IF, Burns TC. A field resource for the glioma cerebrospinal fluid proteome: Impacts of resection and location on biomarker discovery. Neuro Oncol 2025; 27:948-962. [PMID: 39786485 DOI: 10.1093/neuonc/noae277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Indexed: 01/12/2025] Open
Abstract
BACKGROUND While serial sampling of glioma tissue is rarely performed prior to recurrence, cerebrospinal fluid (CSF) is an underutilized longitudinal source of candidate glioma biomarkers for understanding therapeutic impacts. However, the impact of key variables to consider in longitudinal CSF samples for monitoring biomarker discovery, including anatomical location and post-surgical changes, remains unknown. METHODS Aptamer-based proteomics was performed on 147 CSF samples from 74 patients; 71 of whom had grade 2-4 astrocytomas or grade 2-3 oligodendrogliomas. This included pre- versus post-resection intracranial CSF samples obtained at early (1-16 days; n = 20 patients) or delayed (86-153 days; n = 11 patients) time points for patients with glioma. Paired lumbar versus intracranial glioma CSF samples were also obtained (n = 14 patients). RESULTS Significant differences were identified in the CSF proteome between lumbar, subarachnoid, and ventricular CSF in patients with gliomas. Importantly, we found that resection had a significant, evolving longitudinal impact on the CSF proteome, with distinct sets of proteins present at different time points since resection. Our analysis of serial intracranial CSF samples suggests the early potential for disease monitoring and evaluation of pharmacodynamic impact of targeted therapies, such as bevacizumab and immunotherapies. CONCLUSIONS The intracranial glioma CSF proteome serves as a rich and dynamic reservoir of potential biomarkers that can be used to evaluate the effects of resection and other therapies over time. All data within this study, including detailed individual clinical annotations, are shared as a resource for the neuro-oncology community to collectively address these unanswered questions and further understand glioma biology through CSF proteomics.
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Affiliation(s)
| | - Christopher J Graser
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Arthur E Warrington
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew D Hoplin
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Noor Malik
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Elizabeth A Palmer
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Lucas P Carlstrom
- Department of Neurological Surgery, The Ohio State University, Columbus, Ohio, USA
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Surendra Dasari
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Samar Ikram
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Keyvan Ghadimi
- Department of Neurological Surgery, Montefiore/Albert Einstein College of Medicine, Bronx, New York, USA
| | - Benjamin T Himes
- Department of Neurological Surgery, Montefiore/Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Fredric B Meyer
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Jamie J Van Gompel
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Sani H Kizilbash
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ugur Sener
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Franziska Michor
- The Eli and Edythe L. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- The Ludwig Center, Harvard University, Cambridge, Massachusetts, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
- Department of Data Science, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Jian L Campian
- Department of Medical Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ian F Parney
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Terry C Burns
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
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17
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Wu Z, Yang H, Li X, Ji X, Mo C, Zheng Z, Xu Y, Xiong D. Circulating tumor DNA laboratory processes and clinical applications in nasopharyngeal carcinoma. Front Oncol 2025; 15:1520733. [PMID: 40444084 PMCID: PMC12119280 DOI: 10.3389/fonc.2025.1520733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2024] [Accepted: 04/28/2025] [Indexed: 06/02/2025] Open
Abstract
Circulating tumor DNA (ctDNA), a subset of cell-free DNA (cfDNA), originates from primary tumors and metastatic lesions in cancer patients, often carrying genomic variations identical to those of the primary tumor. ctDNA analysis via liquid biopsy has proven to be a valuable biomarker for early cancer detection, minimal residual disease (MRD) assessment, monitoring tumor recurrence, and evaluating treatment efficacy. However, despite advancements in ctDNA analysis technologies, standardized protocols for its extraction and detection have yet to be established. Each step of the process-from pre-analytical variables to detection techniques-significantly impacts the accuracy and reliability of ctDNA analysis. This review examines recent developments in ctDNA detection methods, focusing on pre-analytical factors such as specimen types, collection tubes, centrifugation protocols, and storage conditions, alongside high-throughput and ultra-sensitive detection technologies. It also briefly discusses the clinical potential of liquid biopsy in nasopharyngeal carcinoma (NPC).
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Affiliation(s)
- Ziman Wu
- School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Haiyan Yang
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
| | - Xinying Li
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xiang Ji
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Chan Mo
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Zhou Zheng
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Yafei Xu
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Shenzhen, China
| | - Dan Xiong
- School of Medical Technology, Xinxiang Medical University, Xinxiang, China
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, China
- Shantou University Medical College, Shantou, China
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18
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Zhang L, Zhang Y, Chen L, Wang X, Liu Y, Huang Y, Song Y, Zhang Y, Tai J. Research trends and hotspots of circulating tumor DNA in colorectal cancer: a bibliometric study. Front Oncol 2025; 15:1492880. [PMID: 40438683 PMCID: PMC12116327 DOI: 10.3389/fonc.2025.1492880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2024] [Accepted: 04/23/2025] [Indexed: 06/01/2025] Open
Abstract
Introduction Colorectal cancer (CRC) is the third most common cancer worldwide and the second leading cause of cancer-related deaths. The current standard of care for patients with early-stage CRC includes surgical resection and, in selected patients, adjuvant chemotherapy. Circulating tumor DNA (ctDNA) testing is an important component of liquid biopsy, and with the development of testing technology, its value for clinical application has attracted widespread attention. The aim of this study was to help researchers review what has been achieved and better understand the direction of future research through bibliometric analysis. Methods We used the Web of Science Core Collection database to search for ctDNA in CRC-related articles published between 2014 - 2023. Bibliometric analyses of major keywords, authors, countries, institutions, literature and journals in the field were performed using CiteSpace and VOSviewer. Results The number of publications in the field has continued to increase over the last decade. The United States has the highest number of publications, and Italian research scholars have made outstanding contributions. Cancers is the journal with the highest number of publications. Conclusion This study systematically summarizes the research findings in the field of ctDNA in CRC from 2014 to 2023 and describes the research hotspots and trends worldwide that can guide future research.
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Affiliation(s)
- Lele Zhang
- Department of Colorectal & Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Yuzhe Zhang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Lei Chen
- Department of Colorectal & Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Xu Wang
- Department of Colorectal & Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Yulian Liu
- Department of Traditional Chinese Medicine, Chongqing Hospital of Jiangsu Province Hospital, Chongqing, China
| | - Yishan Huang
- Department of Colorectal & Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Yu Song
- Department of Colorectal & Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
| | - Ye Zhang
- The First Laboratory of Cancer Institute, The First Hospital of China Medical University, Shenyang, China
| | - Jiandong Tai
- Department of Colorectal & Anal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, China
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19
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Miyata M, Hayashi H. Current treatment landscape for patients with non-small cell lung cancer with common EGFR mutations. Respir Investig 2025; 63:576-584. [PMID: 40328075 DOI: 10.1016/j.resinv.2025.04.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2025] [Revised: 04/14/2025] [Accepted: 04/22/2025] [Indexed: 05/08/2025]
Abstract
Common EGFR mutations including exon-19 deletions and the L858R point mutation in exon 21 constitute predominant actionable genomic alterations in individuals with non-small cell lung cancer (NSCLC). The introduction of EGFR tyrosine kinase inhibitors (TKIs) has fundamentally changed the treatment landscape for such patients by improving both progression-free survival (PFS) and overall survival (OS). Among EGFR-TKIs, third-generation agents such as osimertinib have shown marked efficacy and favorable safety profiles and have become the standard of care in the first-line setting. The combination of osimertinib with platinum-based chemotherapy has recently been shown to improve PFS compared with osimertinib monotherapy in the FLAURA2 trial. Similarly, the MARIPOSA trial demonstrated clinical benefit of the combination of the EGFR-MET bispecific antibody, amivantamab, with the third-generation EGFR-TKI, lazertinib, further supporting the use of combination therapies as first-line treatment for EGFR-mutated NSCLC. Despite these advances, however, challenges such as brain metastases remain substantial barriers to successful treatment outcomes. Management of patients with such metastases often requires a multidisciplinary approach that integrates systemic treatment with local interventions such as radiation therapy. Finally, circulating tumor DNA has emerged as a promising biomarker for real-time monitoring of treatment response and evolution of drug resistance mechanisms. Analysis of such biomarkers can facilitate dynamic and personalized therapeutic adjustments, potentially improving outcomes. This review provides a comprehensive overview of the latest clinical evidence supporting therapeutic advances in the management of EGFR-mutated NSCLC, emphasizing the importance of tailoring treatment strategies based on tumor biology, patient-specific factors, and evolving therapeutic options.
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Affiliation(s)
- Masayuki Miyata
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan
| | - Hidetoshi Hayashi
- Department of Medical Oncology, Kindai University Faculty of Medicine, 377-2 Ohno-higashi, Osaka-Sayama, Osaka, 589-8511, Japan.
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20
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Kato T, Shiota M, Nishimoto K, Matsubara N, Osawa T, Abe T, Yasumizu Y, Tanaka N, Yamamoto Y, Ishizuya Y, Abutani H, Bando H, Fujisawa T, Nakamura Y, Oya M, Shinohara N, Eto M, Yoshino T, Nonomura N. Prognostic significance of circulating tumor DNA alterations in advanced renal cell carcinoma from SCRUM-Japan MONSTAR-SCREEN: a nationwide genomic profiling project. Br J Cancer 2025:10.1038/s41416-025-02985-8. [PMID: 40325148 DOI: 10.1038/s41416-025-02985-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2024] [Revised: 01/25/2025] [Accepted: 03/12/2025] [Indexed: 05/07/2025] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is a promising tool for diagnosing and predicting cancer prognosis. However, its clinical utility in metastatic renal cell carcinoma (mRCC) remains unclear, particularly in terms of clinical prognosis. METHODS We enrolled 124 patients with mRCC in the MONSTAR-SCREEN study (UMIN 000036749) between August 2019 and February 2022, a national observational ctDNA-based screening study, and performed ctDNA sequencing before and at the time of resistance to systemic therapy. RESULTS ctDNA were assessed in 178 samples containing 432 mutations. The most frequently altered genes at baseline were VHL (25.0%), PBRM1 (10.9%), TERT2 (8.7%), BAP1 (8.7%), and MTOR (7.6%). Patients receiving first-line therapy with tumor fraction (TF) < 1.2% showed significantly better progression-free survival than those with TF ≥ 1.2% (Hazard ratio (HR) = 0.467; 95% CI 0.229-0.979; p = 0.0425). BAP1 mutational status of ctDNA at baseline led to poor OS (HR = 0.4867; 95% CI 0.322-0.736; p = 0.0003). Serial ctDNA analysis showed that 46.8% of patients developed new ctDNA mutations at disease progression, which was linked to shorter time to progression (p = 0.046). CONCLUSIONS Our findings demonstrated that ctDNA profiling is feasible in mRCC and can predict disease progression after treatment.
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Affiliation(s)
- Taigo Kato
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan.
| | - Masaki Shiota
- Department of Urology, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Koshiro Nishimoto
- Department of Uro-Oncology, Saitama Medical University International Medical Center, Saitama, Japan
- Department of Urology, Faculty of Medicine, Miyazaki University Hospital, Miyazaki, Japan
| | - Nobuaki Matsubara
- Department of Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takahiro Osawa
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Takashige Abe
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Yota Yasumizu
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Nobuyuki Tanaka
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Yoshiyuki Yamamoto
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Yu Ishizuya
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
| | | | - Hideaki Bando
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
| | - Takao Fujisawa
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Head and Neck Medical Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of International Research Promotion Office, National Cancer Center Hospital East, Kashiwa, Japan
| | - Mototsugu Oya
- Department of Urology, Keio University School of Medicine, Tokyo, Japan
| | - Nobuo Shinohara
- Department of Renal and Genitourinary Surgery, Hokkaido University Graduate School of Medicine, Sapporo, Japan
| | - Masatoshi Eto
- Department of Urology, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
- Department of the Promotion of Drug & Diagnostic Development, National Cancer Center Hospital East, Kashiwa, Japan
| | - Norio Nonomura
- Department of Urology, Osaka University Graduate School of Medicine, Osaka, Japan
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21
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Lee TR, Ahn JM, Lee J, Kim D, Park J, Jeong BH, Oh D, Kim SM, Jung GC, Choi BH, Kwon MJ, Wang M, Salmans M, Carson A, Leatham B, Fathe K, Lee BI, Jung B, Ki CS, Park YS, Cho EH. Integrating Plasma Cell-Free DNA Fragment End Motif and Size with Genomic Features Enables Lung Cancer Detection. Cancer Res 2025; 85:1696-1707. [PMID: 40136052 DOI: 10.1158/0008-5472.can-24-1517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 07/28/2024] [Accepted: 11/08/2024] [Indexed: 03/27/2025]
Abstract
Early detection of lung cancer is important for improving patient survival rates. Liquid biopsy using whole-genome sequencing of cell-free DNA (cfDNA) offers a promising avenue for lung cancer screening, providing a potential alternative or complementary approach to current screening modalities. Here, we aimed to develop and validate an approach by integrating fragment and genomic features of cfDNA to enhance lung cancer detection accuracy across diverse populations. Deep learning-based classifiers were trained using comprehensive cfDNA fragmentomic features from participants in multi-institutional studies, including a Korean discovery dataset (218 patients with lung cancer and 2,559 controls), a Korean validation dataset (111 patients with lung cancer and 1,136 controls), and an independent Caucasian validation cohort (50 patients with lung cancer and 50 controls). In the discovery dataset, classifiers using fragment end motif by size, a feature that captures both fragment end motif and size profiles, outperformed standalone fragment end motif and fragment size classifiers, achieving an area under the curve (AUC) of 0.917. The ensemble classifier integrating fragment end motif by size and genomic coverage achieved an improved performance, with an AUC of 0.937. This performance extended to the Korean validation dataset and demonstrated ethnic generalizability in the Caucasian validation cohort. Overall, the development of a deep learning-based classifier integrating cfDNA fragmentomic and genomic features in this study highlights the potential for accurate lung cancer detection across diverse populations. Significance: Evaluating fragment-based features and genomic coverage in cell-free DNA offers an accurate lung cancer screening method, promising improvements in early cancer detection and addressing challenges associated with current screening methods.
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Affiliation(s)
- Tae-Rim Lee
- Genome Research Center, GC Genome, Yongin-si, South Korea
| | - Jin Mo Ahn
- Genome Research Center, GC Genome, Yongin-si, South Korea
| | - Junnam Lee
- Genome Research Center, GC Genome, Yongin-si, South Korea
| | - Dasom Kim
- Genome Research Center, GC Genome, Yongin-si, South Korea
| | - Juntae Park
- Genome Research Center, GC Genome, Yongin-si, South Korea
| | - Byeong-Ho Jeong
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Dongryul Oh
- Department of Radiation Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | | | | | - Min-Jung Kwon
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | | | | | | | | | | | | | - Byoungsok Jung
- Genome Research Center, GC Genome, Yongin-si, South Korea
| | - Chang-Seok Ki
- Genome Research Center, GC Genome, Yongin-si, South Korea
| | - Young Sik Park
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Eun-Hae Cho
- Genome Research Center, GC Genome, Yongin-si, South Korea
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22
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Grancher A, Beaussire-Trouvay L, Vernon V, Dutherage M, Blondin V, Elie C, Bouhier-Leporrier K, Galais MP, Clabaut T, Bignon AL, Parzy A, Gangloff A, Schwarz L, Lévêque E, Sabourin JC, Michel P, Vasseur N, Sefrioui D, Gilibert A, Di Fiore F. ctDNA variations according to treatment intensity in first-line metastatic colorectal cancer. Br J Cancer 2025; 132:814-821. [PMID: 40089635 PMCID: PMC12041588 DOI: 10.1038/s41416-025-02971-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2024] [Revised: 01/14/2025] [Accepted: 02/25/2025] [Indexed: 03/17/2025] Open
Abstract
BACKGROUND Circulating tumor DNA variations (∆ctDNA) were reported to be associated with treatment efficacy in metastatic colorectal cancer (mCRC). The present study evaluated ∆ctDNA according to first-line treatment intensity. METHODS Patients from two prospective ctDNA collections were divided into Group ≤ 2 drugs and Group ≥ 3 drugs. ∆ctDNA were analysed from baseline to cycle 3 or 4 (C3-4) according to three predefined subgroups: ∆ctDNA ≥ 80%_ undetectable, ∆ctDNA ≥ 80%_ detectable, and ∆ctDNA < 80%. Impact of ∆ctDNA on progression-free survival (PFS) and overall survival (OS) were analysed. RESULTS Pretreatment ctDNA was detected in 129/152 (84.9%) of patients. A ∆ctDNA ≥ 80%_undetectable was more frequent in Group ≥ 3 than ≤ 2 drugs (respectively 51.5% vs. 32.7%, p = 0.015). Patients with ∆ctDNA ≥ 80%_undetectable had longer survival than other ∆ctDNA subgroups, in Group ≥ 3 drugs (mPFS 11.5 vs 7.8 vs 6.3 months, p = 0.02: mOS 30.2 vs 18.1 vs 16.4 month, p = 0.04) and in Group ≤ 2 drugs (mPFS 8.4 vs 6.0 vs 5.3 months, p = 0.05; mOS 29.6 vs 14.6 vs 14.6 months, p = 0.007). DISCUSSION Early ∆ctDNA are associated to treatment intensity in first line mCRC with a significant impact on prognosis.
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Affiliation(s)
- Adrien Grancher
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine and Department of Hepato-gastroenterology and Digestive Oncology, Rouen University Hospital, Rouen, France
| | - Ludivine Beaussire-Trouvay
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - Virginie Vernon
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine and Department of Hepato-gastroenterology and Digestive Oncology, Rouen University Hospital, Rouen, France
| | - Marie Dutherage
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine and Department of Hepato-gastroenterology and Digestive Oncology, Rouen University Hospital, Rouen, France
| | - Valérie Blondin
- CHI Elbeuf, Department of Hepatogastroenterology, Elbeuf, France
| | - Caroline Elie
- CHI Elbeuf, Department of Hepatogastroenterology, Elbeuf, France
| | | | - Marie-Pierre Galais
- Department of Hepatogastroenterology, Francois Baclesse Centre, Caen, France
| | - Tifenn Clabaut
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - Anne-Laure Bignon
- Department of Hepatogastroenterology, Caen University Hospital, Caen, France
| | - Aurélie Parzy
- Department of Hepatogastroenterology, Francois Baclesse Centre, Caen, France
| | | | - Lilian Schwarz
- Department of Digestive Surgery, Rouen University Hospital, Rouen, France
| | - Emilie Lévêque
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | | | - Pierre Michel
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine and Department of Hepato-gastroenterology and Digestive Oncology, Rouen University Hospital, Rouen, France
| | - Nasrin Vasseur
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Rouen, France
| | - David Sefrioui
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine and Department of Hepato-gastroenterology and Digestive Oncology, Rouen University Hospital, Rouen, France
| | - André Gilibert
- Department of Biostatistics, Rouen University Hospital, Rouen, France
| | - Frédéric Di Fiore
- Normandie Univ, UNIROUEN, Inserm U1245, IRON group, Normandy Centre for Genomic and Personalized Medicine and Department of Hepato-gastroenterology and Digestive Oncology, Rouen University Hospital, Rouen, France.
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23
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Nguyen VTC, Vo DH, Tran TT, Tran TT, Nguyen THH, Vo TDH, Van TTV, Vu TL, Lam MQ, Nguyen GTH, Tran TH, Pham NT, Trac QT, Nguyen TH, Phan TV, Dao TH, Nguyen HTP, Nguyen LHD, Nguyen DS, Tang HS, Giang H, Phan MD, Nguyen HN, Tran LS. Cost-effective shallow genome-wide sequencing for profiling plasma cfDNA signatures to enhance lung cancer detection. Future Oncol 2025; 21:1391-1402. [PMID: 40133038 PMCID: PMC12051589 DOI: 10.1080/14796694.2025.2483154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2025] [Accepted: 03/19/2025] [Indexed: 03/27/2025] Open
Abstract
BACKGROUND Lung cancer (LC) screening via low-dose computed tomography (LDCT) faces challenges including high false-positive rates and low patient compliance. Circulating tumor DNA (ctDNA)-based tests offer a minimally invasive alternative but are limited by high costs and low sensitivity, particularly in early-stage detection. This study introduces a cost-effective, shallow genome-wide sequencing approach for LC detection by profiling multiple cell-free DNA (cfDNA) signatures. METHODS We developed a multimodal cfDNA assay with shallow sequencing coverage (0.5×) that integrates fragmentomic, nucleosome, end-motif, and copy number alteration analyses. A machine-learning model trained on a discovery cohort (99 LC patients, 168 healthy controls) and validated on an independent cohort (58 LC patients, 71 controls) demonstrated robust performance. RESULTS The ensemble model exhibited outstanding performance, achieving an AUC of 0.97 and a specificity of 92% in both the discovery and validation cohorts, with sensitivities of 94% and 90%, respectively. Notably, it outperformed hotspot mutation-based assays and the multi-cancer SPOT-MAS assay in sensitivity across all LC stages. CONCLUSIONS This assay provides a cost-effective, accurate, and minimally invasive method for LC detection, addressing the limitations of current screening methods. It represents a promising complementary tool to improve early detection and patient outcomes in LC.
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Affiliation(s)
- Van Thien Chi Nguyen
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Dac Ho Vo
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Trang Tran
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thanh Truong Tran
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Hue Hanh Nguyen
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Truong Dang Huy Vo
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Tuong Vi Van
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Luyen Vu
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Minh Quang Lam
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | | | - Trung Hieu Tran
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Ngoc Tan Pham
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Quang Thinh Trac
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Trong Hieu Nguyen
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Van Phan
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Thi Huyen Dao
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Huu Tam Phuc Nguyen
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Luu Hong Dang Nguyen
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Duy Sinh Nguyen
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Hung Sang Tang
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Hoa Giang
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Minh Duy Phan
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Hoai-Nghia Nguyen
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
| | - Le Son Tran
- Research and Development Department, Medical Genetics Institute, Ho Chi Minh, Vietnam
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24
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Balaguer-Lluna L, Olaciregui NG, Aschero R, Resa-Pares C, Paco S, Cuadrado-Vilanova M, Burgueño V, Baulenas-Farres M, Monterrubio C, Manzanares A, Rodríguez E, Lavarino C, Mora J, Carcaboso AM. Establishment of xenografts and methods to evaluate tumor burden for the three most frequent subclasses of pediatric-type diffuse high grade gliomas. J Neurooncol 2025; 172:599-611. [PMID: 39961939 PMCID: PMC11968510 DOI: 10.1007/s11060-025-04954-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2024] [Accepted: 01/25/2025] [Indexed: 04/04/2025]
Abstract
PURPOSE We aimed to expand and refine the experimental models for pediatric-type diffuse high grade gliomas (pHGG) and the methods to follow up disease progression in mouse pHGG xenografts. METHODS Using whole exome sequencing and immunoassays we characterized pHGG primary cultures and xenografts established at hospital SJD Barcelona. We obtained tumor samples and serial CSF samples from mouse xenografts. To assess tumor progression, we evaluated: (1) mouse weight, (2) human cell counts in brain paraffin sections, and (3) tumor DNA amount, quantified through droplet digital polymerase chain reaction (ddPCR) in paraffin sections and cerebrospinal fluid (CSF). RESULTS We established 15 experimental models of three pHGG subclasses, four of which engrafted in mice. Xenografts HSJD-DIPG-007 and HSJD-DMG-005 are diffuse midline glioma (DMG) H3 K27-altered, HSJD-GBM-002 is an H3 G34-mutant diffuse hemispheric glioma, and HSJD-GBM-001 is an H3-wildtype and IDH-wildtype pHGG. ddPCR quantification of human H3F3A K27M, H3F3A G34R, and ACVR1 R206H in paraffin samples is linear and sufficiently sensitive. We required a preamplification step to detect H3F3A K27M in CSF. In HSJD-DIPG-007 xenografts, human cell counts correlated with H3F3A amounts in paraffin for the whole engraftment period. Weight loss correlated with human cell counts and H3F3A amounts in paraffin. Serial collection of CSF was feasible, but H3F3A amounts in the CSF correlated only with weight loss. CONCLUSION The developed methods contribute to the preclinical field of pHGG and introduce for the first time the concept of liquid biopsy in mice, which still needs improvement regarding its use as a preclinical biomarker.
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Affiliation(s)
- Leire Balaguer-Lluna
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Nagore G Olaciregui
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Rosario Aschero
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Claudia Resa-Pares
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Sonia Paco
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Maria Cuadrado-Vilanova
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Victor Burgueño
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Merce Baulenas-Farres
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Carles Monterrubio
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Alejandro Manzanares
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Eva Rodríguez
- Pathology, Hospital Sant Joan de Deu, Barcelona, 08950, Spain
| | - Cinzia Lavarino
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Jaume Mora
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain
| | - Angel M Carcaboso
- Pediatric Cancer Program, Institut de Recerca Sant Joan de Deu (IRSJD), Barcelona, 08950, Spain.
- SJD Pediatric Cancer Center Barcelona, Hospital Sant Joan de Deu, Santa Rosa 39-57, Esplugues de Llobregat, Barcelona, 08950, Spain.
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25
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Uchibori M, Hosomichi K, Hoshimoto Y, Sasaki M, Aoki T, Tajima A, Ota Y, Kimura M. The Efficacy of Liquid Biopsy of Total cfDNA for Predicting Systemic Metastasis in Japanese Patients With Oral Squamous Cell Carcinoma. Head Neck 2025; 47:1411-1420. [PMID: 39731308 PMCID: PMC12038226 DOI: 10.1002/hed.28054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 11/28/2024] [Accepted: 12/17/2024] [Indexed: 12/29/2024] Open
Abstract
BACKGROUND The use of liquid biopsy of total cell-free DNA (cfDNA) to identify otherwise undetectable cancers has attracted interest; however, its efficacy remains unknown. We explored whether analysis using total cfDNA is efficacious for Japanese patients with oral squamous cell carcinoma (OSCC). METHODS We collected total cfDNA from nine patients with OSCC preoperatively, 1 month postoperatively, and every 3 months thereafter to analyze this association. We used a target DNA sequence for genetic mutation analysis of tumor tissues collected from 33 patients, including the aforementioned nine patients. RESULTS Patients with good disease control showed negligible changes in preoperative and postoperative total cfDNA concentrations. A rapid increase in total cfDNA concentration was observed in patients who developed systemic metastases. Patients whose tumor tissue DNA showed genetic mutations had the same mutations in preoperative circulating tumor DNA. CONCLUSIONS Our data suggested that analyzing total cfDNA is efficacious for patients with OSCC.
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Affiliation(s)
- Masahiro Uchibori
- Department of Oral and Maxillofacial SurgeryTokai University School of MedicineIseharaJapan
| | - Kazuyoshi Hosomichi
- Laboratory of Computational Genomics, School of Life ScienceTokyo University of Pharmacy and Life SciencesTokyoJapan
| | - Yasutaka Hoshimoto
- Department of Oral and Maxillofacial SurgeryTokai University School of MedicineIseharaJapan
| | - Masashi Sasaki
- Department of Oral and Maxillofacial SurgeryTokai University School of MedicineIseharaJapan
| | - Takayuki Aoki
- Department of Oral and Maxillofacial SurgeryTokai University School of MedicineIseharaJapan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical SciencesKanazawa UniversityKanazawaJapan
| | - Yoshihide Ota
- Department of Oral and Maxillofacial SurgeryTokai University School of MedicineIseharaJapan
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26
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Zheng MM, Zhou Q, Chen HJ, Jiang BY, Tang LB, Jie GL, Tu HY, Yin K, Sun H, Liu SY, Zhang JT, Xiao FM, Yang JJ, Zhang XC, Zhong WZ, Pan Y, Wang BC, Yan HH, Guo WB, Chen ZH, Wang Z, Xu CR, Li SY, Liu SYM, Zeng L, Cai SL, Wang GQ, Zhu DQ, Li YS, Wu YL. Cerebrospinal fluid circulating tumor DNA profiling for risk stratification and matched treatment of central nervous system metastases. Nat Med 2025; 31:1547-1556. [PMID: 40016451 DOI: 10.1038/s41591-025-03538-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/27/2025] [Indexed: 03/01/2025]
Abstract
Genomic profiling of central nervous system (CNS) metastases has the potential to guide treatments. In the present study, we included 584 patients with non-small-cell lung cancer and CNS metastases and performed a comprehensive analysis of cerebrospinal fluid (CSF) circulating tumor DNA (ctDNA) with clinicopathological annotation. CSF ctDNA-positive detection was independently associated with shorter survival than negative detection (hazard ratio (HR) = 1.9, 95% confidence interval (CI) = 1.56-2.39; P < 0.0001). Matched tumor-CSF analysis characterized the CSF private molecular features causing poor survival (HR = 1.64, 95% CI = 1.15-2.32, P = 0.006). A multimetric CSF ctDNA prognostic model integrating CSF ctDNA features and clinical factors was developed for risk-stratifying CNS metastases and validated in an independent cohort. Among patients with treatment histories available, those positive for a driver alteration by CSF ctDNA showed a survival benefit from CSF-matched therapy (HR = 0.78, 95% CI = 0.65-0.92, P = 0.003). Longitudinal monitoring by CSF identified CNS-specific resistant mechanisms and a second matched targeted therapy indicating improved survival (HR = 0.56, 95% CI = 0.35-0.91, P = 0.018). These findings support the clinical value of CSF ctDNA for risk-stratifying CNS metastases and guiding therapy.
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Affiliation(s)
- Mei-Mei Zheng
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Ben-Yuan Jiang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Li-Bo Tang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Guang-Ling Jie
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hai-Yan Tu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Kai Yin
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hao Sun
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Si-Yang Liu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jia-Tao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Fa-Man Xiao
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Wen-Zhao Zhong
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yi Pan
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Bin-Chao Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Hong-Hong Yan
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Wei-Bang Guo
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhi-Hong Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhen Wang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Chong-Rui Xu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Su-Yun Li
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Si-Yang Maggie Liu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- Department of Hematology, First Affiliated Hospital, Institute of Hematology, School of Medicine; Key Laboratory for Regenerative Medicine of Ministry of Education, Jinan University, Guangzhou, China
| | - Lu Zeng
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | | | | | - Dong-Qin Zhu
- Nanjing Geneseeq Technology Inc., Nanjing, China
| | - Yang-Si Li
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
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27
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Bruhm DC, Vulpescu NA, Foda ZH, Phallen J, Scharpf RB, Velculescu VE. Genomic and fragmentomic landscapes of cell-free DNA for early cancer detection. Nat Rev Cancer 2025; 25:341-358. [PMID: 40038442 DOI: 10.1038/s41568-025-00795-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/24/2025] [Indexed: 03/06/2025]
Abstract
Genomic analyses of cell-free DNA (cfDNA) in plasma are enabling noninvasive blood-based biomarker approaches to cancer detection and disease monitoring. Current approaches for identification of circulating tumour DNA typically use targeted tumour-specific mutations or methylation analyses. An emerging approach is based on the recognition of altered genome-wide cfDNA fragmentation in patients with cancer. Recent studies have revealed a multitude of characteristics that can affect the compendium of cfDNA fragments across the genome, collectively called the 'cfDNA fragmentome'. These changes result from genomic, epigenomic, transcriptomic and chromatin states of an individual and affect the size, position, coverage, mutation, structural and methylation characteristics of cfDNA. Identifying and monitoring these changes has the potential to improve early detection of cancer, especially using highly sensitive multi-feature machine learning approaches that would be amenable to broad use in populations at increased risk. This Review highlights the rapidly evolving field of genome-wide analyses of cfDNA characteristics, their comparison to existing cfDNA methods, and recent related innovations at the intersection of large-scale sequencing and artificial intelligence. As the breadth of clinical applications of cfDNA fragmentome methods have enormous public health implications for cancer screening and personalized approaches for clinical management of patients with cancer, we outline the challenges and opportunities ahead.
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Affiliation(s)
- Daniel C Bruhm
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicholas A Vulpescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zachariah H Foda
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jillian Phallen
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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28
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Nejat Dehkordi A, Maddahi M, Vafa P, Ebrahimi N, Aref AR. Salivary biomarkers: a promising approach for predicting immunotherapy response in head and neck cancers. Clin Transl Oncol 2025; 27:1887-1920. [PMID: 39377974 DOI: 10.1007/s12094-024-03742-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Accepted: 09/21/2024] [Indexed: 04/27/2025]
Abstract
Head and neck cancers, including cancers of the mouth, throat, voice box, salivary glands, and nose, are a significant global health issue. Radiotherapy and surgery are commonly used treatments. However, due to treatment resistance and disease recurrence, new approaches such as immunotherapy are being explored. Immune checkpoint inhibitors (ICIs) have shown promise, but patient responses vary, necessitating predictive markers to guide appropriate treatment selection. This study investigates the potential of non-invasive biomarkers found in saliva, oral rinses, and tumor-derived exosomes to predict ICI response in head and neck cancer patients. The tumor microenvironment significantly impacts immunotherapy efficacy. Oral biomarkers can provide valuable information on composition, such as immune cell presence and checkpoint expression. Elevated tumor mutation load is also associated with heightened immunogenicity and ICI responsiveness. Furthermore, the oral microbiota may influence treatment outcomes. Current research aims to identify predictive salivary biomarkers. Initial studies indicate that tumor-derived exosomes and miRNAs present in saliva could identify immunosuppressive pathways and predict ICI response. While tissue-based markers like PD-L1 have limitations, combining multiple oral fluid biomarkers could create a robust panel to guide treatment decisions and advance personalized immunotherapy for head and neck cancer patients.
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Affiliation(s)
| | - Moein Maddahi
- Faculty of Density, Yeditepe University, Istanbul, Turkey
| | - Parinaz Vafa
- Faculty of Density, Yeditepe University, Istanbul, Turkey
| | - Nasim Ebrahimi
- Genetics Division, Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Amir Reza Aref
- Mass General Cancer Center, Department of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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29
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Ernst SM, Aldea M, von der Thüsen JH, de Langen AJ, Smit EF, Paats MS, Aerts JGJV, Mezquita L, Popat S, Besse B, Remon J, Rolfo C, Dubbink HJ, Dingemans AMC. Utilizing ctDNA to discover mechanisms of resistance to targeted therapies in patients with metastatic NSCLC: towards more informative trials. Nat Rev Clin Oncol 2025; 22:371-378. [PMID: 40087401 DOI: 10.1038/s41571-025-01011-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2025] [Indexed: 03/17/2025]
Abstract
Advances in targeted therapies for patients with non-small-cell lung cancer have substantially improved the outcomes of those with actionable alterations in certain oncogenic driver genes. However, acquired resistance to these targeted therapies remains a major challenge. Understanding the mechanisms underlying acquired resistance will be crucial for the development of strategies that might either overcome this effect or delay the onset. Circulating tumour DNA, owing to the need for only minimally invasive sampling and a potential role as both a prognostic and predictive biomarker, is increasingly being used in both research and clinical practice. Several studies have explored the landscape of acquired resistance to targeted therapies using this approach. However, the methodologies of the published studies vary widely, and several major challenges remain in addressing the practical difficulties associated with these methods. These challenges currently limit the depth of research insight provided by the available data. In this Perspective, we review clinical reports describing the use of circulating tumour DNA to detect mechanisms of acquired resistance to targeted therapies, predominantly in patients with advanced-stage non-small-cell lung cancer, and highlight key unresolved questions with the aim of moving towards more-informative research studies.
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Affiliation(s)
- Sophie M Ernst
- Department of Respiratory Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Mihaela Aldea
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
- Paris-Saclay University, Kremlin Bicetre, France
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jan H von der Thüsen
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Adrianus J de Langen
- Department of Thoracic Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Egbert F Smit
- Department of Respiratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Marthe S Paats
- Department of Respiratory Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Joachim G J V Aerts
- Department of Respiratory Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands
| | - Laura Mezquita
- Medical Oncology Department, Hospital Clinic of Barcelona, Barcelona, Spain
- Laboratory of Translational Genomics and Targeted Therapies in Solid Tumors, IDIBAPS, Barcelona, Spain
| | - Sanjay Popat
- Lung Unit, Royal Marsden Hospital NHS Foundation Trust, London, UK
| | - Benjamin Besse
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
- Paris-Saclay University, Kremlin Bicetre, France
| | - Jordi Remon
- Department of Cancer Medicine, Gustave Roussy, Villejuif, France
| | - Christian Rolfo
- The Arthur G. James Comprehensive Cancer Center, Ohio State University, Columbus, OH, USA
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anne-Marie C Dingemans
- Department of Respiratory Medicine, Erasmus MC Cancer Institute, University Medical Center, Rotterdam, The Netherlands.
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30
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Chennareddy S, Chen S, Levinson C, Genden EM, Posner MR, Roof SA. Circulating tumor DNA in human papillomavirus-associated oropharyngeal cancer management: A systematic review. Oral Oncol 2025; 164:107262. [PMID: 40163959 DOI: 10.1016/j.oraloncology.2025.107262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Accepted: 03/14/2025] [Indexed: 04/02/2025]
Abstract
OBJECTIVE Circulating tumor DNA (ctDNA) has emerged as a promising tool in the treatment of HPV-associated oropharyngeal squamous cell cancer (OPSCC). This systematic review sought to answer the question: what is the current role of ctDNA in the diagnosis, treatment, and surveillance of HPV-associated OPSCC? DATA SOURCES Medline (Ovid), Embase (Ovid), Scopus. REVIEW METHODS Original articles studying the role of ctDNA in the diagnosis or surveillance of HPV-associated OPSCC were eligible for inclusion. Two authors independently reviewed studies for inclusion and abstracted data, including study design, characterization of liquid biopsy technology, and diagnostic outcomes. RESULTS After a preliminary screening of 441 studies, 23 were selected for inclusion. Ten studies were conducted retrospectively, and 13 were conducted prospectively. In these studies, diagnostic testing included plasma-based droplet digital polymerase chain reaction (ddPCR, n = 13), quantitative PCR (qPCR, n = 4), digital PCR (dPCR, n = 3), next-generation sequencing (NGS) (n = 3), or a ctDNA detection kit (n = 1). Diagnostic outcomes were reported for pre-diagnosis (n = 1), pre-treatment (n = 17), during treatment (n = 6), and surveillance/recurrence (n = 11) timepoints. Test sensitivities ranged from 20.6 %-100 % pre-treatment and 72 %-100 % during surveillance, while test specificities ranged from 95 %-100 % pre-treatment and 87.2 %-100 % during surveillance. CONCLUSION The majority of studied ctDNA technologies allow for detection of HPV-associated OPSCC with high diagnostic accuracy. However, heterogeneity is introduced by test type and assay used. These findings highlight the utility, as well as limitations, of ctDNA in the diagnosis, treatment monitoring, and surveillance of HPV-associated OPSCC. Future studies and clinical consensus will need to address acceptable diagnostic accuracy thresholds for clinical use.
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Affiliation(s)
- Susmita Chennareddy
- Department of Otolaryngology-Head& Neck Surgery, Mount Sinai Hospital, New York, NY, USA.
| | - Sida Chen
- Department of Otolaryngology-Head& Neck Surgery, Mount Sinai Hospital, New York, NY, USA
| | - Carrie Levinson
- Gustave L. and Janet W. Levy Library, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric M Genden
- Department of Otolaryngology-Head& Neck Surgery, Mount Sinai Hospital, New York, NY, USA
| | - Marshall R Posner
- TGH/Cancer Center of South Florida, USA; University of Southern Florida, USA
| | - Scott A Roof
- Department of Otolaryngology-Head& Neck Surgery, Mount Sinai Hospital, New York, NY, USA
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31
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Ali MF, Riviere-Cazaux C, Johnson SH, Salvatori R, Penheiter AR, Smadbeck JB, Murphy SJ, Harris FR, McCune LF, Carlstrom LP, Barrett MT, Kosari F, Jones LA, Ida C, Borad MJ, Bendok BR, Quiñones-Hinojosa A, Porter AB, Mrugala MM, Jaeckle KA, Anastasiadis PZ, Kizilbash SH, Cheville JC, Routman DM, Burns TC, Vasmatzis G. Personalized Tumor-Specific Amplified DNA Junctions in Peripheral Blood of Patients with High-Grade Gliomas. Clin Cancer Res 2025; 31:1700-1710. [PMID: 40019927 PMCID: PMC12010965 DOI: 10.1158/1078-0432.ccr-24-3233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2024] [Revised: 12/30/2024] [Accepted: 02/26/2025] [Indexed: 03/06/2025]
Abstract
PURPOSE Monitoring disease progression in patients with high-grade gliomas (HGG) is challenging due to treatment-related changes in imaging and the requirement for neurosurgical intervention to obtain diagnostic tissue. DNA junctions in HGG often amplify oncogenes, making these DNA fragments potentially more abundant in blood than monoallelic mutations. In this study, we piloted a cell-free DNA approach for disease detection in the plasma of patients with HGG by leveraging patient-specific DNA junctions associated with oncogene amplifications. EXPERIMENTAL DESIGN Whole-genome sequencing of grade 3 or 4 isocitrate dehydrogenase-mutant or wild-type astrocytomas was utilized to identify amplified junctions. Individualized qPCR assays were developed using patient-specific primers designed for the amplified junction. ctDNA levels containing these junctions were measured in patient plasma samples. RESULTS Unique amplified junctions were evaluated by individualized semi-qPCR assays in presurgical plasma of 18 patients, 15 with tumor-associated focal amplifications and three without tumor-associated focal amplifications. high copy-number junctions were robustly detected in the plasma of 14 of 15 (93.3%) patients with amplified junctions and none of the controls. Changes in junction abundance correlated with disease trajectory in serial plasma samples from five patients, including increased abundance of amplified junctions preceding radiographic disease progression. CONCLUSIONS In patients with grade 3 or 4 astrocytomas who had tumor-associated amplifications, patient-specific amplified junctions were successfully detected in assayed plasma from most patients. Longitudinal analysis of plasma samples correlated with disease trajectory, including cytoreduction and progression.
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Affiliation(s)
- Mohamed F. Ali
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Sarah H. Johnson
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Rebecca Salvatori
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Alan R. Penheiter
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - James B. Smadbeck
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Stephen J. Murphy
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Faye R. Harris
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Lex F. McCune
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | | | - Michael T. Barrett
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Scottsdale, Arizona
| | - Farhad Kosari
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Leila A. Jones
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Cristiane Ida
- Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Mitesh J. Borad
- Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona
| | - Bernard R. Bendok
- Department of Neurological Surgery, Mayo Clinic, Phoenix, Arizona
- Neurosurgery Simulation and Innovation Laboratory, Mayo Clinic, Phoenix, Arizona
- Precision Neuro-Therapeutics Innovation Laboratory, Mayo Clinic, Phoenix, Arizona
- Department of Radiology, Mayo Clinic, Rochester, Minnesota
- Department of Otolaryngology–Head and Neck Surgery, Mayo Clinic, Phoenix, Arizona
| | | | | | | | | | | | | | - John C. Cheville
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
- Department of Lab Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - David M. Routman
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Terry C. Burns
- Department of Neurologic Surgery, Mayo Clinic, Rochester, Minnesota
| | - George Vasmatzis
- Center for Individualized Medicine and Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
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32
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Cheng AP, Widman AJ, Arora A, Rusinek I, Sossin A, Rajagopalan S, Midler N, Hooper WF, Murray RM, Halmos D, Langanay T, Chu H, Inghirami G, Potenski C, Germer S, Marton M, Manaa D, Helland A, Furatero R, McClintock J, Winterkorn L, Steinsnyder Z, Wang Y, Alimohamed AI, Malbari MS, Saxena A, Callahan MK, Frederick DT, Spain L, Sigouros M, Manohar J, King A, Wilkes D, Otilano J, Elemento O, Mosquera JM, Jaimovich A, Lipson D, Turajlic S, Zody MC, Altorki NK, Wolchok JD, Postow MA, Robine N, Faltas BM, Boland G, Landau DA. Error-corrected flow-based sequencing at whole-genome scale and its application to circulating cell-free DNA profiling. Nat Methods 2025; 22:973-981. [PMID: 40217113 PMCID: PMC12077166 DOI: 10.1038/s41592-025-02648-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 03/04/2025] [Indexed: 05/15/2025]
Abstract
Differentiating sequencing errors from true variants is a central genomics challenge, calling for error suppression strategies that balance costs and sensitivity. For example, circulating cell-free DNA (ccfDNA) sequencing for cancer monitoring is limited by sparsity of circulating tumor DNA, abundance of genomic material in samples and preanalytical error rates. Whole-genome sequencing (WGS) can overcome the low abundance of ccfDNA by integrating signals across the mutation landscape, but higher costs limit its wide adoption. Here, we applied deep (~120×) lower-cost WGS (Ultima Genomics) for tumor-informed circulating tumor DNA detection within the part-per-million range. We further leveraged lower-cost sequencing by developing duplex error-corrected WGS of ccfDNA, achieving 7.7 × 10-7 error rates, allowing us to assess disease burden in individuals with melanoma and urothelial cancer without matched tumor sequencing. This error-corrected WGS approach will have broad applicability across genomics, allowing for accurate calling of low-abundance variants at efficient cost and enabling deeper mapping of somatic mosaicism as an emerging central aspect of aging and disease.
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Affiliation(s)
- Alexandre Pellan Cheng
- New York Genome Center, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
- Département de Génie des Systèmes, École de Technologie Supérieure, Montréal, Québec, Canada.
- Axe Cancer, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), Montréal, Québec, Canada.
| | - Adam J Widman
- New York Genome Center, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Anushri Arora
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Aaron Sossin
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Srinivas Rajagopalan
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nicholas Midler
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Rebecca M Murray
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Daniel Halmos
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Theophile Langanay
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Hoyin Chu
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Giorgio Inghirami
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Catherine Potenski
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Dina Manaa
- New York Genome Center, New York, NY, USA
| | | | | | | | | | | | - Yohyoh Wang
- New York Genome Center, New York, NY, USA
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Asrar I Alimohamed
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Murtaza S Malbari
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Ashish Saxena
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | - Dennie T Frederick
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Lavinia Spain
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Michael Sigouros
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jyothi Manohar
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Abigail King
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - David Wilkes
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - John Otilano
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Juan Miguel Mosquera
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | | | | | - Samra Turajlic
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
- Renal and Skin Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | | | - Nasser K Altorki
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Jedd D Wolchok
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Ludwig Institute for Cancer Research, New York, NY, USA
| | - Michael A Postow
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Bishoy M Faltas
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Genevieve Boland
- Mass General Cancer Center, Massachusetts General Hospital, Boston, MA, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY, USA.
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Szeto S, Kytölä S, Erkan EP, Ahtiainen M, Mecklin J, Kuopio T, Sallinen V, Lepistö A, Koskenvuo L, Renkonen‐Sinisalo L, Anttonen A, Heiskala K, Tulokas S, Mäkelä S, Wirta E, Tuunanen T, Salminen T, Ristimäki A, Seppälä TT. Performance Comparison of Droplet Digital PCR and Next-Generation Sequencing for Circulating Tumor DNA Detection in Non-Metastatic Rectal Cancer. Cancer Med 2025; 14:e70943. [PMID: 40346007 PMCID: PMC12062871 DOI: 10.1002/cam4.70943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 03/16/2025] [Accepted: 04/28/2025] [Indexed: 05/11/2025] Open
Abstract
BACKGROUND AND OBJECTIVES Circulating tumor DNA (ctDNA) can potentially identify rectal cancer patients benefiting from neoadjuvant and adjuvant therapy. This study compared droplet digital PCR (ddPCR) and next-generation sequencing (NGS) for ctDNA detection in localized rectal cancer before and after surgery. METHODS Pre-therapy plasma and rectal tumor samples were collected from a development group (n = 41) and a validation group (n = 26). Mutations in tumor samples were identified using NGS, and ctDNA detection was performed with both ddPCR and NGS. Recurrence was assessed 1 year after surgery in the development group. RESULTS In the development group, ddPCR detected ctDNA in 24/41 (58.5%) and NGS panel in 15/41 (36.6%; p = 0.00075) of the baseline plasma. In the validation group, 21/26 (80.8%) patients had detectable ctDNA in the pre-therapy plasma. A positive ctDNA result was associated with higher clinical tumor stage and with lymph node positivity as detected by MRI. Postoperative ddPCR did not detect ctDNA before most recurrences. CONCLUSIONS We demonstrated a practical oligomarker ctDNA test for localized rectal cancer suitable for clinical workflow, and that ddPCR detects ctNA from pre-therapy plasma at a satisfactory level in advanced rectal cancers. Detecting ctDNA with ddPCR may help to assess the local severity, but the clinical utility of this approach should be evaluated in clinical trials.
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Affiliation(s)
- Säde Szeto
- Applied Tumor Genomics Research Program, Research Program Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
| | - Soili Kytölä
- Department of Genetics, HUS Diagnostic CenterHelsinki University HospitalHelsinkiFinland
- Department of GeneticsUniversity of HelsinkiHelsinkiFinland
| | - Erdogan Pekcan Erkan
- Applied Tumor Genomics Research Program, Research Program Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University HospitalTampereFinland
| | - Maarit Ahtiainen
- Department of Molecular PathologyCentral Finland Hospital Nova, Wellbeing Services County of Central FinlandJyväskyläFinland
| | - Jukka‐Pekka Mecklin
- Department of Education and ScienceCentral Finland Hospital Nova, Wellbeing Services County of Central FinlandJyväskyläFinland
- Faculty of Sports and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Teijo Kuopio
- Department of Molecular PathologyCentral Finland Hospital Nova, Wellbeing Services County of Central FinlandJyväskyläFinland
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Ville Sallinen
- Department of Gastroenterological SurgeryHelsinki University Hospital and University of HelsinkiHelsinkiFinland
- Transplantation and Liver SurgeryHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Anna Lepistö
- Department of Gastroenterological SurgeryHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Laura Koskenvuo
- Department of Gastroenterological SurgeryHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Laura Renkonen‐Sinisalo
- Department of Gastroenterological SurgeryHelsinki University Hospital and University of HelsinkiHelsinkiFinland
| | - Anu Anttonen
- Department of OncologyHUS Comprehensive Cancer Centre and University of HelsinkiHelsinkiFinland
| | - Kukka Heiskala
- Department of OncologyHUS Comprehensive Cancer Centre and University of HelsinkiHelsinkiFinland
| | - Sanni Tulokas
- Department of OncologyHUS Comprehensive Cancer Centre and University of HelsinkiHelsinkiFinland
| | - Siru Mäkelä
- Department of OncologyHUS Comprehensive Cancer Centre and University of HelsinkiHelsinkiFinland
| | - Erkki‐Ville Wirta
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University HospitalTampereFinland
- Department of Gastroenterology and Alimentary Tract SurgeryTampere University HospitalTampereFinland
| | - Tuija Tuunanen
- Department of OncologyTampere University HospitalTampereFinland
| | - Tapio Salminen
- Department of OncologyTampere University HospitalTampereFinland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Program Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Department of PathologyHUS Diagnostic Center, Helsinki University HospitalHelsinkiFinland
| | - Toni T. Seppälä
- Applied Tumor Genomics Research Program, Research Program Unit, Faculty of MedicineUniversity of HelsinkiHelsinkiFinland
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University HospitalTampereFinland
- Department of Gastroenterology and Alimentary Tract SurgeryTampere University HospitalTampereFinland
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Rounge TB, Paulsen J. Highly sensitive method captures rare RNAs in blood to search for disease. Nature 2025; 641:599-600. [PMID: 40240820 DOI: 10.1038/d41586-025-01127-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2025]
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Choudalakis S, Kastis GA, Dikaios N. Intra-clustering analysis reveals tissue-specific mutational patterns. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2025; 263:108681. [PMID: 40050208 DOI: 10.1016/j.cmpb.2025.108681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 02/06/2025] [Accepted: 02/18/2025] [Indexed: 03/14/2025]
Abstract
BACKGROUND AND OBJECTIVE The identification of tissue-specific mutational patterns associated with cancer is challenging due to the low frequency of certain mutations and the high variability among tumors within the same cancer type. To address the inter-tumoral heterogeneity issue, our study aims to uncover infrequent mutational patterns by proposing a novel intra-clustering analysis. METHODS A Network Graph of 8303 patients and 198 genes was constructed using single-point-mutation data from The Cancer Genome Atlas (TCGA). Patient-gene groups were retrieved with the parallel use of two separate methodologies based on the: (a) Barber's modularity index, and (b) network dynamics. An intra-clustering analysis was employed to explore the patterns within smaller patient subgroups in two phases: i) to determine the significant presence of a gene with a cancer type using the Fisher's exact test and ii) to determine gene-to-gene patterns using multiple correspondence analysis and DISCOVER. The results are followed by a Benjamini-Hochberg false discovery rate of 5%. RESULTS This analysis was applied over 24 statistically meaningful groups of 2619 patients spanning 21 cancer types and it recovered 42 mutational patterns that are not reported in the TCGA consortium publications. Notably, our findings: (i) suggest that AMER1 mutations are a putative separative element between colon and rectal adenocarcinomas, (ii) highlight the significant presence of RAC1 in head and neck squamous cell carcinoma (iii) suggest that EP300 mutations in head and neck squamous cell carcinoma are irrelevant of the HPV status of the patients and (iv) show that mutational-based clusters can contain patients with contrasting genetic alterations. CONCLUSIONS The proposed intra-clustering analysis extracted statistically significant relationships within clusters, uncovering putative clinically relevant connections and disentangling mutational heterogeneity.
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Affiliation(s)
- Stamatis Choudalakis
- Mathematics Research Center, Academy of Athens, 4, Soranou Efesiou str., 11527 Athens, Greece; Medical School of Athens, National and Kapodistrian University of Athens, 75, Mikras Asias str., 11527 Athens, Greece.
| | - George A Kastis
- Mathematics Research Center, Academy of Athens, 4, Soranou Efesiou str., 11527 Athens, Greece.
| | - Nikolaos Dikaios
- Mathematics Research Center, Academy of Athens, 4, Soranou Efesiou str., 11527 Athens, Greece.
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36
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Venkataraman J, Crook T, Mokbel K. Liquid biopsy in breast cancer: a practical guide for surgeons. Gland Surg 2025; 14:754-760. [PMID: 40405948 PMCID: PMC12093179 DOI: 10.21037/gs-2025-11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Accepted: 04/17/2025] [Indexed: 05/24/2025]
Abstract
Breast cancer remains a global health challenge, requiring innovative strategies for early detection, diagnosis, treatment monitoring, and recurrence detection. Liquid biopsy-leveraging circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), microRNAs (miRNAs), exosomes, immune-based biomarkers, and tumor-educated platelets (TEPs)-has emerged as a promising tool to address these needs. CTCs and ctDNA provide critical insights into tumor heterogeneity, therapeutic targets, and resistance mechanisms, while miRNAs, exosomes, and other non-CTC-based markers reflect the tumor microenvironment and offer potential biomarkers for disease progression. Importantly, liquid biopsy offers distinct advantages in early detection and precise diagnosis, as well as in identifying therapeutic resistance in real time, allowing clinicians to adapt treatment strategies effectively. The non-invasive nature of liquid biopsy further enables real-time tumor monitoring, paving the way for personalized treatment approaches. However, several challenges hinder its routine clinical adoption, including technical complexity, economic constraints, and variations in detection sensitivity due to low biomarker abundance. Additionally, a lack of standardization in methodology and interpretation limits its widespread application. Rigorous standardization and clinical validation are essential to address these barriers, ensuring equitable access across diverse healthcare settings and transforming breast cancer care for millions worldwide. Future directions include integrating artificial intelligence and multi-omic approaches to enhance diagnostic accuracy and clinical utility.
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Affiliation(s)
- Janhavi Venkataraman
- The London Breast Institute, Princess Grace Hospital, HCA Healthcare pvt Ltd., London, UK
| | - Timothy Crook
- The London Breast Institute, Princess Grace Hospital, HCA Healthcare pvt Ltd., London, UK
| | - Kefah Mokbel
- The London Breast Institute, Princess Grace Hospital, HCA Healthcare pvt Ltd., London, UK
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37
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Dwarshuis G, Kroon LL, Brandsma D, Noske DP, Best MG, Sol N. Liquid biopsies for the monitoring of gliomas and brain metastases in adults. Acta Neuropathol 2025; 149:37. [PMID: 40285800 PMCID: PMC12033197 DOI: 10.1007/s00401-025-02880-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Revised: 04/11/2025] [Accepted: 04/12/2025] [Indexed: 04/29/2025]
Abstract
Clinical evaluation and MR imaging are currently the cornerstone of brain tumor progression monitoring. However, this is complicated by the occurrence of treatment effects such as pseudoprogression and radionecrosis. While essential for patient management, the distinction from true progression remains a significant challenge. Moreover, MR imaging provides limited real-time insights into tumor heterogeneity, genetic divergence, and treatment resistance. Although surgical histopathological biopsies can yield additional valuable information, they are not always conclusive, invasive, and therefore, not suitable for longitudinal measurements. In the era of precision medicine, there is a critical need for minimally invasive, accurate, and cost-effective monitoring methods for both primary brain tumors and brain metastases. Liquid biopsies have emerged as a potential candidate. Various analytes, including circulating nucleic acids, extracellular vesicles, platelet RNAs, and circulating tumor cells, can be obtained from whole blood and its derivatives, as well as other body fluids such as cerebrospinal fluid. In this narrative review, we outline the potential of liquid biopsies for the management of gliomas and brain metastases in adults and emphasize their utility in monitoring disease progression and treatment response. We discuss the most studied biofluids and analytes, along with their respective advantages and downsides. Furthermore, we address key considerations for future research and biobanking to pave the way for clinical implementation.
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Affiliation(s)
- Govert Dwarshuis
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Lente L Kroon
- Department of Neurology, Netherlands Cancer Institute-Antoni Van Leeuwenhoek, Amsterdam, The Netherlands
| | - Dieta Brandsma
- Department of Neurology, Netherlands Cancer Institute-Antoni Van Leeuwenhoek, Amsterdam, The Netherlands
| | - David P Noske
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Myron G Best
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Cancer Center Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands
| | - Nik Sol
- Department of Neurology, Netherlands Cancer Institute-Antoni Van Leeuwenhoek, Amsterdam, The Netherlands.
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38
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Kitagawa S, Seike M. Liquid biopsy in lung cancer. Jpn J Clin Oncol 2025; 55:453-458. [PMID: 40104865 DOI: 10.1093/jjco/hyaf013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 03/13/2025] [Indexed: 03/20/2025] Open
Abstract
Precision medicine based on biomarkers, such as genetic abnormalities and PD-L1 expression, has been established for the treatment of nonsmall cell lung cancer. Recently, liquid biopsy has emerged as a valuable and minimally invasive alternative. This method analyzes blood and other bodily fluids to detect cancer-related genetic abnormalities and molecular residual disease (MRD). Liquid biopsy, which includes testing for circulating tumor cells, circulating tumor DNA (ctDNA), and microRNA (miRNA), offers several advantages over conventional methods. It is minimally invasive, can be performed repeatedly, and provides crucial information for early cancer diagnosis, genotyping, and treatment monitoring. Elevated ctDNA levels and miRNA markers show promise for early diagnosis. Liquid biopsy complements traditional tissue biopsy during genotyping, particularly when tumor samples are insufficient. Tests such as Cobas® EGFR Mutation Test v2 and Guardant360® CDx have been shown to be effective in detecting genetic mutations and guiding treatment decisions. Although the accuracy of liquid biopsy is still lower than that of tissue biopsy, its clinical utility continues to improve. For cancer prediction recurrence and treatment monitoring, ctDNA analysis can detect MRD earlier than conventional imaging, offering potential benefits for treatment adjustment and early relapse detection. The continuous development and validation of liquid biopsy methods are essential for improving personalized lung cancer treatment strategies.
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Affiliation(s)
- Shingo Kitagawa
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
| | - Masahiro Seike
- Department of Pulmonary Medicine and Oncology, Graduate School of Medicine, Nippon Medical School, Tokyo, Japan
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39
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An Y, Feng Q, Jia L, Sha X, Zhang T, Lu L, Wang R, Bai B. Present progress in biomarker discovery of endometrial cancer by multi-omics approaches. Clin Proteomics 2025; 22:15. [PMID: 40281423 PMCID: PMC12032760 DOI: 10.1186/s12014-025-09528-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 01/14/2025] [Indexed: 04/29/2025] Open
Abstract
Endometrial cancer (EC), a prevalent and intricate disease, is associated with a poor prognosis among gynecological malignancies. Its incidence rising globally underscores the urgent need for biomarkers detection in both research and clinical settings. Over the past decade, we've witnessed rapid advancements in biological methodologies and techniques. A multitude of omics technologies, encompassing genomic/transcriptomic sequencing and proteomic/metabolomic mass spectrometry, have been extensively employed to analyze both tissue and liquid samples derived from EC patients. The integration of multi-omics data has not only broadened our understanding of the disease but also unearthed valuable biomarkers specific to EC. This review encapsulates the recent progress and future prospects in the application of multi-omics technologies in EC research, emphasizing the potential of multi-omics in uncovering novel biomarkers and enhancing clinical assessments.
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Affiliation(s)
- Yuhao An
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518020, China.
| | - Quanxin Feng
- Department of Gastrointestinal Surgery, Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, 710032, China
| | - Li Jia
- Faculty of Pharmacy and Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia
| | - Xinrui Sha
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518020, China
| | - Tuanjie Zhang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518020, China
| | - Linlin Lu
- Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China
| | - Rui Wang
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, Guangdong, 518020, China.
| | - Bin Bai
- Department of Gastrointestinal Surgery, Xijing Hospital of Digestive Diseases, Xijing Hospital, Fourth Military Medical University, Xi'an, Shanxi, 710032, China.
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40
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Netti GS, De Luca F, Camporeale V, Khalid J, Leccese G, Troise D, Sanguedolce F, Stallone G, Ranieri E. Liquid Biopsy as a New Tool for Diagnosis and Monitoring in Renal Cell Carcinoma. Cancers (Basel) 2025; 17:1442. [PMID: 40361369 PMCID: PMC12070982 DOI: 10.3390/cancers17091442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2025] [Revised: 04/19/2025] [Accepted: 04/23/2025] [Indexed: 05/15/2025] Open
Abstract
Renal cell carcinoma (RCC) presents a significant diagnostic challenge, particularly in small renal masses. The search for non-invasive screening methods and biomarkers has directed research toward liquid biopsy, which focuses on microRNAs (miRNAs), exosomes, and circulating tumor cells (CTCs). miRNAs are small non-coding RNA molecules that show considerable dysregulation in RCC, and they have potential for both diagnostic and prognostic applications. Research has highlighted their utility on biofluids, such as plasma, serum, and urine, in detecting RCC and characterizing its subtypes. Promising miRNA signatures have been associated with overall survival, suggesting their potential importance in the management of RCC. Exosomes, which carry a variety of molecular components, including miRNAs, are emerging as valuable biomarkers, whereas CTCs, released from primary tumors into the bloodstream, provide critical information on cancer progression. However, translation of these findings into clinical practice requires additional validation and standardization through large-scale studies and robust evidence. Although there are currently no approved diagnostic tests for RCC, the future potential of liquid biopsy in monitoring, treatment decision-making, and outcome prediction in patients with this disease is significant. This review examined and discussed recent developments in liquid biopsy for RCC, assessing both the strengths and limitations of these approaches for managing this disease.
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Affiliation(s)
- Giuseppe Stefano Netti
- Unit of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
| | - Federica De Luca
- Unit of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
| | - Valentina Camporeale
- Unit of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
| | - Javeria Khalid
- Unit of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
| | - Giorgia Leccese
- Unit of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
| | - Dario Troise
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Unit of Nephrology, Dialysis and Transplantation, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Renal Medicine and Baxter Novum, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, 141 52 Stockholm, Sweden
| | - Francesca Sanguedolce
- Unit of Pathology, Department of Clinical and Experimental Medicine, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
| | - Giovanni Stallone
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Unit of Nephrology, Dialysis and Transplantation, Advanced Research Center on Kidney Aging (A.R.K.A.), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
| | - Elena Ranieri
- Unit of Clinical Pathology, Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
- Center for Research and Innovation in Medicine (CREATE), Department of Medical and Surgical Sciences, University of Foggia–University Hospital “Policlinico Riuniti”, Viale Luigi Pinto, 71122 Foggia, Italy
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Tsukahara S, Shiota M, Matsumoto T, Takamatsu D, Nagakawa S, Noda N, Matsumoto S, Yagi M, Uchiumi T, Kunisaki Y, Kang D, Eto M. Monitoring circulating tumor DNA by recurrent hotspot mutations in bladder cancer. BJC REPORTS 2025; 3:26. [PMID: 40274976 PMCID: PMC12022302 DOI: 10.1038/s44276-025-00143-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2024] [Revised: 03/11/2025] [Accepted: 04/03/2025] [Indexed: 04/26/2025]
Abstract
BACKGROUND Liquid biopsy can evaluate minimally residual disease. Hotspot mutations are also common in non-coding regions among the MIBC patients. We evaluated the status of MIBC with hotspot mutations with cfDNA. METHODS Tumor and blood from MIBC patients were collected prospectively. We evaluate the VAF of mutations (TERT, PLEKHS1, ADGRG6 and WDR74) with digital PCR in tumor and cfDNA as somatic mutation. We originally designed and validated primers and probes. VAF of cfDNA and clinical imaging were matched. This study was approved by the Institutional Review Board (#2022-157). RESULT 37 MIBC patients were enrolled and 28 (76%) patients had any hotspot. Among the 21 patients of follow-up cohort, cfDNA predicted recurrence 58 days earlier than the diagnosis by CT scan. Furthermore, the detection of ctDNA at the first visit after radical cystectomy was associated with recurrence free survival (P = 0.0043) and overall survival (P = 0.017). The patient who received neoadjuvant chemotherapy (NAC) and diagnosed as ypT0 belonged to the nonrecurrence group with negative ctDNA. CONCLUSION Hotspot mutation is promising biomarker to predict earlier recurrence than CT-scan. Multiple detection of mutations in cfDNA contributes to reliable recurrence prediction.
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Affiliation(s)
- Shigehiro Tsukahara
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masaki Shiota
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
| | - Takashi Matsumoto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Dai Takamatsu
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Anatomic Pathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shohei Nagakawa
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nozomi Noda
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shinya Matsumoto
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Mikako Yagi
- Department of Health and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Uchiumi
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Department of Health and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuya Kunisaki
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Kashiigaoka Rehabilitation Hospital, Fukuoka, Japan
| | - Masatoshi Eto
- Department of Urology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Tougeron D, Louvet C, Desramé J, Evesque L, Angelergues A, Carnot A, Breysacher G, Zaanan A, Etchepare N, Mabro M, Kaluzinski L, Petorin C, Chibaudel B, Aparicio T, Bodere A, Rinaldi Y, Le Malicot K, Emile JF, Lepage C, Baures A, Djamai H, Taly V, Laurent-Puig P. Circulating tumor DNA strongly predicts efficacy of chemotherapy plus immune checkpoint inhibitors in patients with advanced gastro-esophageal adenocarcinoma. COMMUNICATIONS MEDICINE 2025; 5:136. [PMID: 40275077 PMCID: PMC12022060 DOI: 10.1038/s43856-025-00867-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Accepted: 04/14/2025] [Indexed: 04/26/2025] Open
Abstract
BACKGROUND Efficacy of 2nd line treatment in advanced gastric or gastro-esophageal junction (GEJ) adenocarcinoma remains limited with no identified strong predictor of treatment efficacy. We evaluated the prognostic value of circulating tumor DNA (ctDNA) in predicting the efficacy of immune checkpoint inhibitors (ICI) plus chemotherapy in the randomized PRODIGE 59-FFCD 1707-DURIGAST trial. METHODS ctDNA was evaluated before treatment (baseline) and at 4 weeks (before the third cycle of treatment, C3) using droplet-digital PCR assays based on the detection of CpG methylation. RESULTS Progression-free survival (PFS) and overall survival (OS) were shorter in patients with a high (>1.1 ng/mL) versus low (<1.1 ng/mL) ctDNA concentration at baseline (2.3 vs. 5.8 months; HR = 2.19; 95% CI, 1.09-4.41; p = 0.03 and 4.5 vs. 12.9 months; HR = 2.73; 95% CI, 1.29-5.75; p < 0.01), respectively, after adjustment for identified prognostic variables. Patients with a ctDNA decrease ≤75% between baseline and C3 versus a ctDNA decrease >75% had a worse objective response rate (p = 0.007), shorter PFS (2.2 vs. 7.4 months, HR = 1.90; 95% CI, 1.03-3.51; p = 0.04) and OS (6.6 vs 16.0 months; HR = 2.18; 95% CI, 1.09-4.37; p = 0.03). CONCLUSIONS An early decrease in ctDNA concentration is a strong predictor of the therapeutic efficacy of ICI plus chemotherapy in advanced gastric/GEJ adenocarcinoma. Clinical Trial Information NCT03959293 (DURIGAST).
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Affiliation(s)
- David Tougeron
- Department of Gastroenterology and Hepatology, Poitiers University Hospital, Poitiers, France.
| | - Christophe Louvet
- Department of Medical Oncology, Institute Mutualiste Montsouris, Paris, France
| | - Jérôme Desramé
- Department of Gastroenterology, Mermoz Hospital, Lyon, France
| | - Ludovic Evesque
- Department of Medical Oncology, Centre Antoine Lacassagne, Nice, France
| | | | - Aurélien Carnot
- Department of Gastroenterology and Digestive Oncology, Oscar Lambret Centre, Lille, France
| | - Gilles Breysacher
- Department of Gastroenterology and Hepatology, Colmar Hospital, Colmar, France
| | - Aziz Zaanan
- Department of Digestive Oncology, Georges Pompidou European Hospital, AP-HP, Université Paris Cité, Paris Cancer Institute CARPEM, Paris, France
| | | | - May Mabro
- Department of Oncology, Foch Hospital, Suresnes, France
| | - Laure Kaluzinski
- Department of Oncology, Cherbourg-en-Cotentin Hospital, Cherbourg-en-Cotentin, France
| | - Caroline Petorin
- Department of Oncology, Clermont-Ferrand University Hospital, Clermont-Ferrand, France
| | - Benoist Chibaudel
- Department of Oncology, Franco-Britannique Hospital - Fondation Cognacq-Jay, Levallois, France
| | - Thomas Aparicio
- Department of Gastroenterology and Digestive Oncology, Saint Louis Hospital, Paris, France
| | | | - Yves Rinaldi
- Department of Gastroenterology, Marseille European Hospital, Marseille, France
| | - Karine Le Malicot
- Fédération Francophone de Cancérologie Digestive, EPICAD INSERM LNC-UMR 1231, Bourgogne Franche-Comté University, Dijon, France
| | - Jean-François Emile
- Pathology Department, Paris-Saclay University, Versailles SQY University, EA4340-BECCOH, Assistance Publique-Hôpitaux de Paris (APHP), Ambroise-Paré Hospital, Boulogne, France
| | - Côme Lepage
- Fédération Francophone de Cancérologie Digestive, EPICAD INSERM LNC-UMR 1231, Bourgogne Franche-Comté University, Dijon, France
| | - Aurélia Baures
- Centre de recherche des cordeliers, Université Paris Cité, Sorbonne Université, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Paris, France
| | - Hanane Djamai
- Centre de recherche des cordeliers, Université Paris Cité, Sorbonne Université, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Paris, France
| | - Valérie Taly
- Centre de recherche des cordeliers, Université Paris Cité, Sorbonne Université, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Paris, France
- METHYS Dx, Paris, France
| | - Pierre Laurent-Puig
- Centre de recherche des cordeliers, Université Paris Cité, Sorbonne Université, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Paris, France
- Department of Genomic Medicine of Tumors and Cancers APHP, Institut Cancer Paris Carpem, APHP, Paris, France
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Hum M, Lee ASG. DNA methylation in breast cancer: early detection and biomarker discovery through current and emerging approaches. J Transl Med 2025; 23:465. [PMID: 40269936 PMCID: PMC12020129 DOI: 10.1186/s12967-025-06495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2024] [Accepted: 04/13/2025] [Indexed: 04/25/2025] Open
Abstract
Breast cancer remains one of the most common cancers in women worldwide. Early detection is critical for improving patient outcomes, yet current screening methods have limitations. Therefore, there is a pressing need for more sensitive and specific approaches to detect breast cancer in its earliest stages. Liquid biopsy has emerged as a promising non-invasive method for early cancer detection and management. DNA methylation, an epigenetic alteration that often precedes genetic changes, has been observed in precancerous or early cancer stages, making it a valuable biomarker. This review explores the role of DNA methylation in breast cancer and its potential for developing blood-based tests. We discuss advancements in DNA methylation detection methods, recent discoveries of potential DNA methylation biomarkers from both single-omics and multi-omics integration studies, and the role of machine learning in enhancing diagnostic accuracy. Challenges and future directions are also addressed. Although challenges remain, advances in multi-omics integration and machine learning continue to enhance the clinical potential of methylation-based biomarkers. Ongoing research is crucial to further refine these approaches and improve early detection and patient outcomes.
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Affiliation(s)
- Melissa Hum
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Republic of Singapore
| | - Ann S G Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Republic of Singapore.
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593, Singapore.
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Juthani R, Manne A. Blood-based biomarkers in pancreatic ductal adenocarcinoma: developments over the last decade and what holds for the future- a review. Front Oncol 2025; 15:1555963. [PMID: 40330826 PMCID: PMC12052548 DOI: 10.3389/fonc.2025.1555963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Accepted: 03/24/2025] [Indexed: 05/08/2025] Open
Abstract
Pancreatic Ductal Adenocarcinoma (PDAC) accounts for a significant burden of global cancer deaths worldwide. The dismal outcomes associated with PDAC can be overcome by detecting the disease early and developing tools that predict response to treatment, allowing the selection of the most optimal treatment. Over the last couple of years, significant progress has been made in the development of novel biomarkers that aid in diagnosis, prognosis, treatment selection, and monitoring response. Blood-based biomarkers offer an alternative to tissue-based diagnosis and offer immense potential in managing PDAC. In this review, we have discussed the advances in blood-based biomarkers in PDAC, such as DNA (mutations and methylations), RNA, protein biomarkers and circulating tumor cells (CTC) over the last decade and also elucidated all aspects of practical implementation of these biomarkers in clinical practice. We have also discussed implementing multiomics utilizing more than one biomarker and targeted therapies that have been developed using these biomarkers.
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Affiliation(s)
- Ronit Juthani
- Department of Medicine, Saint Vincent Hospital, Worcester, MA, United States
| | - Ashish Manne
- Department of Internal Medicine, Division of Medical Oncology at the Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
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Ghoreyshi N, Heidari R, Farhadi A, Chamanara M, Farahani N, Vahidi M, Behroozi J. Next-generation sequencing in cancer diagnosis and treatment: clinical applications and future directions. Discov Oncol 2025; 16:578. [PMID: 40253661 PMCID: PMC12009796 DOI: 10.1007/s12672-025-01816-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2024] [Accepted: 01/15/2025] [Indexed: 04/22/2025] Open
Abstract
Next-generation sequencing (NGS) has emerged as a pivotal technology in the field of oncology, transforming the approach to cancer diagnosis and treatment. This paper provides a comprehensive overview of the integration of NGS into clinical settings, emphasizing its significant contributions to precision medicine. NGS enables detailed genomic profiling of tumors, identifying genetic alterations that drive cancer progression and facilitating personalized treatment plans targeting specific mutations, thereby improving patient outcomes. This capability facilitates the development of personalized treatment plans targeting specific mutations, leading to improved patient outcomes and the potential for better prognosis. The application of NGS extends beyond identifying actionable mutations; it is instrumental in detecting hereditary cancer syndromes, thus aiding in early diagnosis and preventive strategies. Furthermore, NGS plays a crucial role in monitoring minimal residual disease, offering a sensitive method to detect cancer recurrence at an early stage. Its use in guiding immunotherapy by identifying biomarkers that predict response to treatment is also highlighted. Ethical issues related to genetic testing, such as concerns around patient consent and data privacy, are also important considerations that need to be addressed for the broader implementation of NGS. These include the complexities of data interpretation, the need for robust bioinformatics support, cost considerations, and ethical issues related to genetic testing. Addressing these challenges is essential for the widespread adoption of NGS. Looking forward, advancements such as single-cell sequencing and liquid biopsies promise to further enhance the precision of cancer diagnostics and treatment. This review emphasizes the transformative impact of NGS in oncology and advocates for its incorporation into routine clinical practice to promote molecularly driven cancer care.
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Affiliation(s)
- Nima Ghoreyshi
- Cancer Epidemiology Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Reza Heidari
- Cancer Epidemiology Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Arezoo Farhadi
- Department of Genetics and Molecular Medicine, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohsen Chamanara
- Department of Clinical Pharmacy, Faculty of Medicine, AJA University of Medical Sciences, Tehran, Iran
- Toxicology Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Nastaran Farahani
- Department of Genetics and Biotechnology, Faculty of Life Science, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Mahmood Vahidi
- Cancer Epidemiology Research Center, AJA University of Medical Sciences, Tehran, Iran.
- Department of Medical Laboratory Sciences, School of Allied Health Medicine, AJA University of Medical Sciences, Tehran, Iran.
| | - Javad Behroozi
- Cancer Epidemiology Research Center, AJA University of Medical Sciences, Tehran, Iran.
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
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Fukuda A, Mizuno T, Yoshida T, Sunami K, Kubo T, Koyama T, Yonemori K, Okusaka T, Kato K, Ohe Y, Yatabe Y, Yamamoto N. Upfront liquid biopsy in patients with advanced solid tumors who were not feasible for tissue-based next-generation sequencing. Jpn J Clin Oncol 2025:hyaf065. [PMID: 40251768 DOI: 10.1093/jjco/hyaf065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2024] [Revised: 02/03/2025] [Accepted: 04/09/2025] [Indexed: 04/21/2025] Open
Abstract
BACKGROUND Liquid biopsy has been developed as an alternative to tissue-based sequencing for detecting genomic alterations in solid tumors. However, the clinical utility of liquid biopsy in patients with solid tumors for whom tissue-based next-generation sequencing (NGS) is infeasible has not been well-characterized, particularly in previously untreated individuals. METHODS This prospective study evaluated the clinical impact of liquid biopsy, focusing on six solid tumor types. Overall, 109 patients were enrolled and underwent liquid biopsy using Guardant360 (Guardant Health, Redwood City, CA, USA). Among these, 94 (86.3%) patients were previously untreated. RESULTS The most common cancer type was non-small cell lung cancer (n = 57, 52.3%), followed by pancreatic (n = 35, 32.1%), biliary tract (n = 8, 7.3%), gastric (n = 5, 4.6%), colorectal (n = 3, 2.8%), and triple-negative breast (n = 1, 0.9%) cancers. The success rate of liquid biopsy was 99.1%, and the median turnaround time from blood collection to results was 7 days (range: 5-22 days). Actionable alterations were detected in 31 (28.4%) patients, and 8.3% of them received matched therapy based on alterations identified by liquid biopsy. Among previously untreated patients, actionable mutations were identified in 29.8%, and 8.5% received matched therapy. CONCLUSIONS In patients with advanced solid tumors for which tissue-based NGS is not feasible, performing upfront liquid biopsy could lead to the detection of actionable alterations and help guide targeted therapies. CLINICAL TRIAL REGISTRY UMIN Clinical Trials Registry (UMIN000041722).
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Affiliation(s)
- Akito Fukuda
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takaaki Mizuno
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Tatsuya Yoshida
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Kuniko Sunami
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Takashi Kubo
- Department of Laboratory Medicine, National Cancer Center Hospital, Tokyo, Japan
| | - Takafumi Koyama
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
| | - Kan Yonemori
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
- Department of Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Takuji Okusaka
- Department of Hepatobiliary and Pancreatic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Ken Kato
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
- Department of Head and Neck, Esophageal Medical Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuichiro Ohe
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Yatabe
- Department of Diagnostic Pathology, National Cancer Center Hospital, Tokyo, Japan
| | - Noboru Yamamoto
- Department of Thoracic Oncology, National Cancer Center Hospital, Tokyo, Japan
- Department of Experimental Therapeutics, National Cancer Center Hospital, Tokyo, Japan
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Liu L, He Y, Du H, Tang M, Wang T, Tan J, Zha L, Yang L, Ashrafizadeh M, Tian Y, Zhou H. Biological profile of breast cancer brain metastasis. Acta Neuropathol Commun 2025; 13:78. [PMID: 40253355 PMCID: PMC12008903 DOI: 10.1186/s40478-025-01983-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Accepted: 03/08/2025] [Indexed: 04/21/2025] Open
Abstract
Breast cancer is one of the leading causes of death worldwide. The aggressive behaviour of breast tumor results from their metastasis. Notably, the brain tissue is one of the common regions of metastasis, thereby reducing the overall survival of patients. Moreover, the metastatic tumors demonstrate poor response or resistance to therapies. In addition, breast cancer brain metastasis provides the poor prognosis of patients. Therefore, it is of importance to understand the mechanisms in breast cancer brain metastasis. Both cell lines and animal models have been developed for the evaluation of breast cancer brain metastasis. Moreover, different tumor microenvironment components and other factors such as lymphocytes and astrocytes can affect brain metastasis. The breast cancer cells can disrupt the blood-brain barrier (BBB) during their metastasis into brain, developing blood-tumor barrier to enhance carcinogenesis. The breast cancer brain metastasis can be increased by the dysregulation of chemokines, STAT3, Wnt, Notch and PI3K/Akt. On the other hand, the effective therapeutics have been developed for the brain metastasis such as introduction of nanoparticles. Moreover, the disruption of BBB by ultrasound can increase the entrance of bioactive compounds to the brain tissue. In order to improve specificity and selectivity, the nanoparticles for the delivery of therapeutics and crossing over BBB have been developed to suppress breast cancer brain metastasis.
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Affiliation(s)
- Li Liu
- Department of Oncology, Suining Central Hospital, Suning, 629000, China
| | - Yuan He
- Department of Oncology, Yunyang County People's Hospital, Chongqing, 404500, China
| | - Hongyu Du
- Department of General Medicine, The Seventh People's Hospital of Chongqing, The Central Hospital Affiliated to Chongging University of Technology, Chongqing, 400054, China
| | - Min Tang
- Department of Oncology, Chongqing General Hospital, Chongqing University, Chongqing, 401120, China
| | - Tingting Wang
- Department of Gynecology and Obstetrics, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Jieren Tan
- School of Biomedical Sciences, Hunan University, Changsha, Hunan, 410082, PR China
| | - Lisha Zha
- School of Biomedical Sciences, Hunan University, Changsha, Hunan, 410082, PR China
| | - Li Yang
- Department of Nephrology, Nanfang Hospital, Southern Medical University, No. 1838 North Guangzhou Avenue, Guangzhou, Guangdong Province, 510515, China
| | - Milad Ashrafizadeh
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University, Shandong Academy of Medical Sciences, Jinan, Shandong, 250000, China.
| | - Yu Tian
- School of Public Health, Benedictine University, No.5700 College Road, Lisle, IL, 60532, USA.
- Research Center, the Huizhou Central People's Hospital, Guangdong Medical University, Huizhou, Guangdong, China.
| | - Hui Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, No. 19 Nonglinxia Road, Guangzhou, 510080, China.
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Feng S, Liu H, Yun C, Zhu W, Pan Y. Application of EGFR-TKIs in brain tumors, a breakthrough in future? J Transl Med 2025; 23:449. [PMID: 40241139 PMCID: PMC12004797 DOI: 10.1186/s12967-025-06448-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2025] [Accepted: 04/01/2025] [Indexed: 04/18/2025] Open
Abstract
Brain tumors, both primary and secondary, represent a significant clinical challenge due to their high mortality and limited treatment options. Primary brain tumors, such as gliomas and meningiomas, and brain metastases from cancers such as non-small cell lung cancer and breast cancer require innovative therapeutic strategies. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR -TKIs) have emerged as a promising treatment option, particularly for tumors harboring EGFR mutations. This review examines the use of EGFR-TKIs in brain tumors, highlighting both laboratory and clinical research findings. In primary brain tumors and brain metastases, EGFR-TKIs have shown potential in controlling tumor growth and improving patient outcomes. Advanced applications, such as nano-formulated EGFR-TKIs and combination therapies with other pathway inhibitors, are being investigated to improve efficacy and overcome resistance. Challenges such as treatment-related events, resistance mechanisms and blood-brain barrier penetration remain significant hurdles. Addressing tumor heterogeneity through personalized medicine approaches is critical to optimizing EGFR-TKI therapies. This review highlights the need for continued research to refine these therapies and improve survival for patients with brain tumors.
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Affiliation(s)
- Shiying Feng
- Central Clinical Medical School, Baotou Medical College, Baotou, Inner Mongolia, 014040, China
- Department of Oncology, Inner Mongolia Baotou City Central Hospital, Baotou, Inner Mongolia, 014040, China
| | - Huiqin Liu
- Department of Gynecology & Obstetrics, Inner Mongolia Baotou City Central Hospital, Baotou, Inner Mongolia, 014040, China
| | - Cuilan Yun
- Department of Gynecology & Obstetrics, Inner Mongolia Baotou City Central Hospital, Baotou, Inner Mongolia, 014040, China
| | - Wei Zhu
- Department of Oncology, Inner Mongolia Baotou City Central Hospital, Baotou, Inner Mongolia, 014040, China.
| | - Yuanming Pan
- Cancer Research Center, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China.
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Chen LT, Jager M, Rebergen D, Brink GJ, van den Ende T, Vanderlinden W, Kolbeck P, Pagès-Gallego M, van der Pol Y, Besselink N, Moldovan N, Hami N, Kloosterman WP, van Laarhoven H, Mouliere F, Zweemer R, Lipfert J, Derks S, Marcozzi A, de Ridder J. Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling. Genome Res 2025; 35:886-899. [PMID: 39805703 PMCID: PMC12047234 DOI: 10.1101/gr.279144.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 01/06/2025] [Indexed: 01/16/2025]
Abstract
Shallow genome-wide cell-free DNA sequencing holds great promise for noninvasive cancer monitoring by providing reliable copy number alteration (CNA) and fragmentomic profiles. Single-nucleotide variations (SNVs) are, however, much harder to identify with low sequencing depth due to sequencing errors. Here, we present Nanopore Rolling Circle Amplification (RCA)-enhanced Consensus Sequencing (NanoRCS), which leverages RCA and consensus calling based on genome-wide long-read nanopore sequencing to enable simultaneous multimodal tumor fraction (TF) estimation through SNVs, CNAs, and fragmentomics. The efficacy of NanoRCS is tested on 18 cancer patient samples and seven healthy controls, demonstrating its ability to reliably detect TFs as low as 0.24%. In vitro experiments confirm that SNV measurements are essential for detecting TFs below 3%. NanoRCS provides an opportunity for cost-effective and rapid sample processing, which aligns well with clinical needs, particularly in settings where quick and accurate cancer monitoring is essential for personalized treatment strategies.
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Affiliation(s)
- Li-Ting Chen
- Center for Molecular Medicine University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Myrthe Jager
- Center for Molecular Medicine University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | | | - Geertruid J Brink
- Department of Gynecologic Oncology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Tom van den Ende
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, 1105 AZ, Amsterdam, The Netherlands
| | - Willem Vanderlinden
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
- School of Physics and Astronomy, University of Edinburgh, EH9 3FD Edinburgh, United Kingdom
| | - Pauline Kolbeck
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
- Department of Physics and Center for NanoScience, LMU Munich, 80799 Munich, Germany
| | - Marc Pagès-Gallego
- Center for Molecular Medicine University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Ymke van der Pol
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
- Oncode Institute, 3521 AL Utrecht, The Netherlands
| | - Norbert Moldovan
- Cancer Center Amsterdam, Imaging and Biomarkers, 1105 AZ, Amsterdam, The Netherlands
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | - Nizar Hami
- Department of Gynecologic Oncology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | | | - Hanneke van Laarhoven
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, 1105 AZ, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, 1105 AZ, Amsterdam, The Netherlands
| | - Florent Mouliere
- Cancer Center Amsterdam, Imaging and Biomarkers, 1105 AZ, Amsterdam, The Netherlands
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1105 AZ, Amsterdam, The Netherlands
- Cancer Research UK National Biomarker Centre, University of Manchester, Manchester M20 4BX, United Kingdom
| | - Ronald Zweemer
- Department of Gynecologic Oncology, University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands
| | - Jan Lipfert
- Soft Condensed Matter and Biophysics, Department of Physics and Debye Institute for Nanomaterials Science, Utrecht University, 3584 CC Utrecht, The Netherlands
| | - Sarah Derks
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Department of Pathology, Cancer Centre Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, 1105 AZ, Amsterdam, The Netherlands
| | | | - Jeroen de Ridder
- Center for Molecular Medicine University Medical Center Utrecht, Utrecht University, 3584 CX Utrecht, The Netherlands;
- Oncode Institute, 3521 AL Utrecht, The Netherlands
- Cyclomics, 3584 CG Utrecht, The Netherlands
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Tataranu LG. Liquid Biopsy as a Diagnostic and Monitoring Tool in Glioblastoma. MEDICINA (KAUNAS, LITHUANIA) 2025; 61:716. [PMID: 40283007 PMCID: PMC12028463 DOI: 10.3390/medicina61040716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2025] [Revised: 03/26/2025] [Accepted: 03/31/2025] [Indexed: 04/29/2025]
Abstract
Glioblastoma (GBM) is the most prevalent and aggressive primary central nervous system (CNS) tumor in adults. GBMs exhibit genetic and epigenetic heterogeneity, posing difficulties in surveillance and being associated with high rates of recurrence and mortality. Nevertheless, due to the high infiltrating ability of glioblastoma cells, and regardless of the considerable progress made in radiotherapeutic, chemotherapeutic, and surgical protocols, the treatment of GBM is still inefficient. Conventional diagnostic approaches, such as neuroimaging techniques and tissue biopsies, which are invasive maneuvers, present certain challenges and limitations in providing real-time information, and are incapable of differentiating pseudo-progression related to treatment from real tumor progression. Liquid biopsy, the analysis of biomarkers such as nucleic acids (DNA/RNA), circulating tumor cells (CTCs), extracellular vesicles (EVs), or tumor-educated platelets (TEPs) that are present in body fluids, provides a minimally invasive and dynamic method of diagnosis and continuous monitoring for GBM. It represents a new preferred approach that enables a superior manner to obtain data on possible tumor risk, prognosis, and recurrence assessment. This article is a literature review that aims to provide updated information about GBM biomarkers in body fluids and to analyze their clinical efficiency.
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Affiliation(s)
- Ligia Gabriela Tataranu
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
- Department of Neurosurgery, Bagdasar-Arseni Emergency Clinical Hospital, 041915 Bucharest, Romania
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