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Hanna GJ, Chang SSW, Siddiqui F, Bain PA, Takiar V, Ward MC, Shukla ME, Hu KS, Robbins J, Witek ME, Bakst R, Chandra RA, Galloway T, Margalit DN. Imaging and Biomarker Surveillance for Head and Neck Squamous Cell Carcinoma: A Systematic Review and American Radium Society Appropriate Use Criteria Statement. Int J Radiat Oncol Biol Phys 2024; 119:786-802. [PMID: 38168554 DOI: 10.1016/j.ijrobp.2023.12.024] [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: 04/18/2023] [Revised: 12/10/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
Surveillance for survivors of head and neck cancer (HNC) is focused on early detection of recurrent or second primary malignancies. After initial restaging confirms disease-free status, the use of surveillance imaging for asymptomatic patients with HNC is controversial. Our objective was to comprehensively review literature pertaining to imaging and biomarker surveillance of asymptomatic patients treated for head and neck squamous cell carcinoma and to convene a multidisciplinary expert panel to provide appropriate use criteria for surveillance in representative clinical scenarios. The evidence base for the appropriate use criteria was gathered through a librarian-mediated search of literature published from 1990 to 2022 focused on surveillance imaging and circulating tumor-specific DNA for nonmetastatic head and neck squamous cell carcinoma using MEDLINE (Ovid), Embase, Web of Science Core Collection, and the Cochrane Central Register of Controlled Trials. The systematic review was reported according to PRISMA guidelines. Using the modified Delphi process, the expert panel voted on appropriate use criteria, providing recommendations for appropriate use of surveillance imaging and human papillomavirus (HPV) circulating tumor DNA. Of 5178 studies identified, 80 met inclusion criteria (5 meta-analyses/systematic reviews, 1 randomized control trial, 1 post hoc analysis, 25 prospective, and 48 retrospective cohort studies [with ≥50 patients]), reporting on 27,525 patients. No large, randomized, prospective trials examined whether asymptomatic patients who receive surveillance imaging or HPV circulating tumor DNA monitoring benefit from earlier detection of recurrence or second primary tumors in terms of disease-specific or quality-of-life outcomes. In the absence of prospective data, surveillance imaging for HNC survivors should rely on individualized recurrence-risk assessment accounting for initial disease staging, HPV disease status, and tobacco use history. There is an emerging surveillance role for circulating tumor biomarkers.
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Affiliation(s)
- Glenn J Hanna
- Center for Head and Neck Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
| | - Steven Shih-Wei Chang
- Department of Otolaryngology Head and Neck Surgery, Henry Ford Cancer Institute and Hospital, Detroit, Michigan
| | - Farzan Siddiqui
- Department of Radiation Oncology, Henry Ford Cancer Institute and Hospital, Detroit, Michigan
| | - Paul A Bain
- Countway Library, Harvard Medical School, Boston, Massachusetts
| | - Vinita Takiar
- Department of Radiation Oncology, University of Cincinnati, Cincinnati, Ohio
| | - Matthew C Ward
- Atrium Health Levine Cancer Institute Radiation Therapy Center, Charlotte, North Carolina
| | - Monica E Shukla
- Radiation Oncology, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Kenneth S Hu
- New York University Langone Hospitals, New York, New York
| | - Jared Robbins
- Radiation Oncology, College of Medicine Tucson, University of Arizona, Tucson, Arizona
| | - Matthew E Witek
- University of Maryland School of Medicine, Baltimore, Maryland
| | - Richard Bakst
- Mount Sinai Icahn School of Medicine, New York, New York
| | - Ravi A Chandra
- Mid-Atlantic Permanente Medical Group, Kaiser Permanente Health, Rockville, Maryland
| | - Thomas Galloway
- Fox Chase Cancer Center, Temple Health, Philadelphia, Pennsylvania
| | - Danielle N Margalit
- Center for Head and Neck Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts; Department of Radiation Oncology, Dana-Farber Brigham and Women's Cancer Center, Harvard Medical School, Boston, Massachusetts
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Stutheit-Zhao EY, Sanz-Garcia E, Liu Z(A, Wong D, Marsh K, Abdul Razak AR, Spreafico A, Bedard PL, Hansen AR, Lheureux S, Torti D, Lam B, Yang SYC, Burgener J, Luo P, Zeng Y, Cheng N, Awadalla P, Bratman SV, Ohashi PS, Pugh TJ, Siu LL. Early Changes in Tumor-Naive Cell-Free Methylomes and Fragmentomes Predict Outcomes in Pembrolizumab-Treated Solid Tumors. Cancer Discov 2024; 14:1048-1063. [PMID: 38393391 PMCID: PMC11145176 DOI: 10.1158/2159-8290.cd-23-1060] [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: 10/01/2023] [Revised: 01/18/2024] [Accepted: 02/21/2024] [Indexed: 02/25/2024]
Abstract
Early kinetics of circulating tumor DNA (ctDNA) in plasma predict response to pembrolizumab but typically requires sequencing of matched tumor tissue or fixed gene panels. We analyzed genome-wide methylation and fragment-length profiles using cell-free methylated DNA immunoprecipitation and sequencing (cfMeDIP-seq) in 204 plasma samples from 87 patients before and during treatment with pembrolizumab from a pan-cancer phase II investigator-initiated trial (INSPIRE). We trained a pan-cancer methylation signature using independent methylation array data from The Cancer Genome Atlas to quantify cancer-specific methylation (CSM) and fragment-length score (FLS) for each sample. CSM and FLS are strongly correlated with tumor-informed ctDNA levels. Early kinetics of CSM predict overall survival and progression-free survival, independently of tumor type, PD-L1, and tumor mutation burden. Early kinetics of FLS are associated with overall survival independently of CSM. Our tumor-naïve mutation-agnostic ctDNA approach integrating methylomics and fragmentomics could predict outcomes in patients treated with pembrolizumab. SIGNIFICANCE Analysis of methylation and fragment length in plasma using cfMeDIP-seq provides a tumor-naive approach to measure ctDNA with results comparable with a tumor-informed bespoke ctDNA. Early kinetics within the first weeks of treatment in methylation and fragment quantity can predict outcomes with pembrolizumab in patients with various advanced solid tumors. This article is featured in Selected Articles from This Issue, p. 897.
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Affiliation(s)
- Eric Y. Stutheit-Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Enrique Sanz-Garcia
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhihui (Amy) Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Philippe L. Bedard
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Aaron R. Hansen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Stephanie Lheureux
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Shih Yu Cindy Yang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Justin Burgener
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yong Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nicholas Cheng
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Philip Awadalla
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Pamela S. Ohashi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
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Li M, Xie S, Hou T, Shao T, Kuang J, Liu C, Qu Y, Lu C, Liu J, Liu X, Zhu L, Zhu L. Circulating Tumor DNA Profiling Approach Based on In Silico Background Elimination Guides Chemotherapy in Nasopharyngeal Carcinoma. Clin Pharmacol Ther 2024; 115:993-1006. [PMID: 38037868 DOI: 10.1002/cpt.3125] [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: 08/06/2023] [Accepted: 11/17/2023] [Indexed: 12/02/2023]
Abstract
Circulating tumor DNA (ctDNA) analysis increasingly provides a promising minimally invasive alternative to tissue biopsies in precision oncology. However, there are no ctDNA analysis approaches available in nasopharyngeal carcinoma (NPC) and current methods of ctDNA mutation profiling have limited resolution because of the high background noise and false-positive rate caused by benign variants in plasma cell-free DNA (cfDNA), majorly generated during clonal hematopoiesis. Although personalized parallel white blood cell genome sequencing suppresses the noise of clonal hematopoiesis variances, the system cost and complexity restrict its extensive application in clinical settings. We developed Matched WBC Genome sequencing Independent CtDNA profiling (MaGIC) approaches, which synergically integrated a ctDNA capturing panel for a hybrid capture cfDNA deep sequencing, in silico background elimination, and a reliable readout measurement. We profiled the ctDNAs of 80 plasma samples from 40 patients with NPC before and during chemotherapy by MaGICs. In addition, the public cfDNA sequencing data and The Cancer Genome Atlas project data were analyzed by MaGICs to evaluate their application in other scenarios of patient classification. The MaGIC version-2 has the ability to predict the chemosensitivity of patients with NPC with high accuracy by utilizing a single sample of liquid biopsy from each patient prior to a standardized treatment regimen. Moreover, both versions of MaGICs are of ideal performance in the diagnosis of patients with prostate cancer by liquid biopsy and prognosis prediction of multiple cancers by tissue biopsy. This study has the potential to enhance the sensitivity and expand the application scope of ctDNA detection, independently of other paired genome sequencing methods. As a result, it might further increase the clinical utilization of liquid biopsy based on ctDNA.
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Affiliation(s)
- Ming Li
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
- Jiuquan Satellite Launch Centre, Jiuquan, China
| | - Sisi Xie
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Tao Hou
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Tong Shao
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Jingyu Kuang
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Chuanyang Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Ying Qu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Chenyu Lu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Jiali Liu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Xianling Liu
- Department of Oncology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Lingyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
| | - Lvyun Zhu
- Department of Biology and Chemistry, College of Sciences, National University of Defense Technology, Changsha, China
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4
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Payne KFB, Brotherwood P, Suriyanarayanan H, Brooks JM, Batis N, Beggs AD, Gendoo DMA, Mehanna H, Nankivell P. Circulating tumour DNA detects somatic variants contributing to spatial and temporal intra-tumoural heterogeneity in head and neck squamous cell carcinoma. Front Oncol 2024; 14:1374816. [PMID: 38846976 PMCID: PMC11154907 DOI: 10.3389/fonc.2024.1374816] [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: 01/22/2024] [Accepted: 04/09/2024] [Indexed: 06/09/2024] Open
Abstract
Background As circulating tumour DNA (ctDNA) liquid biopsy analysis is increasingly incorporated into modern oncological practice, establishing the impact of genomic intra-tumoural heterogeneity (ITH) upon data output is paramount. Despite advances in other cancer types the evidence base in head and neck squamous cell carcinoma (HNSCC) remains poor. We sought to investigate the utility of ctDNA to detect ITH in HNSCC. Methods In a pilot cohort of 9 treatment-naïve HNSCC patients, DNA from two intra-tumoural sites (core and margin) was whole-exome sequenced. A 9-gene panel was designed to perform targeted sequencing on pre-treatment plasma cell-free DNA and selected post-treatment samples. Results Rates of genomic ITH among the 9 patients was high. COSMIC variants from 19 TCGA HNSCC genes demonstrated an 86.9% heterogeneity rate (present in one tumour sub-site only). Across all patients, cell-free DNA (ctDNA) identified 12.9% (range 7.5-19.8%) of tumour-specific variants, of which 55.6% were specific to a single tumour sub-site only. CtDNA identified 79.0% (range: 55.6-90.9%) of high-frequency variants (tumour VAF>5%). Analysis of ctDNA in serial post-treatment blood samples in patients who suffered recurrence demonstrated dynamic changes in both tumour-specific and acquired variants that predicted recurrence ahead of clinical detection. Conclusion We demonstrate that a ctDNA liquid biopsy identified spatial genomic ITH in HNSCC and reliably detected high-frequency driver mutations. Serial sampling allowed post-treatment surveillance and early identification of treatment failure.
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Affiliation(s)
- Karl F. B. Payne
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Peter Brotherwood
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Harini Suriyanarayanan
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Jill M. Brooks
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Nikolaos Batis
- School of Biomedical Sciences, Institute of Clinical Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Deena M. A. Gendoo
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Institute for Interdisciplinary Data Science and AI, University of Birmingham, Birmingham, United Kingdom
| | - Hisham Mehanna
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Paul Nankivell
- Institute of Head and Neck Studies and Education, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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Sanz-Garcia E, Zou J, Avery L, Spreafico A, Waldron J, Goldstein D, Hansen A, Cho BCJ, de Almeida J, Hope A, Hosni A, Hahn E, Perez-Ordonez B, Zhao Z, Smith C, Zheng Y, Singaravelan N, Bratman SV, Siu LL. Multimodal detection of molecular residual disease in high-risk locally advanced squamous cell carcinoma of the head and neck. Cell Death Differ 2024; 31:460-468. [PMID: 38409276 PMCID: PMC11043441 DOI: 10.1038/s41418-024-01272-y] [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: 12/03/2023] [Revised: 02/11/2024] [Accepted: 02/14/2024] [Indexed: 02/28/2024] Open
Abstract
Up to 30% of patients with locally advanced head and neck squamous cell carcinoma (LA-HNSCC) relapse. Molecular residual disease (MRD) detection using multiple assays after definitive therapy has not been reported. In this study, we included patients with LA-HNSCC (stage III Human Papilloma virus (HPV)-positive, III-IVB HPV-negative) treated with curative intent. Plasma was collected pre-treatment, at 4-6 weeks (FU1) and 8-12 weeks (FU2) post-treatment. Circulating tumor DNA (ctDNA) was analyzed using a tumor-informed (RaDaR®) and a tumor-naïve (CAPP-seq) assay. HPV DNA was measured using HPV-sequencing (HPV-seq) and digital PCR (dPCR). A total of 86 plasma samples from 32 patients were analyzed; all patients with at least 1 follow-up sample. Most patients were stage III HPV-positive (50%) and received chemoradiation (78%). No patients had radiological residual disease at FU2. With a median follow-up of 25 months, there were 7 clinical relapses. ctDNA at baseline was detected in 15/17 (88%) by RaDaR and was not associated with recurrence free survival (RFS). Two patients relapsed within a year after definitive therapy and showed MRD at FU2 using RaDaR; detection of ctDNA during follow-up was associated with shorter RFS (p < 0.001). ctDNA detection by CAPP-seq pre-treatment and during follow-up was not associated with RFS (p = 0.09). HPV DNA using HPV-seq or dPCR during follow-up was associated with shorter RFS (p < 0.001). Sensitivity and specificity for MRD at FU2 using RaDaR was 40% and 100% versus 20 and 90.5% using CAPP-seq. Sensitivity and specificity for MRD during follow-up using HPV-seq was 100% and 91.7% versus 50% and 100% using dPCR. In conclusion, HPV DNA and ctDNA can be detected in LA-HNSCC before definitive therapy. The RaDaR assay but not CAPP-seq may detect MRD in patients who relapse within 1 year. HPV-seq may be more sensitive than dPCR for MRD detection.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Jinfeng Zou
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Lisa Avery
- Department of Biostatistics, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - John Waldron
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - David Goldstein
- Department of Surgical Oncology, Division of ENT, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Aaron Hansen
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - B C John Cho
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - John de Almeida
- Department of Surgical Oncology, Division of ENT, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Andrew Hope
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Ali Hosni
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Ezra Hahn
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Bayardo Perez-Ordonez
- Department of Pathology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | | | - Yangqiao Zheng
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Nitthusha Singaravelan
- Cancer Genomics Program, Princess Margaret Cancer Center, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Research Institute, University Health Network, University of Toronto, Toronto, ON, Canada
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada
| | - Lillian L Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, ON, Canada.
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6
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Passaro A, Al Bakir M, Hamilton EG, Diehn M, André F, Roy-Chowdhuri S, Mountzios G, Wistuba II, Swanton C, Peters S. Cancer biomarkers: Emerging trends and clinical implications for personalized treatment. Cell 2024; 187:1617-1635. [PMID: 38552610 PMCID: PMC7616034 DOI: 10.1016/j.cell.2024.02.041] [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: 12/13/2023] [Revised: 02/21/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
The integration of cancer biomarkers into oncology has revolutionized cancer treatment, yielding remarkable advancements in cancer therapeutics and the prognosis of cancer patients. The development of personalized medicine represents a turning point and a new paradigm in cancer management, as biomarkers enable oncologists to tailor treatments based on the unique molecular profile of each patient's tumor. In this review, we discuss the scientific milestones of cancer biomarkers and explore future possibilities to improve the management of patients with solid tumors. This progress is primarily attributed to the biological characterization of cancers, advancements in testing methodologies, elucidation of the immune microenvironment, and the ability to profile circulating tumor fractions. Integrating these insights promises to continually advance the precision oncology field, fostering better patient outcomes.
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Affiliation(s)
- Antonio Passaro
- Division of Thoracic Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Maise Al Bakir
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emily G Hamilton
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Fabrice André
- Gustave-Roussy Cancer Center, Paris Saclay University, Villejuif, France
| | - Sinchita Roy-Chowdhuri
- Department of Anatomic Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giannis Mountzios
- Fourth Department of Medical Oncology and Clinical Trials Unit, Henry Dunant Hospital Center, Athens, Greece
| | - Ignacio I Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK; Department of Oncology, University College London Hospitals, London, UK
| | - Solange Peters
- Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland.
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7
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Murray JC, Sivapalan L, Hummelink K, Balan A, White JR, Niknafs N, Rhymee L, Pereira G, Rao N, Weksler B, Bahary N, Phallen J, Leal A, Bartlett DL, Marrone KA, Naidoo J, Goel A, Levy B, Rosner S, Hann CL, Scott SC, Feliciano J, Lam VK, Ettinger DS, Li QK, Illei PB, Monkhorst K, Scharpf RB, Brahmer JR, Velculescu VE, Zaidi AH, Forde PM, Anagnostou V. Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer. Clin Cancer Res 2024; 30:389-403. [PMID: 37939140 PMCID: PMC10792359 DOI: 10.1158/1078-0432.ccr-23-1469] [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: 05/26/2023] [Revised: 09/05/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
PURPOSE Although immunotherapy is the mainstay of therapy for advanced non-small cell lung cancer (NSCLC), robust biomarkers of clinical response are lacking. The heterogeneity of clinical responses together with the limited value of radiographic response assessments to timely and accurately predict therapeutic effect-especially in the setting of stable disease-calls for the development of molecularly informed real-time minimally invasive approaches. In addition to capturing tumor regression, liquid biopsies may be informative in capturing immune-related adverse events (irAE). EXPERIMENTAL DESIGN We investigated longitudinal changes in circulating tumor DNA (ctDNA) in patients with metastatic NSCLC who received immunotherapy-based regimens. Using ctDNA targeted error-correction sequencing together with matched sequencing of white blood cells and tumor tissue, we tracked serial changes in cell-free tumor load (cfTL) and determined molecular response. Peripheral T-cell repertoire dynamics were serially assessed and evaluated together with plasma protein expression profiles. RESULTS Molecular response, defined as complete clearance of cfTL, was significantly associated with progression-free (log-rank P = 0.0003) and overall survival (log-rank P = 0.01) and was particularly informative in capturing differential survival outcomes among patients with radiographically stable disease. For patients who developed irAEs, on-treatment peripheral blood T-cell repertoire reshaping, assessed by significant T-cell receptor (TCR) clonotypic expansions and regressions, was identified on average 5 months prior to clinical diagnosis of an irAE. CONCLUSIONS Molecular responses assist with the interpretation of heterogeneous clinical responses, especially for patients with stable disease. Our complementary assessment of the peripheral tumor and immune compartments provides an approach for monitoring of clinical benefits and irAEs during immunotherapy.
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Affiliation(s)
- Joseph C. Murray
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Lung Cancer Precision Medicine Center of Excellence, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lavanya Sivapalan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karlijn Hummelink
- Antoni van Leeuwenhoek Nederlands Kanker Instituut, Amsterdam, the Netherlands
| | - Archana Balan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - James R. White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Lamia Rhymee
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Gavin Pereira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Nisha Rao
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Benny Weksler
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Nathan Bahary
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Jillian Phallen
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alessandro Leal
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David L. Bartlett
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Kristen A. Marrone
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Lung Cancer Precision Medicine Center of Excellence, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jarushka Naidoo
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Beaumont RCSI Cancer Centre, Dublin, Ireland
| | - Akul Goel
- California Institute of Technology, 1200 E California Blvd, Pasadena, California
| | - Benjamin Levy
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Samuel Rosner
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine L. Hann
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Susan C. Scott
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Josephine Feliciano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Vincent K. Lam
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David S. Ettinger
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Qing Kay Li
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Peter B. Illei
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Kim Monkhorst
- Antoni van Leeuwenhoek Nederlands Kanker Instituut, Amsterdam, the Netherlands
| | - Robert B. Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Julie R. Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Lung Cancer Precision Medicine Center of Excellence, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Victor E. Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ali H. Zaidi
- Allegheny Health Network Cancer Institute, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Patrick M. Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, Maryland
- The Lung Cancer Precision Medicine Center of Excellence, Johns Hopkins University School of Medicine, Baltimore, Maryland
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8
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Moldovan N, van der Pol Y, van den Ende T, Boers D, Verkuijlen S, Creemers A, Ramaker J, Vu T, Bootsma S, Lenos KJ, Vermeulen L, Fransen MF, Pegtel M, Bahce I, van Laarhoven H, Mouliere F. Multi-modal cell-free DNA genomic and fragmentomic patterns enhance cancer survival and recurrence analysis. Cell Rep Med 2024; 5:101349. [PMID: 38128532 PMCID: PMC10829758 DOI: 10.1016/j.xcrm.2023.101349] [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: 02/03/2023] [Revised: 09/22/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
The structure of cell-free DNA (cfDNA) is altered in the blood of patients with cancer. From whole-genome sequencing, we retrieve the cfDNA fragment-end composition using a new software (FrEIA [fragment end integrated analysis]), as well as the cfDNA size and tumor fraction in three independent cohorts (n = 925 cancer from >10 types and 321 control samples). At 95% specificity, we detect 72% cancer samples using at least one cfDNA measure, including 64% early-stage cancer (n = 220). cfDNA detection correlates with a shorter overall (p = 0.0086) and recurrence-free (p = 0.017) survival in patients with resectable esophageal adenocarcinoma. Integrating cfDNA measures with machine learning in an independent test set (n = 396 cancer, 90 controls) achieve a detection accuracy of 82% and area under the receiver operating characteristic curve of 0.96. In conclusion, harnessing the biological features of cfDNA can improve, at no extra cost, the diagnostic performance of liquid biopsies.
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Affiliation(s)
- Norbert Moldovan
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Ymke van der Pol
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Tom van den Ende
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Dries Boers
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Sandra Verkuijlen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Aafke Creemers
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Jip Ramaker
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Trang Vu
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Sanne Bootsma
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Kristiaan J Lenos
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Louis Vermeulen
- Amsterdam UMC, University of Amsterdam, Center for Experimental and Molecular Medicine, Laboratory for Experimental Oncology and Radiobiology, Amsterdam, the Netherlands; Cancer Center Amsterdam, Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands; Oncode Institute, Amsterdam, the Netherlands
| | - Marieke F Fransen
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Centre Amsterdam, Amsterdam, the Netherlands
| | - Michiel Pegtel
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - Idris Bahce
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pulmonology, Cancer Centre Amsterdam, Amsterdam, the Netherlands
| | - Hanneke van Laarhoven
- Amsterdam UMC, University of Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam, the Netherlands
| | - Florent Mouliere
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Cancer Centre Amsterdam, Amsterdam, the Netherlands; Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands.
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9
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Sacdalan DB, Ul Haq S, Lok BH. Plasma Cell-Free Tumor Methylome as a Biomarker in Solid Tumors: Biology and Applications. Curr Oncol 2024; 31:482-500. [PMID: 38248118 PMCID: PMC10814449 DOI: 10.3390/curroncol31010033] [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: 11/24/2023] [Revised: 12/30/2023] [Accepted: 01/10/2024] [Indexed: 01/23/2024] Open
Abstract
DNA methylation is a fundamental mechanism of epigenetic control in cells and its dysregulation is strongly implicated in cancer development. Cancers possess an extensively hypomethylated genome with focal regions of hypermethylation at CPG islands. Due to the highly conserved nature of cancer-specific methylation, its detection in cell-free DNA in plasma using liquid biopsies constitutes an area of interest in biomarker research. The advent of next-generation sequencing and newer computational technologies have allowed for the development of diagnostic and prognostic biomarkers that utilize methylation profiling to diagnose disease and stratify risk. Methylome-based predictive biomarkers can determine the response to anti-cancer therapy. An additional emerging application of these biomarkers is in minimal residual disease monitoring. Several key challenges need to be addressed before cfDNA-based methylation biomarkers become fully integrated into practice. The first relates to the biology and stability of cfDNA. The second concerns the clinical validity and generalizability of methylation-based assays, many of which are cancer type-specific. The third involves their practicability, which is a stumbling block for translating technologies from bench to clinic. Future work on developing pan-cancer assays with their respective validities confirmed using well-designed, prospective clinical trials is crucial in pushing for the greater use of these tools in oncology.
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Affiliation(s)
- Danielle Benedict Sacdalan
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
| | - Sami Ul Haq
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Schulich School of Medicine & Dentistry, Western University, 1151 Richmond St, London, ON N6A 5C1, Canada
| | - Benjamin H. Lok
- Institute of Medical Science, Temerty Faculty of Medicine, University of Toronto, 1 King’s College Circle, Medical Sciences Building, Room 2374, Toronto, ON M5S 1A8, Canada
- Radiation Medicine Program, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5G 2C4, Canada
- Department of Medical Biophysics, Temerty Faculty of Medicine, University of Toronto, 101 College Street, Room 15-701, Toronto, ON M5G 1L7, Canada
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10
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Wong D, Luo P, Oldfield LE, Gong H, Brunga L, Rabinowicz R, Subasri V, Chan C, Downs T, Farncombe KM, Luu B, Norman M, Sobotka JA, Uju P, Eagles J, Pedersen S, Wellum J, Danesh A, Prokopec SD, Stutheit-Zhao EY, Znassi N, Heisler LE, Jovelin R, Lam B, Lujan Toro BE, Marsh K, Sundaravadanam Y, Torti D, Man C, Goldenberg A, Xu W, Veit-Haibach P, Doria AS, Malkin D, Kim RH, Pugh TJ. Early Cancer Detection in Li-Fraumeni Syndrome with Cell-Free DNA. Cancer Discov 2024; 14:104-119. [PMID: 37874259 PMCID: PMC10784744 DOI: 10.1158/2159-8290.cd-23-0456] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/07/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
People with Li-Fraumeni syndrome (LFS) harbor a germline pathogenic variant in the TP53 tumor suppressor gene, face a near 100% lifetime risk of cancer, and routinely undergo intensive surveillance protocols. Liquid biopsy has become an attractive tool for a range of clinical applications, including early cancer detection. Here, we provide a proof-of-principle for a multimodal liquid biopsy assay that integrates a targeted gene panel, shallow whole-genome, and cell-free methylated DNA immunoprecipitation sequencing for the early detection of cancer in a longitudinal cohort of 89 LFS patients. Multimodal analysis increased our detection rate in patients with an active cancer diagnosis over uni-modal analysis and was able to detect cancer-associated signal(s) in carriers prior to diagnosis with conventional screening (positive predictive value = 67.6%, negative predictive value = 96.5%). Although adoption of liquid biopsy into current surveillance will require further clinical validation, this study provides a framework for individuals with LFS. SIGNIFICANCE By utilizing an integrated cell-free DNA approach, liquid biopsy shows earlier detection of cancer in patients with LFS compared with current clinical surveillance methods such as imaging. Liquid biopsy provides improved accessibility and sensitivity, complementing current clinical surveillance methods to provide better care for these patients. See related commentary by Latham et al., p. 23. This article is featured in Selected Articles from This Issue, p. 5.
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Affiliation(s)
- Derek Wong
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Ping Luo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Leslie E. Oldfield
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Haifan Gong
- The Hospital for Sick Children, Toronto, Canada
| | | | | | - Vallijah Subasri
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Clarissa Chan
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Tiana Downs
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | - Beatrice Luu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Maia Norman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Julia A. Sobotka
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Precious Uju
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Jenna Eagles
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Stephanie Pedersen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Johanna Wellum
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Nadia Znassi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
| | | | | | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Kayla Marsh
- Ontario Institute for Cancer Research, Toronto, Canada
| | | | - Dax Torti
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Carina Man
- The Hospital for Sick Children, Toronto, Canada
| | - Anna Goldenberg
- The Hospital for Sick Children, Toronto, Canada
- Vector Institute, Toronto, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Patrick Veit-Haibach
- Joint Department of Medical Imaging, Toronto General Hospital, University Health Network, University of Toronto, Toronto, Canada
| | | | - David Malkin
- The Hospital for Sick Children, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Raymond H. Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- The Hospital for Sick Children, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Ontario Institute for Cancer Research, Toronto, Canada
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11
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Dong Q, Chen C, Hu Y, Zhang W, Yang X, Qi Y, Zhu C, Chen X, Shen X, Ji W. Clinical application of molecular residual disease detection by circulation tumor DNA in solid cancers and a comparison of technologies: review article. Cancer Biol Ther 2023; 24:2274123. [PMID: 37955635 PMCID: PMC10653633 DOI: 10.1080/15384047.2023.2274123] [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: 05/11/2023] [Accepted: 08/04/2023] [Indexed: 11/14/2023] Open
Abstract
Molecular residual disease (MRD), detected by circulating tumor DNA (ctDNA) can be involved in the entire process of solid tumor management, including recurrence prediction, efficacy evaluation, and risk stratification. Currently, the detection technologies are divided into two main categories, as follows: tumor-agnostic and tumor informed. Tumor-informed assay obtains mutation information by sequencing tumor tissue samples before blood MRD monitoring, followed by formulation of a personalized MRD panel. Tumor-agnostic assays are carried out using a fixed panel without the mutation information from primary tumor tissue. The choice of testing strategy may depend on the level of evidence from ongoing randomized clinical trials, investigator preference, cost-effectiveness, patient economics, and availability of tumor tissue. The review describes the difference between tumor informed and tumor agnostic detection. In addition, the clinical application of ctDNA MRD in solid tumors was introduced, with emphasis on lung cancer, colorectal cancer, Urinary system cancer, and breast cancer.
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Affiliation(s)
- Qiantong Dong
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Chenbin Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yuanbo Hu
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiteng Zhang
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xinxin Yang
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Yingxue Qi
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Chan Zhu
- The Medical Department, Jiangsu Simcere Diagnostics Co.Ltd, The state Key Laboratory of Neurology and Oncology Drug Development, Nanjing, China
| | - Xiaodong Chen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
| | - Xian Shen
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
| | - Weiping Ji
- Department of Gastrointestinal Surveillance, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Lucheng District, Wenzhou, Zhejiang, China
- Department of Gastrointestinal Surveillance, The First Affiliated Hospital of Wenzhou Medical University, Ouhai District, Wenzhou City, Zhejiang, China
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12
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Honoré N, van Marcke C, Galot R, Helaers R, Ambroise J, van Maanen A, Mendola A, Dahou H, Marbaix E, Van Eeckhout P, Longton E, Magremanne M, Schmitz S, Limaye N, Machiels JP. Tumor-agnostic plasma assay for circulating tumor DNA detects minimal residual disease and predicts outcome in locally advanced squamous cell carcinoma of the head and neck. Ann Oncol 2023; 34:1175-1186. [PMID: 37879442 DOI: 10.1016/j.annonc.2023.09.3102] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/08/2023] [Accepted: 09/11/2023] [Indexed: 10/27/2023] Open
Abstract
BACKGROUND Forty to fifty percent of patients with locally advanced squamous cell carcinoma of the head and neck (LA SCCHN) relapse despite multimodal treatment. Circulating tumor DNA (ctDNA) has the potential to detect minimal residual disease (MRD) after curative-intent therapy and to identify earlier which patients will progress. We developed a tumor-agnostic plasma ctDNA assay to detect MRD in unselected LA SCCHN with the aim of predicting progression-free survival (PFS) and overall survival without the need for tumor sequencing. PATIENTS AND METHODS A 26-gene next-generation sequencing panel was constructed that included the most frequently mutated genes in SCCHN and two HPV-16 genes. MRD was assessed in each patient through an in-house informatic workflow informed by somatic mutations identified in the corresponding pre-treatment plasma sample. The presence of MRD was defined as the detection of ctDNA in one plasma sample collected within 1-12 weeks of the end of curative treatment. The primary endpoint was the PFS rate at 2 years. At least 32 patients were planned for inclusion with the hypothesis that PFS at 2 years was >80% in MRD-negative patients and <30% in MRD-positive patients (α = 0.05, β = 0.9). RESULTS We sequenced DNA from 116 plasma samples derived from 53 LA SCCHN patients who underwent curative-intent treatment. ctDNA was detected in 41/53 (77%) patients in the pre-treatment samples. Out of these 41 patients, 17 (41%) were MRD positive after treatment. The 2-year PFS rate was 23.53% (9.9% to 55.4%) and 86.6% (73.4% to 100%) in MRD-positive and MRD-negative patients, respectively (P < 0.05). Median survival was 28.37 months (14.30 months-not estimable) for MRD-positive patients and was not reached for the MRD-negative cohort (P = 0.011). CONCLUSIONS Our ctDNA assay detects MRD in LA SCCHN and predicts disease progression and survival without the need for tumor sequencing, making this approach easily applicable in daily practice.
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Affiliation(s)
- N Honoré
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - C van Marcke
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - R Galot
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - R Helaers
- Human Molecular Genetics, de Duve Institute, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - J Ambroise
- Center for Applied Molecular Technologies, Institute of Clinical and Experimental Research, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - A van Maanen
- Statistical Support Unit, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - A Mendola
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - H Dahou
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - E Marbaix
- Department of Pathology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - P Van Eeckhout
- Department of Pathology, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - E Longton
- Department of Radiotherapy, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - M Magremanne
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium; Department of Maxillo-facial Surgery, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - S Schmitz
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium; Department of ENT and Head and Neck Surgery, Cliniques Universitaires Saint-Luc, Brussels, Belgium
| | - N Limaye
- Department of Genetics of Autoimmune Diseases and Cancer, de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - J-P Machiels
- Pôle oncologie, Institut de Recherche Clinique et Expérimentale, Université catholique de Louvain (UCLouvain), Brussels, Belgium; Department of Medical Oncology, Institut Roi Albert II, Cliniques universitaires Saint-Luc, Brussels, Belgium.
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13
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Rapado-González Ó, Rodríguez-Ces AM, López-López R, Suárez-Cunqueiro MM. Liquid biopsies based on cell-free DNA as a potential biomarker in head and neck cancer. JAPANESE DENTAL SCIENCE REVIEW 2023; 59:289-302. [PMID: 37680614 PMCID: PMC10480573 DOI: 10.1016/j.jdsr.2023.08.004] [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: 02/09/2023] [Revised: 07/31/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
In the era of 'precision medicine', liquid biopsies based on cell-free DNA (cfDNA) have emerged as a promising tool in the oncology field. cfDNA from cancer patients is a mixture of tumoral (ctDNA) and non-tumoral DNA originated from healthy, cancer and tumor microenvironmental cells. Apoptosis, necrosis, and active secretion from extracellular vesicles represent the main mechanisms of cfDNA release into the physiological body fluids. Focused on HNC, two main types of cfDNA can be identified: the circulating cfDNA (ccfDNA) and the salivary cfDNA (scfDNA). Numerous studies have reported on the potential of cfDNA analysis as potential diagnostic, prognostic, and monitoring biomarker for HNC. Thus, ctDNA has emerged as an attractive strategy to detect cancer specific genetic and epigenetic alterations including DNA somatic mutations and DNA methylation patterns. This review aims to provide an overview of the up-to-date studies evaluating the value of the analysis of total cfDNA, cfDNA fragment length, and ctDNA analysis at DNA mutation and methylation level in HNC patients.
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Affiliation(s)
- Óscar Rapado-González
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Ana María Rodríguez-Ces
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Santiago de Compostela, Spain
| | - Rafael López-López
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
| | - María Mercedes Suárez-Cunqueiro
- Department of Surgery and Medical-Surgical Specialties, Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), 15782 Santiago de Compostela, Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School, Universidade de Santiago de Compostela (USC), Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
- Translational Medical Oncology Group (ONCOMET), Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS), 15706 Santiago de Compostela, Spain
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14
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Temilola DO, Adeola HA, Grobbelaar J, Chetty M. Liquid Biopsy in Head and Neck Cancer: Its Present State and Future Role in Africa. Cells 2023; 12:2663. [PMID: 37998398 PMCID: PMC10670726 DOI: 10.3390/cells12222663] [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: 10/10/2023] [Revised: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023] Open
Abstract
The rising mortality and morbidity rate of head and neck cancer (HNC) in Africa has been attributed to factors such as the poor state of health infrastructures, genetics, and late presentation resulting in the delayed diagnosis of these tumors. If well harnessed, emerging molecular and omics diagnostic technologies such as liquid biopsy can potentially play a major role in optimizing the management of HNC in Africa. However, to successfully apply liquid biopsy technology in the management of HNC in Africa, factors such as genetic, socioeconomic, environmental, and cultural acceptability of the technology must be given due consideration. This review outlines the role of circulating molecules such as tumor cells, tumor DNA, tumor RNA, proteins, and exosomes, in liquid biopsy technology for the management of HNC with a focus on studies conducted in Africa. The present state and the potential opportunities for the future use of liquid biopsy technology in the effective management of HNC in resource-limited settings such as Africa is further discussed.
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Affiliation(s)
- Dada Oluwaseyi Temilola
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Henry Ademola Adeola
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town 7925, South Africa
| | - Johan Grobbelaar
- Division of Otorhinolaryngology, Department of Surgical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg Hospital, Cape Town 7505, South Africa;
| | - Manogari Chetty
- Department of Craniofacial Biology, Faculty of Dentistry, University of the Western Cape, Tygerberg Hospital, Cape Town 7505, South Africa;
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15
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van den Ende T, van der Pol Y, Creemers A, Moldovan N, Boers D, van Berge Henegouwen MI, Hulshof MC, Cillessen SA, van Grieken NC, Pegtel DM, Derks S, Bijlsma MF, Mouliere F, van Laarhoven HW. Genome-wide and panel-based cell-free DNA characterization of patients with resectable esophageal adenocarcinoma. J Pathol 2023; 261:286-297. [PMID: 37615198 DOI: 10.1002/path.6175] [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: 03/13/2023] [Revised: 06/08/2023] [Accepted: 07/06/2023] [Indexed: 08/25/2023]
Abstract
Circulating tumor DNA (ctDNA) holds promise in resectable esophageal adenocarcinoma (EAC) to predict patient outcome but is not yet sensitive enough to be clinically applicable. Our aim was to combine ctDNA mutation data with shallow whole-genome sequencing (sWGS)-derived copy number tumor fraction estimates (ichorCNA) to improve pathological response and survival prediction in EAC. In total, 111 stage II/III EAC patients with baseline (n = 111), post-neoadjuvant chemoradiotherapy (nCRT) (n = 68), and pre-surgery (n = 92) plasma samples were used for ctDNA characterization. sWGS (<5× coverage) was performed on all time-point samples, and copy number aberrations were estimated using ichorCNA. Baseline and pre-surgery samples were sequenced using a custom amplicon panel for mutation detection. Detection of baseline ctDNA was successful in 44.3% of patients by amplicon sequencing and 10.5% by ichorCNA. Combining both, ctDNA could be detected in 50.5% of patients. Baseline ctDNA positivity was related to higher T stage (cT3, 4) (p = 0.017). There was no relationship between pathological response and baseline ctDNA positivity. However, baseline ctDNA metrics (variant allele frequency > 1% or ichorCNA > 3%) were associated with a high risk of disease progression [HR = 2.23 (95% CI 1.22-4.07), p = 0.007]. The non-clearance of a baseline variant or ichorCNA > 3% in pre-surgery samples was related to early progression [HR = 4.58 (95% CI 2.22-9.46), p < 0.001]. Multi-signal analysis improves detection of ctDNA and can be used for prognostication of resectable EAC patients. Future studies should explore the potential of multi-modality sequencing for risk stratification and treatment adaptation based on ctDNA results. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Tom van den Ende
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Ymke van der Pol
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Aafke Creemers
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Norbert Moldovan
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Dries Boers
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Mark I van Berge Henegouwen
- Department of Surgery, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
| | - Maarten Ccm Hulshof
- Cancer Center Amsterdam, Cancer Treatment and Quality of Life, Amsterdam, The Netherlands
- Department of Radiotherapy, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Saskia Agm Cillessen
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - Nicole Ct van Grieken
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - D Michiel Pegtel
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Sarah Derks
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Department of Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Maarten F Bijlsma
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Florent Mouliere
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
- Department of Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
| | - Hanneke Wm van Laarhoven
- Department of Medical Oncology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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16
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Anagnostou V, Ho C, Nicholas G, Juergens RA, Sacher A, Fung AS, Wheatley-Price P, Laurie SA, Levy B, Brahmer JR, Balan A, Niknafs N, Avrutin E, Zhu L, Sausen M, Bradbury PA, O'Donnell-Tormey J, Gaudreau PO, Ding K, Dancey J. ctDNA response after pembrolizumab in non-small cell lung cancer: phase 2 adaptive trial results. Nat Med 2023; 29:2559-2569. [PMID: 37814061 PMCID: PMC10579094 DOI: 10.1038/s41591-023-02598-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Circulating tumor DNA (ctDNA) has shown promise in capturing primary resistance to immunotherapy. BR.36 is a multi-center, randomized, ctDNA-directed, phase 2 trial of molecular response-adaptive immuno-chemotherapy for patients with lung cancer. In the first of two independent stages, 50 patients with advanced non-small cell lung cancer received pembrolizumab as standard of care. The primary objectives of stage 1 were to ascertain ctDNA response and determine optimal timing and concordance with radiologic Response Evaluation Criteria in Solid Tumors (RECIST) response. Secondary endpoints included the evaluation of time to ctDNA response and correlation with progression-free and overall survival. Maximal mutant allele fraction clearance at the third cycle of pembrolizumab signified molecular response (mR). The trial met its primary endpoint, with a sensitivity of ctDNA response for RECIST response of 82% (90% confidence interval (CI): 52-97%) and a specificity of 75% (90% CI: 56.5-88.5%). Median time to ctDNA response was 2.1 months (90% CI: 1.5-2.6), and patients with mR attained longer progression-free survival (5.03 months versus 2.6 months) and overall survival (not reached versus 7.23 months). These findings are incorporated into the ctDNA-driven interventional molecular response-adaptive second stage of the BR.36 trial in which patients at risk of progression are randomized to treatment intensification or continuation of therapy. ClinicalTrials.gov ID: NCT04093167 .
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Affiliation(s)
- Valsamo Anagnostou
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Cheryl Ho
- BCCA-Vancouver Cancer Centre, Vancouver, BC, Canada
| | | | | | - Adrian Sacher
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Andrea S Fung
- Kingston Health Sciences Centre, Kingston, ON, Canada
| | | | | | - Benjamin Levy
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julie R Brahmer
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Archana Balan
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noushin Niknafs
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Egor Avrutin
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Liting Zhu
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Mark Sausen
- Personal Genome Diagnostics (LabCorp), Baltimore, MD, USA
| | - Penelope A Bradbury
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | | | - Keyue Ding
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Janet Dancey
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada.
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17
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Kampel L, Feldstein S, Tsuriel S, Hannes V, Carmel Neiderman NN, Horowitz G, Warshavsky A, Leider-Trejo L, Hershkovitz D, Muhanna N. Mutated TP53 in Circulating Tumor DNA as a Risk Level Biomarker in Head and Neck Squamous Cell Carcinoma Patients. Biomolecules 2023; 13:1418. [PMID: 37759818 PMCID: PMC10527516 DOI: 10.3390/biom13091418] [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: 06/25/2023] [Revised: 08/28/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
Circulating tumor DNA (ctDNA) has been suggested as a surrogate biomarker for early detection of cancer recurrence. We aimed to explore the utility of ctDNA as a noninvasive prognostic biomarker in newly diagnosed head and neck squamous cell carcinoma (HNSCC) patients. Seventy HNSCC specimens were analysed for the detection of TP53 genetic alterations utilizing next-generation sequencing (NGS). TP53 mutations were revealed in 55 (79%). Upon detection of a significant TP53 mutation, circulating cell-free DNA was scrutinized for the presence of the tumor-specific mutation. ctDNA was identified at a minimal allele frequency of 0.08% in 21 out of 30 processed plasma samples. Detectable ctDNA correlated with regional spread (N stage ≥ 1, p = 0.011) and poorer 5-year progression-free survival (20%, 95% CI 10.9 to 28.9, p = 0.034). The high-risk worst pattern of invasion (WPOI grade 4-5) and deep invasion were frequently found in patients whose ctDNA was detected (p = 0.087 and p = 0.072, respectively). Detecting mutated TP53 ctDNA was associated with poor progression-free survival and regional metastases, indicating its potential role as a prognostic biomarker. However, ctDNA detectability in early-stage disease and the mechanisms modulating its release into the bloodstream must be further elucidated.
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Affiliation(s)
- Liyona Kampel
- The Head and Neck Cancer Research Laboratory, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (L.K.); (N.N.C.N.)
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
| | - Sara Feldstein
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Shlomo Tsuriel
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Victoria Hannes
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Narin N. Carmel Neiderman
- The Head and Neck Cancer Research Laboratory, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (L.K.); (N.N.C.N.)
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
| | - Gilad Horowitz
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Anton Warshavsky
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Leonor Leider-Trejo
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Dov Hershkovitz
- The Cancer Research and Pathology Institute, Tel Aviv Sourasky Medical Center, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (S.F.); (S.T.); (V.H.); (L.L.-T.); (D.H.)
| | - Nidal Muhanna
- The Head and Neck Cancer Research Laboratory, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (L.K.); (N.N.C.N.)
- The Department of Otolaryngology, Head and Neck Surgery and Maxillofacial Surgery, The Sackler School of Medicine, Tel-Aviv University, 6 Weizman St., Tel-Aviv 6423906, Israel; (G.H.); (A.W.)
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18
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Dietrich D, Weider S, de Vos L, Vogt TJ, Färber M, Zarbl R, Hunecke A, Glosch AK, Gabrielpillai J, Bootz F, Bauernfeind FG, Kramer FJ, Kristiansen G, Brossart P, Strieth S, Franzen A. Circulating Cell-Free SEPT9 DNA Methylation in Blood Is a Biomarker for Minimal Residual Disease Detection in Head and Neck Squamous Cell Carcinoma Patients. Clin Chem 2023; 69:1050-1061. [PMID: 37477541 DOI: 10.1093/clinchem/hvad084] [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: 11/23/2022] [Accepted: 05/11/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Tumorous SEPT9 (septin 9, SEPTIN9) circulating cell-free DNA (ccfDNA) methylation in blood plasma is a powerful biomarker for diagnosis, molecular staging, prognosis, and recurrence monitoring in head and neck squamous cell carcinoma (HNSCC) patients. The present study aimed to evaluate the clinical performance of SEPT9 ccfDNA methylation to detect post-surgical minimal residual disease (MRD) in patients with localized or locally advanced HNSCC treated with curative intent. METHODS We applied quasi-digital methylation-specific real-time PCR to quantify SEPT9 ccfDNA methylation levels 2 to 30 days post-surgically in plasma from n = 219 prospectively enrolled HNSCC patients. We tested the associations of SEPT9 ccfDNA methylation with clinicopathological parameters and used Kaplan-Meier and Cox proportional hazards analyses for univariate, pairwise bivariate, and multivariate analyses of disease-free survival. RESULTS Of 219 patients, 26.5% (58/219) were post-surgically SEPT9 ccfDNA methylation positive. SEPT9 ccfDNA methylation positivity was significantly associated with tumor site, American Joint Committee on Cancer/Union for International Cancer Control (AJCC/UICC; 8th edition) tumor stage, nodal category and extracapsular extension, lymphatic and vascular invasion, and surgical margin. Bivariate Cox proportional hazards analysis proved post-surgical SEPT9 ccfDNA methylation positivity to be an independent prognostic factor tested together with AJCC/UICC tumor stage (SEPT9: hazard ratio [HR] = 2.43, 95% CI, 1.37-4.30, P = 0.002; AJCC/UICC stage: HR = 1.48, 95% CI, 1.11-1.98, P = 0.008). CONCLUSIONS Post-surgical SEPT9 ccfDNA methylation may aid to identify high-risk HNSCC patients who could benefit from an intensified adjuvant treatment and surveillance.
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Affiliation(s)
- Dimo Dietrich
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Simone Weider
- Department of Oral and Maxillofacial Surgery, University Medical Center Bonn (UKB), Bonn, Germany
| | - Luka de Vos
- Department of Dermatology and Allergology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Timo Jakob Vogt
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Moritz Färber
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Romina Zarbl
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Alina Hunecke
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Ann-Kathrin Glosch
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Jennis Gabrielpillai
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Friedrich Bootz
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Franz-Georg Bauernfeind
- Department of Oncology, Hematology and Rheumatology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Franz-Josef Kramer
- Department of Oral and Maxillofacial Surgery, University Medical Center Bonn (UKB), Bonn, Germany
| | - Glen Kristiansen
- Department of Pathology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Peter Brossart
- Department of Oncology, Hematology and Rheumatology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Sebastian Strieth
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
| | - Alina Franzen
- Department of Otorhinolaryngology, University Medical Center Bonn (UKB), Bonn, Germany
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19
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Huang X, Duijf PHG, Sriram S, Perera G, Vasani S, Kenny L, Leo P, Punyadeera C. Circulating tumour DNA alterations: emerging biomarker in head and neck squamous cell carcinoma. J Biomed Sci 2023; 30:65. [PMID: 37559138 PMCID: PMC10413618 DOI: 10.1186/s12929-023-00953-z] [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: 02/09/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023] Open
Abstract
Head and Neck cancers (HNC) are a heterogeneous group of upper aero-digestive tract cancer and account for 931,922 new cases and 467,125 deaths worldwide. About 90% of these cancers are of squamous cell origin (HNSCC). HNSCC is associated with excessive tobacco and alcohol consumption and infection with oncogenic viruses. Genotyping tumour tissue to guide clinical decision-making is becoming common practice in modern oncology, but in the management of patients with HNSCC, cytopathology or histopathology of tumour tissue remains the mainstream for diagnosis and treatment planning. Due to tumour heterogeneity and the lack of access to tumour due to its anatomical location, alternative methods to evaluate tumour activities are urgently needed. Liquid biopsy approaches can overcome issues such as tumour heterogeneity, which is associated with the analysis of small tissue biopsy. In addition, liquid biopsy offers repeat biopsy sampling, even for patients with tumours with access limitations. Liquid biopsy refers to biomarkers found in body fluids, traditionally blood, that can be sampled to provide clinically valuable information on both the patient and their underlying malignancy. To date, the majority of liquid biopsy research has focused on blood-based biomarkers, such as circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), and circulating microRNA. In this review, we will focus on ctDNA as a biomarker in HNSCC because of its robustness, its presence in many body fluids, adaptability to existing clinical laboratory-based technology platforms, and ease of collection and transportation. We will discuss mechanisms of ctDNA release into circulation, technological advances in the analysis of ctDNA, ctDNA as a biomarker in HNSCC management, and some of the challenges associated with translating ctDNA into clinical and future perspectives. ctDNA provides a minimally invasive method for HNSCC prognosis and disease surveillance and will pave the way in the future for personalized medicine, thereby significantly improving outcomes and reducing healthcare costs.
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Affiliation(s)
- Xiaomin Huang
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia
| | - Pascal H G Duijf
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Data Science, Queensland University of Technology, Brisbane, QLD, Australia
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
- University Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - Sharath Sriram
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Ganganath Perera
- Functional Materials and Microsystems Research Group and the Micro Nano Research Facility, RMIT University, Melbourne, Australia
| | - Sarju Vasani
- Department of Otolaryngology, Royal Brisbane Women's Hospital, Brisbane, QLD, Australia
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Lizbeth Kenny
- The School of Medicine, University of Queensland, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - Paul Leo
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, QLD, Australia
- Australian Translational Genomics Centre, Brisbane, QLD, Australia
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, Griffith Institute for Drug Discovery (GRIDD), School of Environment and Science, Griffith University, QLD, Brisbane, Australia.
- Menzies Health Institute Queensland (MIHQ), Griffith University, Gold coast, QLD, Australia.
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20
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Ma Y, Gan J, Bai Y, Cao D, Jiao Y. Minimal residual disease in solid tumors: an overview. Front Med 2023; 17:649-674. [PMID: 37707677 DOI: 10.1007/s11684-023-1018-6] [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: 02/22/2023] [Accepted: 06/24/2023] [Indexed: 09/15/2023]
Abstract
Minimal residual disease (MRD) is termed as the small numbers of remnant tumor cells in a subset of patients with tumors. Liquid biopsy is increasingly used for the detection of MRD, illustrating the potential of MRD detection to provide more accurate management for cancer patients. As new techniques and algorithms have enhanced the performance of MRD detection, the approach is becoming more widely and routinely used to predict the prognosis and monitor the relapse of cancer patients. In fact, MRD detection has been shown to achieve better performance than imaging methods. On this basis, rigorous investigation of MRD detection as an integral method for guiding clinical treatment has made important advances. This review summarizes the development of MRD biomarkers, techniques, and strategies for the detection of cancer, and emphasizes the application of MRD detection in solid tumors, particularly for the guidance of clinical treatment.
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Affiliation(s)
- Yarui Ma
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jingbo Gan
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yinlei Bai
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Dandan Cao
- Genetron Health (Beijing) Co. Ltd., Beijing, 102206, China
| | - Yuchen Jiao
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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21
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Heft Neal ME, Walline HM, Haring CT. Circulating Tumor DNA in Human Papillomavirus-Mediated Oropharynx Cancer: Leveraging Early Data to Inform Future Directions. Cancer J 2023; 29:215-219. [PMID: 37471611 DOI: 10.1097/ppo.0000000000000670] [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: 07/22/2023]
Abstract
ABSTRACT Circulating tumor DNA (ctDNA) has become an area of intense study in many solid malignancies including head and neck cancer. This is of particular interest for human papillomavirus-mediated oropharyngeal squamous cell carcinoma as this cohort of patients has excellent survival and is undergoing current clinical trials aimed at treatment de-escalation. Recent studies have demonstrated the prognostic implications of pretreatment ctDNA and the utility of monitoring ctDNA during and posttreatment; however, there is a need for a more critical understanding of ctDNA as it is beginning to be incorporated into clinical trials. This review discusses the current state of ctDNA in oropharynx cancer focusing on ctDNA kinetics and minimal residual disease detection and ends with a discussion of future applications.
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Affiliation(s)
| | - Heather M Walline
- From the Department of Otolaryngology-Head and Neck Surgery, University of Michigan, Ann Arbor, MI
| | - Catherine T Haring
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University, Columbus, OH
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22
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Zeng Y, Ye W, Stutheit-Zhao EY, Han M, Bratman SV, Pugh TJ, He HH. MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis. Bioinformatics 2023; 39:btad423. [PMID: 37402621 PMCID: PMC10348834 DOI: 10.1093/bioinformatics/btad423] [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: 04/04/2023] [Revised: 06/06/2023] [Accepted: 07/03/2023] [Indexed: 07/06/2023] Open
Abstract
SUMMARY Cell-free methylated DNA immunoprecipitation and high-throughput sequencing (cfMeDIP-seq) has emerged as a promising liquid biopsy technology to detect cancers and monitor treatments. While several bioinformatics tools for DNA methylation analysis have been adapted for cfMeDIP-seq data, an end-to-end pipeline and quality control framework specifically for this data type is still lacking. Here, we present the MEDIPIPE, which provides a one-stop solution for cfMeDIP-seq data quality control, methylation quantification, and sample aggregation. The major advantages of MEDIPIPE are: (i) ease of implementation and reproducibility with Snakemake containerized execution environments that will be automatically deployed via Conda; (ii) flexibility to handle different experimental settings with a single configuration file; and (iii) computationally efficiency for large-scale cfMeDIP-seq profiling data analysis and aggregation. AVAILABILITY AND IMPLEMENTATION This pipeline is an open-source software under the MIT license and it is freely available at https://github.com/pughlab/MEDIPIPE.
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Affiliation(s)
- Yong Zeng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wenbin Ye
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Eric Y Stutheit-Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Ming Han
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Housheng Hansen He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
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23
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Taylor K, Zou J, Magalhaes M, Oliva M, Spreafico A, Hansen AR, McDade SS, Coyle VM, Lawler M, Elimova E, Bratman SV, Siu LL. Circulating tumour DNA kinetics in recurrent/metastatic head and neck squamous cell cancer patients. Eur J Cancer 2023; 188:29-38. [PMID: 37182343 DOI: 10.1016/j.ejca.2023.04.014] [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: 03/10/2023] [Revised: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 05/16/2023]
Abstract
PURPOSE Immune checkpoint blockade (ICB) has become a standard of care in the treatment of recurrent/metastatic head and neck squamous cell cancer (R/M HNSCC). However, only a subset of patients benefit from treatment. Quantification of plasma circulating tumour DNA (ctDNA) levels and on-treatment kinetics may permit real-time assessment of disease burden under selective pressures of treatment. PATIENTS AND METHODS R/M HNSCC patients treated with systemic therapy, platinum-based chemotherapy (CT) or ICB, underwent serial liquid biopsy sampling. Biomarkers tested included ctDNA measured by CAncer Personalized Profiling by deep Sequencing (CAPP-Seq) and markers of host inflammation measured by neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR). RESULTS Among 53 eligible patients, 16 (30%) received CT, 30 (57%) ICB [anti-PD1/L1] monotherapy and 7 (13%) combination immunotherapy (IO). Median progression-free survival (PFS) and overall survival (OS) were 2.8 months (95% CI, 1.3-4.3) and 8.2 months (95% CI, 5.6-10.8), respectively. Seven (13%) patients experienced a partial response and 21 (40%) derived clinical benefit. At baseline, median ctDNA variant allele frequency (VAF) was 4.3%. Baseline ctDNA abundance was not associated with OS (p = 0.56) nor PFS (p = 0.54). However, a change in ctDNA VAF after one cycle of treatment (ΔVAF (T1-2)) was predictive of both PFS (p< 0.01) and OS (p< 0.01). Additionally, decrease in ΔVAF identified patients with longer OS despite early radiological progression, 8.2 vs 4.6 months, hazard ratio 0.44 (95% CI, 0.19-0.87) p = 0.03. After incorporating NLR and PLR into multivariable Cox models, ctDNA ∆VAF retained an association with OS. CONCLUSIONS Early dynamic changes in ctDNA abundance, after one cycle of treatment, compared to baseline predicted both OS and PFS in R/M HNSCC patients on systemic therapy.
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Affiliation(s)
- Kirsty Taylor
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada; Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Jinfeng Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marcos Magalhaes
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Marc Oliva
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Anna Spreafico
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Aaron R Hansen
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Simon S McDade
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Vicky M Coyle
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Mark Lawler
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, Northern Ireland, UK
| | - Elena Elimova
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Scott V Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lillian L Siu
- Division of Medical Oncology & Haematology, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
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24
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Earland N, Chen K, Semenkovich NP, Chauhan PS, Zevallos JP, Chaudhuri AA. Emerging Roles of Circulating Tumor DNA for Increased Precision and Personalization in Radiation Oncology. Semin Radiat Oncol 2023; 33:262-278. [PMID: 37331781 DOI: 10.1016/j.semradonc.2023.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Recent breakthroughs in circulating tumor DNA (ctDNA) technologies present a compelling opportunity to combine this emerging liquid biopsy approach with the field of radiogenomics, the study of how tumor genomics correlate with radiotherapy response and radiotoxicity. Canonically, ctDNA levels reflect metastatic tumor burden, although newer ultrasensitive technologies can be used after curative-intent radiotherapy of localized disease to assess ctDNA for minimal residual disease (MRD) detection or for post-treatment surveillance. Furthermore, several studies have demonstrated the potential utility of ctDNA analysis across various cancer types managed with radiotherapy or chemoradiotherapy, including sarcoma and cancers of the head and neck, lung, colon, rectum, bladder, and prostate . Additionally, because peripheral blood mononuclear cells are routinely collected alongside ctDNA to filter out mutations associated with clonal hematopoiesis, these cells are also available for single nucleotide polymorphism analysis and could potentially be used to detect patients at high risk for radiotoxicity. Lastly, future ctDNA assays will be utilized to better assess locoregional MRD in order to more precisely guide adjuvant radiotherapy after surgery in cases of localized disease, and guide ablative radiotherapy in cases of oligometastatic disease.
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Affiliation(s)
- Noah Earland
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Kevin Chen
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Nicholas P Semenkovich
- Division of Endocrinology, Metabolism, and Lipid Research, Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Pradeep S Chauhan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO
| | - Jose P Zevallos
- Department of Otolaryngology, University of Pittsburgh Medical School, Pittsburgh, PA
| | - Aadel A Chaudhuri
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO; Department of Radiation Oncology, Washington University School of Medicine, St. Louis, MO; Siteman Cancer Center, Barnes Jewish Hospital and Washington University School of Medicine, St. Louis, MO; Department of Genetics, Washington University School of Medicine, St. Louis, MO; Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO; Department of Computer Science and Engineering, Washington University in St. Louis, St. Louis, MO.
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25
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Murray JC, Sivapalan L, Hummelink K, Balan A, White JR, Niknafs N, Rhymee L, Pereira G, Rao N, Phallen J, Leal A, Bartlett DL, Marrone KA, Naidoo J, Levy B, Rosner S, Hann CL, Scott SC, Feliciano J, Lam VK, Ettinger DS, Li QK, Illei PB, Monkhorst K, Zaidi AH, Scharpf RB, Brahmer JR, Velculescu VE, Forde PM, Anagnostou V. Elucidating the heterogeneity of immunotherapy response and immune-related toxicities by longitudinal ctDNA and immune cell compartment tracking in lung cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546338. [PMID: 37425893 PMCID: PMC10327039 DOI: 10.1101/2023.06.23.546338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Purpose Although immunotherapy is the mainstay of therapy for advanced non-small cell lung cancer (NSCLC), robust biomarkers of clinical response are lacking. The heterogeneity of clinical responses together with the limited value of radiographic response assessments to timely and accurately predict therapeutic effect -especially in the setting of stable disease-call for the development of molecularly-informed real-time minimally invasive predictive biomarkers. In addition to capturing tumor regression, liquid biopsies may be informative in evaluating immune-related adverse events (irAEs). Experimental design We investigated longitudinal changes in circulating tumor DNA (ctDNA) in patients with metastatic NSCLC who received immunotherapy-based regimens. Using ctDNA targeted error-correction sequencing together with matched sequencing of white blood cells and tumor tissue, we tracked serial changes in cell-free tumor load (cfTL) and determined molecular response for each patient. Peripheral T-cell repertoire dynamics were serially assessed and evaluated together with plasma protein expression profiles. Results Molecular response, defined as complete clearance of cfTL, was significantly associated with progression-free (log-rank p=0.0003) and overall survival (log-rank p=0.01) and was particularly informative in capturing differential survival outcomes among patients with radiographically stable disease. For patients who developed irAEs, peripheral blood T-cell repertoire reshaping, assessed by significant TCR clonotypic expansions and regressions were noted on-treatment. Conclusions Molecular responses assist with interpretation of heterogeneous clinical responses especially for patients with stable disease. Our complementary assessment of the tumor and immune compartments by liquid biopsies provides an approach for monitoring of clinical benefit and immune-related toxicities for patients with NSCLC receiving immunotherapy. Statement of translational relevance Longitudinal dynamic changes in cell-free tumor load and reshaping of the peripheral T-cell repertoire capture clinical outcomes and immune-related toxicities during immunotherapy for patients with non-small cell lung cancer.
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Lin LH, Chang KW, Cheng HW, Liu CJ. Identification of Somatic Mutations in Plasma Cell-Free DNA from Patients with Metastatic Oral Squamous Cell Carcinoma. Int J Mol Sci 2023; 24:10408. [PMID: 37373553 DOI: 10.3390/ijms241210408] [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: 05/08/2023] [Revised: 06/01/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
The accurate diagnosis and treatment of oral squamous cell carcinoma (OSCC) requires an understanding of its genomic alterations. Liquid biopsies, especially cell-free DNA (cfDNA) analysis, are a minimally invasive technique used for genomic profiling. We conducted comprehensive whole-exome sequencing (WES) of 50 paired OSCC cell-free plasma with whole blood samples using multiple mutation calling pipelines and filtering criteria. Integrative Genomics Viewer (IGV) was used to validate somatic mutations. Mutation burden and mutant genes were correlated to clinico-pathological parameters. The plasma mutation burden of cfDNA was significantly associated with clinical staging and distant metastasis status. The genes TTN, PLEC, SYNE1, and USH2A were most frequently mutated in OSCC, and known driver genes, including KMT2D, LRP1B, TRRAP, and FLNA, were also significantly and frequently mutated. Additionally, the novel mutated genes CCDC168, HMCN2, STARD9, and CRAMP1 were significantly and frequently present in patients with OSCC. The mutated genes most frequently found in patients with metastatic OSCC were RORC, SLC49A3, and NUMBL. Further analysis revealed that branched-chain amino acid (BCAA) catabolism, extracellular matrix-receptor interaction, and the hypoxia-related pathway were associated with OSCC prognosis. Choline metabolism in cancer, O-glycan biosynthesis, and protein processing in the endoplasmic reticulum pathway were associated with distant metastatic status. About 20% of tumors carried at least one aberrant event in BCAA catabolism signaling that could possibly be targeted by an approved therapeutic agent. We identified molecular-level OSCC that were correlated with etiology and prognosis while defining the landscape of major altered events of the OSCC plasma genome. These findings will be useful in the design of clinical trials for targeted therapies and the stratification of patients with OSCC according to therapeutic efficacy.
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Affiliation(s)
- Li-Han Lin
- Department of Medical Research, MacKay Memorial Hospital No. 92, Sec. 2, Chung San N. Rd., Taipei 10449, Taiwan
| | - Kuo-Wei Chang
- Institute of Oral Biology, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Stomatology, Taipei Veterans General Hospital, Taipei 11121, Taiwan
| | - Hui-Wen Cheng
- Department of Medical Research, MacKay Memorial Hospital No. 92, Sec. 2, Chung San N. Rd., Taipei 10449, Taiwan
| | - Chung-Ji Liu
- Department of Medical Research, MacKay Memorial Hospital No. 92, Sec. 2, Chung San N. Rd., Taipei 10449, Taiwan
- Institute of Oral Biology, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
- Department of Oral and Maxillofacial Surgery, Taipei MacKay Memorial Hospital, Taipei 10449, Taiwan
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27
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Tinhofer I, Staudte S, George S. Liquid biopsy in head neck cancer: ready for clinical routine diagnostics? Curr Opin Oncol 2023; 35:151-157. [PMID: 36966499 DOI: 10.1097/cco.0000000000000935] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2023]
Abstract
PURPOSE OF REVIEW The bodily fluids of patients with solid cancers representing a minimally-invasive source of clinically exploitable biomarkers have attracted an increasing amount of attention in recent years. In patients with head and neck squamous cell carcinoma (HNSCC), cell-free tumour DNA (ctDNA) belongs to the most promising liquid biomarkers for monitoring disease burden and identifying patients at high risk of recurrence. In this review, we highlight recent studies, evaluating the analytical validity and clinical utility of ctDNA as a dynamic biomarker in HNSCC, especially as it relates to risk stratification and contrasting human papilloma virus (HPV+ and HPV-) and carcinomas. RECENT FINDINGS The clinical potential of minimal residual disease monitoring through viral ctDNA in identifying HPV+ oropharyngeal carcinoma patients at higher risk of recurrence has recently been demonstrated. Furthermore, accumulating evidence supports a potential diagnostic value of ctDNA dynamics in HPV-negative HNSCC. Altogether, recent data suggest that ctDNA analysis may be a valuable tool in guiding (de)escalation of surgical interventions as well as adaptation in radiotherapy dosage, both in the definitive and adjuvant settings. SUMMARY Rigorous clinical trials with patient-relevant endpoints are critical in order to demonstrate that treatment decisions based on ctDNA dynamics result in better outcomes in HNSCC.
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Affiliation(s)
- Ingeborg Tinhofer
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Berlin, Germany
| | - Stephanie Staudte
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Berlin, Germany
| | - Stephen George
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Department of Radiooncology and Radiotherapy
- German Cancer Research Center (DKFZ), Heidelberg, Germany and German Cancer Consortium (DKTK) partner site Berlin, Germany
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Patel KB, Padhya TA, Huang J, Hernandez-Prera JC, Li T, Chung CH, Wang L, Wang X. Plasma cell-free DNA methylome profiling in pre- and post-surgery oral cavity squamous cell carcinoma. Mol Carcinog 2023; 62:493-502. [PMID: 36636912 PMCID: PMC10023468 DOI: 10.1002/mc.23501] [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: 09/28/2022] [Revised: 11/29/2022] [Accepted: 12/30/2022] [Indexed: 01/14/2023]
Abstract
Head and neck squamous cell carcinoma (HNSCC), a highly heterogeneous disease that involves multiple anatomic sites, is a leading cause of cancer-related mortality worldwide. Although the utility of noninvasive biomarkers based on circulating cell-free DNA (cfDNA) methylation profiling has been widely recognized, limited studies have been reported so far regarding the dynamics of cfDNA methylome in oral cavity squamous cell carcinoma (OCSCC). It is hypothesized in this study that comparison of methylation profiles in pre- and postsurgery plasma samples will reveal OCSCC-specific prognostic and diagnostic biomarkers. As a strategy to further prioritize tumor-specific targets, top differential methylated regions (DMRs) were called by reanalyzing methylation data from paired tumor and normal tissue collected in the the cancer genome atlas head-neck squamous cell carcinoma (TCGA) head and neck cancer cohort. Matched plasma samples from eight patients with OCSCC were collected at Moffitt Cancer Center before and after surgical resection. Plasma-derived cfDNA was analyzed by cfMBD-seq, which is a high-sensitive methylation profiling assay. Differential methylation analysis was then performed based on the matched samples profiled. In the top 200 HNSCC-specific DMRs detected based on the TCGA data set, a total of 23 regions reached significance in the plasma-based DMR test. The top five validated DMR regions (ranked by the significance in the plasma study) are located in the promoter regions of genes PENK, NXPH1, ZIK1, TBXT, and CDO1, respectively. The genome-wide cfDNA DMR analysis further highlighted candidate biomarkers located in genes SFRP4, SOX1, IRF4, and PCDH17. The prognostic relevance of candidate genes was confirmed by survival analysis using the TCGA data. This study supports the utility of cfDNA-based methylome profiling as a promising noninvasive biomarker source for OCSCC and HNSCC.
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Affiliation(s)
- Krupal B Patel
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Tapan A Padhya
- Otolaryngology - Head and Neck Surgery, University of South Florida Morsani College of Medicine, Tampa, USA
| | - Jinyong Huang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Juan C Hernandez-Prera
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Tingyi Li
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Liang Wang
- Department of Tumor Biology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - Xuefeng Wang
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
- Moffitt Cancer Center Immuno-Oncology Program, Tampa, FL 33612, USA
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29
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Huang Q, Ji M, Li F, Li Y, Zhou X, Hsueh CY, Zhou L. Diagnostic and prognostic value of plasma cell-free DNA combined with VEGF-C in laryngeal squamous cell carcinoma. Mol Cell Probes 2023; 67:101895. [PMID: 36682577 DOI: 10.1016/j.mcp.2023.101895] [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: 09/12/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023]
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) and vascular endothelial growth factor-C (VEGF-C) can be utilized to detect cancer and predict its prognosis. However, their potential application in laryngeal squamous cell carcinoma (LSCC) is unclear. PURPOSE This study aimed to identify the diagnostic and prognostic value of cfDNA and VEGF-C in LSCC patients. METHODS The plasma cfDNA of 148 LSCC patients and 43 non-tumor patients were isolated. Quantitative real-time PCR (qRT-PCR) was performed to assess long and short DNA fragments in plasma by amplifying the ALU repeats. ALU-qPCR results (ALU247/ALU115) were used to calculate cfDNA integrity index. Vascular endothelial growth factor-C (VEGF-C) level was detected by ELISA assay. Correlation between cfDNA and clinical features was analyzed. For detecting the sensitivity and specificity of cfDNA and VEGF-C alone or in combination for diagnosing LSCC, receiver operator characteristic (ROC) was established. For evaluating the overall survival (OS) of LSCC, Kaplan-Meier curves were established. RESULTS LSCC patients had significantly higher levels of plasma cfDNA (ALU115, ALU247, and cfDNA integrity index) and VEGF-C than those without cancer (p < 0.05), showing area under the curve (AUC) values of 0.79, 0.74, 0.62 and 0.80, when cutoff value was correspondingly defined at 2.14 ng/mL, 1.39 ng/mL, 0.73 and 412.90 pg/mL, respectively. The AUC for distinguishing LSCC patients from non-tumor patients by plasma cfDNA combined with VEGF-C was 0.89 (95% CI: 0.83-0.94). A significant correlation was found between plasma cfDNA levels and Ki-67, tumor size, pT stage, and smoking history (p < 0.05). Based on survival analysis, low VEGF-C concentration groups had longer OS than those with high VEGF-C concentration (p = 0.02). CONCLUSION Indicators such as plasma cfDNA and VEGF-C may be used to diagnose and monitor LSCC for its noninvasiveness and rapid accessibility.
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Affiliation(s)
- Qiang Huang
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Mengyou Ji
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Feiran Li
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Yufeng Li
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Xuehua Zhou
- Department of Anesthesiology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China
| | - Chi-Yao Hsueh
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
| | - Liang Zhou
- Department of Otorhinolaryngology, Eye & ENT Hospital, Fudan University, Shanghai, 200031, China.
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30
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Chen G, Zhang J, Fu Q, Taly V, Tan F. Integrative analysis of multi-omics data for liquid biopsy. Br J Cancer 2023; 128:505-518. [PMID: 36357703 PMCID: PMC9938261 DOI: 10.1038/s41416-022-02048-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
The innovation of liquid biopsy holds great potential to revolutionise cancer management through early diagnosis and timely treatment of cancer. Integrative analysis of different tumour-derived omics data (such as genomics, epigenetics, fragmentomics, and proteomics) from body fluids for cancer detection and monitoring could outperform the analysis of single modality data alone. In this review, we focussed on the discussion of early cancer detection and molecular residual disease surveillance based on multi-omics data of blood. We summarised diverse types of tumour-derived components, current popular platforms for profiling cancer-associated signals, machine learning approaches for joint analysis of liquid biopsy data, as well as multi-omics-based early detection of cancers, molecular residual disease monitoring, and treatment response surveillance. We also discussed the challenges and future directions of multi-omics-based liquid biopsy. With the development of both experimental protocols and computational methods dedicated to liquid biopsy, the implementation of multi-omics strategies into the clinical workflow will likely benefit the clinical management of cancers including decision-making guidance and patient outcome improvement.
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Affiliation(s)
- Geng Chen
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Center for Bioinformatics and Computational Biology, School of Life Sciences, East China Normal University, 200241, Shanghai, China.
| | - Jing Zhang
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China
| | - Qiaoting Fu
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China
| | - Valerie Taly
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe labélisée Ligue Nationale contre le cancer, Centre de Recherche des Cordeliers, Paris, France.
| | - Fei Tan
- Shanghai Skin Disease Hospital, School of Medicine, Tongji University, 200443, Shanghai, China.
- Shanghai Skin Disease Clinical College, The Fifth Clinical Medical College, Anhui Medical University, 200443, Shanghai, China.
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Sivapalan L, Murray JC, Canzoniero JV, Landon B, Jackson J, Scott S, Lam V, Levy BP, Sausen M, Anagnostou V. Liquid biopsy approaches to capture tumor evolution and clinical outcomes during cancer immunotherapy. J Immunother Cancer 2023; 11:jitc-2022-005924. [PMID: 36657818 PMCID: PMC9853269 DOI: 10.1136/jitc-2022-005924] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2022] [Indexed: 01/20/2023] Open
Abstract
Circulating cell-free tumor DNA (ctDNA) can serve as a real-time biomarker of tumor burden and provide unique insights into the evolving molecular landscape of cancers under the selective pressure of immunotherapy. Tracking the landscape of genomic alterations detected in ctDNA may reveal the clonal architecture of the metastatic cascade and thus improve our understanding of the molecular wiring of therapeutic responses. While liquid biopsies may provide a rapid and accurate evaluation of tumor burden dynamics during immunotherapy, the complexity of antitumor immune responses is not fully captured through single-feature ctDNA analyses. This underscores a need for integrative studies modeling the tumor and the immune compartment to understand the kinetics of tumor clearance in association with the quality of antitumor immune responses. Clinical applications of ctDNA testing in patients treated with immune checkpoint inhibitors have shown both predictive and prognostic value through the detection of genomic biomarkers, such as tumor mutational burden and microsatellite instability, as well as allowing for real-time monitoring of circulating tumor burden and the assessment of early on-therapy responses. These efforts highlight the emerging role of liquid biopsies in selecting patients for cancer immunotherapy, monitoring therapeutic efficacy, determining the optimal duration of treatment and ultimately guiding treatment selection and sequencing. The clinical translation of liquid biopsies is propelled by the increasing number of ctDNA-directed interventional clinical trials in the immuno-oncology space, signifying a critical step towards implementation of liquid biopsies in precision immuno-oncology.
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Affiliation(s)
- Lavanya Sivapalan
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Joseph C Murray
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jenna VanLiere Canzoniero
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Blair Landon
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Susan Scott
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Vincent Lam
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benjamin P. Levy
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Sausen
- Personal Genome Diagnostics, Baltimore, Maryland, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA,The Bloomberg-Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Spiliopoulou P, Vornicova O, Genta S, Spreafico A. Shaping the Future of Immunotherapy Targets and Biomarkers in Melanoma and Non-Melanoma Cutaneous Cancers. Int J Mol Sci 2023; 24:ijms24021294. [PMID: 36674809 PMCID: PMC9862040 DOI: 10.3390/ijms24021294] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
Recent advances in treating cutaneous melanoma have resulted in impressive patient survival gains. Refinement of disease staging and accurate patient risk classification have significantly improved our prognostic knowledge and ability to accurately stratify treatment. Undoubtedly, the most important step towards optimizing patient outcomes has been the advent of cancer immunotherapy, in the form of immune checkpoint inhibition (ICI). Immunotherapy has established its cardinal role in the management of both early and late-stage melanoma. Through leveraging outcomes in melanoma, immunotherapy has also extended its benefit to other types of skin cancers. In this review, we endeavor to summarize the current role of immunotherapy in melanoma and non-melanoma skin cancers, highlight the most pertinent immunotherapy-related molecular biomarkers, and lastly, shed light on future research directions.
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Affiliation(s)
- Pavlina Spiliopoulou
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Olga Vornicova
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Mount Sinai Hospital, University Health Network, Toronto, ON M5G 1X5, Canada
| | - Sofia Genta
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
| | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2C1, Canada
- Correspondence: ; Tel.: +1-416-946-4501 (ext. 5083)
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Eickelschulte S, Riediger AL, Angeles AK, Janke F, Duensing S, Sültmann H, Görtz M. Biomarkers for the Detection and Risk Stratification of Aggressive Prostate Cancer. Cancers (Basel) 2022; 14:cancers14246094. [PMID: 36551580 PMCID: PMC9777028 DOI: 10.3390/cancers14246094] [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: 11/17/2022] [Revised: 12/05/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Current strategies for the clinical management of prostate cancer are inadequate for a precise risk stratification between indolent and aggressive tumors. Recently developed tissue-based molecular biomarkers have refined the risk assessment of the disease. The characterization of tissue biopsy components and subsequent identification of relevant tissue-based molecular alterations have the potential to improve the clinical decision making and patient outcomes. However, tissue biopsies are invasive and spatially restricted due to tumor heterogeneity. Therefore, there is an urgent need for complementary diagnostic and prognostic options. Liquid biopsy approaches are minimally invasive with potential utility for the early detection, risk stratification, and monitoring of tumors. In this review, we focus on tissue and liquid biopsy biomarkers for early diagnosis and risk stratification of prostate cancer, including modifications on the genomic, epigenomic, transcriptomic, and proteomic levels. High-risk molecular alterations combined with orthogonal clinical parameters can improve the identification of aggressive tumors and increase patient survival.
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Affiliation(s)
- Samaneh Eickelschulte
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Anja Lisa Riediger
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany
| | - Arlou Kristina Angeles
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Florian Janke
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
| | - Stefan Duensing
- Molecular Urooncology, Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
| | - Holger Sültmann
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), National Center for Tumor Diseases (NCT), 69120 Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Magdalena Görtz
- Junior Clinical Cooperation Unit, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Department of Urology, University Hospital Heidelberg, 69120 Heidelberg, Germany
- Correspondence: ; Tel.: +49-6221-42-2603
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Janke F, Angeles AK, Riediger AL, Bauer S, Reck M, Stenzinger A, Schneider MA, Muley T, Thomas M, Christopoulos P, Sültmann H. Longitudinal monitoring of cell-free DNA methylation in ALK-positive non-small cell lung cancer patients. Clin Epigenetics 2022; 14:163. [PMID: 36461127 PMCID: PMC9719130 DOI: 10.1186/s13148-022-01387-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND DNA methylation (5-mC) signals in cell-free DNA (cfDNA) of cancer patients represent promising biomarkers for minimally invasive tumor detection. The high abundance of cancer-associated 5-mC alterations permits parallel and highly sensitive assessment of multiple 5-mC biomarkers. Here, we performed genome-wide 5-mC profiling in the plasma of metastatic ALK-rearranged non-small cell lung cancer (NSCLC) patients receiving tyrosine kinase inhibitor therapy. We established a strategy to identify ALK-specific 5-mC changes from cfDNA and demonstrated the suitability of the identified markers for cancer detection, prognosis, and therapy monitoring. METHODS Longitudinal plasma samples (n = 79) of 21 ALK-positive NSCLC patients and 13 healthy donors were collected alongside 15 ALK-positive tumor tissue and 10 healthy lung tissue specimens. All plasma and tissue samples were analyzed by cell-free DNA methylation immunoprecipitation sequencing to generate genome-wide 5-mC profiles. Information on genomic alterations (i.e., somatic mutations/fusions and copy number alterations) determined in matched plasma samples was available from previous studies. RESULTS We devised a strategy that identified tumor-specific 5-mC biomarkers by reducing 5-mC background signals derived from hematopoietic cells. This was followed by differential methylation analysis (cases vs. controls) and biomarker validation using 5-mC profiles of ALK-positive tumor tissues. The resulting 245 differentially methylated regions were enriched for lung adenocarcinoma-specific 5-mC patterns in TCGA data and indicated transcriptional repression of several genes described to be silenced in NSCLC (e.g., PCDH10, TBX2, CDO1, and HOXA9). Additionally, 5-mC-based tumor DNA (5-mC score) was highly correlated with other genomic alterations in cell-free DNA (Spearman, ρ > 0.6), while samples with high 5-mC scores showed significantly shorter overall survival (log-rank p = 0.025). Longitudinal 5-mC scores reflected radiologic disease assessments and were significantly elevated at disease progression compared to the therapy start (p = 0.0023). In 7 out of 8 instances, rising 5-mC scores preceded imaging-based evaluation of disease progression. CONCLUSION We demonstrated a strategy to identify 5-mC biomarkers from the plasma of cancer patients and integrated them into a quantitative measure of cancer-associated 5-mC alterations. Using longitudinal plasma samples of ALK-positive NSCLC patients, we highlighted the suitability of cfDNA methylation for prognosis and therapy monitoring.
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Affiliation(s)
- Florian Janke
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany
| | - Arlou Kristina Angeles
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany
| | - Anja Lisa Riediger
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584Helmholtz Young Investigator Group, Multiparametric Methods for Early Detection of Prostate Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Urology, Heidelberg University Hospital, Heidelberg, Germany ,grid.7700.00000 0001 2190 4373Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Simone Bauer
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany
| | - Martin Reck
- grid.452624.3Lung Clinic Grosshansdorf, Airway Research Center North, German Center for Lung Research, Grosshansdorf, Germany
| | - Albrecht Stenzinger
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marc A. Schneider
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Thomas Muley
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Translational Research Unit, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
| | - Michael Thomas
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Oncology, Thoraxklinik and National Center for Tumor Disease (NCT) at Heidelberg University Hospital, Heidelberg, Germany
| | - Petros Christopoulos
- grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.5253.10000 0001 0328 4908Department of Oncology, Thoraxklinik and National Center for Tumor Disease (NCT) at Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Sültmann
- grid.5253.10000 0001 0328 4908Division of Cancer Genome Research, German Cancer Research Center, National Center for Tumor Diseases, Heidelberg, Germany ,grid.452624.3German Center for Lung Research (DZL), TLRC Heidelberg, Heidelberg, Germany ,grid.7497.d0000 0004 0492 0584German Cancer Consortium (DKTK), Heidelberg, Germany
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Rapado‐González Ó, Brea‐Iglesias J, Rodríguez‐Casanova A, Bao‐Caamano A, López‐Cedrún J, Triana‐Martínez G, Díaz‐Peña R, Santos MA, López‐López R, Muinelo‐Romay L, Martínez‐Fernández M, Díaz‐Lagares Á, Suárez‐Cunqueiro MM. Somatic mutations in tumor and plasma of locoregional recurrent and/or metastatic head and neck cancer using a next‐generation sequencing panel: A preliminary study. Cancer Med 2022; 12:6615-6622. [PMID: 36420687 PMCID: PMC10067107 DOI: 10.1002/cam4.5436] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/13/2022] [Accepted: 11/01/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND We explore the utility of TruSight Tumor 170 panel (TST170) for detecting somatic mutations in tumor and cfDNA from locoregional recurrent and/or metastatic head and neck squamous cell carcinoma (HNSCC). METHODS Targeted NGS of tumor DNA and plasma cfDNA was performed using TST170 panel. In addition, a set of somatic mutations previously described in HNSCC were selected for validating in tumor, plasma, and saliva by digital droplet PCR. RESULTS The TST170 panel identified 13 non-synonymous somatic mutations, of which five were detected in tumoral tissue, other five in plasma cfDNA, and three in both tissue and plasma cfDNA. Of the eight somatic mutations identified in tissue, three were also identified in plasma cfDNA, showing an overall concordance rate of 37.5%. CONCLUSIONS This preliminary study shows the possibility to detect somatic mutations in tumor and plasma of HNSCC patients using a single assay that would facilitate the clinical implementation of personalized medicine in the clinic.
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Affiliation(s)
- Óscar Rapado‐González
- Department of Surgery and Medical‐Surgical Specialties, Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS) Santiago de Compostela Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC) Instituto de Salud Carlos III Madrid Spain
| | - Jenifer Brea‐Iglesias
- Translational Molecular Oncology Unit, Galicia Sur Health Research Institute (IIS Galicia Sur) SERGAS‐UVIGO, Hospital Álvaro Cunqueiro Vigo Spain
| | - Aitor Rodríguez‐Casanova
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS,SERGAS) Santiago de Compostela Spain
- Roche‐Chus Joint Unit, Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS) Santiago de Compostela Spain
- Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
| | - Aida Bao‐Caamano
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS,SERGAS) Santiago de Compostela Spain
- Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
| | - José‐Luis López‐Cedrún
- Department of Oral and Maxillofacial Surgery Complexo Hospitalario Universitario de A Coruña (CHUAC, SERGAS) A Coruña Spain
| | | | - Roberto Díaz‐Peña
- Fundación Pública Galega de Medicina Xenómica, SERGAS, Grupo de Medicina Xenómica‐USC Health Research Institute of Santiago de Compostela (IDIS) Santiago de Compostela Spain
- Faculty of Health Sciences Universidad Autónoma de Chile Talca Chile
| | - María Arminda Santos
- Department of Surgery and Medical‐Surgical Specialties, Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Department of Oral Rehabilitation Instituto Universitario de Ciências da Saúde (IUCS) Gandra Portugal
| | - Rafael López‐López
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC) Instituto de Salud Carlos III Madrid Spain
- Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS) Santiago de Compostela Spain
| | - Laura Muinelo‐Romay
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Liquid Biopsy Analysis Unit, Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS) Santiago de Compostela Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC) Instituto de Salud Carlos III Madrid Spain
| | - Mónica Martínez‐Fernández
- Translational Molecular Oncology Unit, Galicia Sur Health Research Institute (IIS Galicia Sur) SERGAS‐UVIGO, Hospital Álvaro Cunqueiro Vigo Spain
| | - Ángel Díaz‐Lagares
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC) Instituto de Salud Carlos III Madrid Spain
- Epigenomics Unit, Cancer Epigenomics, Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS,SERGAS) Santiago de Compostela Spain
| | - María Mercedes Suárez‐Cunqueiro
- Department of Surgery and Medical‐Surgical Specialties, Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Galician Precision Oncology Research Group (ONCOGAL), Medicine and Dentistry School Universidade de Santiago de Compostela (USC) Santiago de Compostela Spain
- Centro de Investigación Biomédica en Red en Cáncer (CIBERONC) Instituto de Salud Carlos III Madrid Spain
- Translational Medical Oncology Group (ONCOMET) Health Research Institute of Santiago (IDIS), Complexo Hospitalario Universitario de Santiago de Compostela (CHUS, SERGAS) Santiago de Compostela Spain
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The cell-free DNA methylome captures distinctions between localized and metastatic prostate tumors. Nat Commun 2022; 13:6467. [PMID: 36309516 PMCID: PMC9617856 DOI: 10.1038/s41467-022-34012-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 10/07/2022] [Indexed: 12/25/2022] Open
Abstract
Metastatic prostate cancer remains a major clinical challenge and metastatic lesions are highly heterogeneous and difficult to biopsy. Liquid biopsy provides opportunities to gain insights into the underlying biology. Here, using the highly sensitive enrichment-based sequencing technology, we provide analysis of 60 and 175 plasma DNA methylomes from patients with localized and metastatic prostate cancer, respectively. We show that the cell-free DNA methylome can capture variations beyond the tumor. A global hypermethylation in metastatic samples is observed, coupled with hypomethylation in the pericentromeric regions. Hypermethylation at the promoter of a glucocorticoid receptor gene NR3C1 is associated with a decreased immune signature. The cell-free DNA methylome is reflective of clinical outcomes and can distinguish different disease types with 0.989 prediction accuracy. Finally, we show the ability of predicting copy number alterations from the data, providing opportunities for joint genetic and epigenetic analysis on limited biological samples.
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Bredno J, Venn O, Chen X, Freese P, Ofman JJ. Circulating Tumor DNA Allele Fraction: A Candidate Biological Signal for Multicancer Early Detection Tests to Assess the Clinical Significance of Cancers. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1368-1378. [PMID: 35948080 DOI: 10.1016/j.ajpath.2022.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/02/2022] [Accepted: 07/07/2022] [Indexed: 05/28/2023]
Abstract
Current imaging-based cancer screening approaches provide useful but limited prognostic information. Complementary to existing screening tests, cell-free DNA-based multicancer early detection (MCED) tests account for cancer biology [manifested through circulating tumor allele fraction (cTAF)], which could inform prognosis and help assess the cancer's clinical significance. This review discusses the factors affecting circulating tumor DNA (ctDNA) levels and cTAF, and their correlation with the cancer's clinical significance. Furthermore, it discusses the influence of cTAF on MCED test performance, which could help inform prognosis. Clinically significant cancers show higher ctDNA levels quantified by cTAF than indolent phenotype cancers within each stage. This is because more frequent mitosis and cell death combined with increased trafficking of cell-free DNA into circulation leads to greater vascularization and depth of tumor invasion. cTAF has been correlated with biomarkers for cancer aggressiveness and overall survival; cancers with lower cTAF had better survival when compared with cancers as determined by the higher cTAF and Surveillance, Epidemiology, and End Results-based survival for that cancer type at each stage. MCED-detected cancers in case-control studies had comparable survival to Surveillance, Epidemiology, and End Results-based survival at each stage. Because many MCED tests use ctDNA as an analyte, cTAF could provide a common metric to compare performance. The prognostic value of cTAF may allow MCED tests to preferentially detect clinically significant cancers at early stages when outcomes are favorable and this may avoid overdiagnosis.
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Affiliation(s)
- Joerg Bredno
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
| | - Oliver Venn
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California.
| | - Xiaoji Chen
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
| | - Peter Freese
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
| | - Joshua J Ofman
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
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Chikuie N, Urabe Y, Ueda T, Hamamoto T, Taruya T, Kono T, Yumii K, Takeno S. Utility of plasma circulating tumor DNA and tumor DNA profiles in head and neck squamous cell carcinoma. Sci Rep 2022; 12:9316. [PMID: 35661138 PMCID: PMC9167274 DOI: 10.1038/s41598-022-13417-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 05/17/2022] [Indexed: 12/24/2022] Open
Abstract
Early recurrence detection of head and neck squamous cell carcinoma (HNSCC) is important for improving prognosis. Recently, circulating tumor DNA (ctDNA) has been reported to be useful in early detection or treatment response determination in various carcinomas. This study aimed to identify the utility of ctDNA for predicting recurrent metastasis in patients with HNSCC. We collected pre-treatment tissues (malignant and normal tissues) and multiple plasma samples before and after treatment for 20 cases of HNSCC treated with radical therapy. ctDNA was detected in pre-treatment plasma in 10 cases; however, there were no significant associations with tumor recurrence and staging. During follow-up, ctDNA was detected in 5 of the 7 plasma samples of recurrent cases but not in the 13 recurrence-free cases. Moreover, there was a significant difference in post-treatment relapse-free survival time between the groups with and without detected ctDNA (20.6 ± 7.7 vs. 9.6 ± 9.1 months, respectively; log-rank test, p < 0.01). Moreover, for two of the five cases with ctDNA detected after treatment, ctDNA detection was a more sensitive predictor of recurrence than imaging studies. ctDNA detection during treatment follow-up was useful in patients with HNSCC for predicting the response to treatment and recurrent metastasis.
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Affiliation(s)
- Nobuyuki Chikuie
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Yuji Urabe
- Division of Regeneration and Medicine Center for Translational and Clinical Research, Hiroshima University Hospital, Hiroshima, Japan
| | - Tsutomu Ueda
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan.
| | - Takao Hamamoto
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Takayuki Taruya
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Takashi Kono
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Kohei Yumii
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
| | - Sachio Takeno
- Department of Otorhinolaryngology, Head and Neck Surgery, Graduate School of Biomedical and Health Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima, 734-8551, Japan
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Li CL, Yeh SH, Chen PJ. Circulating Virus–Host Chimera DNAs in the Clinical Monitoring of Virus-Related Cancers. Cancers (Basel) 2022; 14:cancers14102531. [PMID: 35626135 PMCID: PMC9139492 DOI: 10.3390/cancers14102531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/18/2022] [Accepted: 05/18/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Cell-free tumor DNA (ctDNA), the DNA released into circulation from tumors, is a promising tumor marker with versatile applications. The associations of the amount, somatic mutation frequency, and epigenetic modifications of ctDNA with the tumor burden, tumor behavior, and prognosis have been widely investigated in different types of tumors. However, there are still some challenging issues to be resolved before ctDNA can complement or even replace current serum tumor markers. We propose employing exogenous viral DNA integration that produces unique virus–host chimera DNA (vh-DNA) at junction sites. Cell-free vh-DNA may become a new biomarker because it overcomes background interference detection problems, takes advantage of virus tropism to localize the tumor, and acts as a universal marker for monitoring clonal expansion or tumor loads in tumors related to oncogenic viruses. Abstract The idea of using tumor-specific cell-free DNA (ctDNA) as a tumor biomarker has been widely tested and validated in various types of human cancers and different clinical settings. ctDNA can reflect the presence or size of tumors in a real-time manner and can enable longitudinal monitoring with minimal invasiveness, allowing it to be applied in treatment response assessment and recurrence monitoring for cancer therapies. However, tumor detection by ctDNA remains a great challenge due to the difficulty in enriching ctDNA from a large amount of homologous non-tumor cell-free DNA (cfDNA). Only ctDNA with nonhuman sequences (or rearrangements) can be selected from the background of cfDNA from nontumor DNAs. This is possible for several virus-related cancers, such as hepatitis B virus (HBV)-related HCC or human papillomavirus (HPV)-related cervical or head and neck cancers, which frequently harbor randomly integrated viral DNA. The junction fragments of the integrations, namely virus–host chimera DNA (vh-DNA), can represent the signatures of individual tumors and are released into the blood. Such ctDNA can be enriched by capture with virus-specific probes and therefore exploited as a circulating biomarker to track virus-related cancers in clinical settings. Here, we review virus integrations in virus-related cancers to evaluate the feasibility of vh-DNA as a cell-free tumor marker and update studies on the development of detection and applications. vh-DNA may be a solution to the development of specific markers to manage virus-related cancers in the future.
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Affiliation(s)
- Chiao-Ling Li
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
| | - Shiou-Hwei Yeh
- Graduate Institute of Microbiology, College of Medicine, National Taiwan University, Taipei 100, Taiwan;
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
| | - Pei-Jer Chen
- Center for Genomic Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei 100, Taiwan
- Division of Gastroenterology, Department of Internal Medicine, National Taiwan University Hospital, Taipei 100, Taiwan
- Correspondence: (S.-H.Y.); (P.-J.C.)
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Verduijn GM, Capala ME, Sijtsema ND, Lauwers I, Hernandez Tamames JA, Heemsbergen WD, Sewnaik A, Hardillo JA, Mast H, van Norden Y, Jansen MPHM, van der Lugt A, van Gent DC, Hoogeman MS, Mostert B, Petit SF. The COMPLETE trial: HolistiC early respOnse assessMent for oroPharyngeaL cancEr paTiEnts; Protocol for an observational study. BMJ Open 2022; 12:e059345. [PMID: 35584883 PMCID: PMC9119182 DOI: 10.1136/bmjopen-2021-059345] [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] [Indexed: 11/24/2022] Open
Abstract
INTRODUCTION The locoregional failure (LRF) rate in human papilloma virus (HPV)-negative oropharyngeal squamous cell carcinoma (OPSCC) remains disappointingly high and toxicity is substantial. Response prediction prior to or early during treatment would provide opportunities for personalised treatment. Currently, there are no accurate predictive models available for correct OPSCC patient selection. Apparently, the pivotal driving forces that determine how a OPSCC responds to treatment, have yet to be elucidated. Therefore, the holistiC early respOnse assessMent for oroPharyngeaL cancer paTiEnts study focuses on a holistic approach to gain insight in novel potential prognostic biomarkers, acquired before and early during treatment, to predict response to treatment in HPV-negative patients with OPSCC. METHODS AND ANALYSIS This single-centre prospective observational study investigates 60 HPV-negative patients with OPSCC scheduled for primary radiotherapy (RT) with cisplatin or cetuximab, according to current clinical practice. A holistic approach will be used that aims to map the macroscopic (with Intra Voxel Incoherent Motion Diffusion Kurtosis Imaging (IVIM-DKI); before, during, and 3 months after RT), microscopic (with biopsies of the primary tumour acquired before treatment and irradiated ex vivo to assess radiosensitivity), and molecular landscape (with circulating tumour DNA (ctDNA) analysed before, during and 3 months after treatment). The main end point is locoregional control (LRC) 2 years after treatment. The primary objective is to determine whether a relative change in the mean of the diffusion coefficient D (an IVIM-DKI parameter) in the primary tumour early during treatment, improves the performance of a predictive model consisting of tumour volume only, for 2 years LRC after treatment. The secondary objectives investigate the potential of other IVIM-DKI parameters, ex vivo sensitivity characteristics, ctDNA, and combinations thereof as potential novel prognostic markers. ETHICS AND DISSEMINATION The study was approved by the Medical Ethical Committee of Erasmus Medical Center. The main results of the trial will be presented in international meetings and medical journals. TRIAL REGISTRATION NUMBER NL8458.
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Affiliation(s)
- Gerda M Verduijn
- Radiotherapy, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Marta E Capala
- Radiotherapy, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Nienke D Sijtsema
- Radiotherapy, Erasmus Medical Center, Rotterdam, The Netherlands
- Radiology and Nuclear Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Iris Lauwers
- Radiotherapy, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Aniel Sewnaik
- Otorhinolaryngology and Head and Neck surgery, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Jose A Hardillo
- Otorhinolaryngology and Head and Neck surgery, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Hetty Mast
- Oral and Maxillofacial surgery, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | | | - Aad van der Lugt
- Radiology and Nuclear Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Dik C van Gent
- Molecular Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Bianca Mostert
- Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Steven F Petit
- Radiotherapy, Erasmus Medical Center, Rotterdam, The Netherlands
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41
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Yang X, Xu X, Zhang C, Ji T, Wan T, Liu W. The diagnostic value and prospects of gene mutations in circulating tumor DNA for head and neck cancer monitoring. Oral Oncol 2022; 128:105846. [DOI: 10.1016/j.oraloncology.2022.105846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 03/24/2022] [Indexed: 10/18/2022]
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Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
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43
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Lim JU, Yeo CD. Update on adjuvant therapy in completely resected NSCLC patients. Thorac Cancer 2021; 13:277-283. [PMID: 34898012 PMCID: PMC8807337 DOI: 10.1111/1759-7714.14277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/27/2021] [Accepted: 11/29/2021] [Indexed: 12/25/2022] Open
Abstract
In patients with completely resected non‐small cell lung cancer (NSCLC), postoperative adjuvant chemotherapy has been associated with improvement in survival by minimizing the risk of recurrence. For years, systemic chemotherapy including platinum based regimen has been a mainstay treatment modality of adjuvant treatment after complete resection. ADAURA study showed that among completely resected IB to IIIA NSCLC, disease‐free survival was significantly better in patients under adjuvant osimertinib than a placebo group. After the advent of a variety of new treatment regimens, such as third generation TKI and immunotherapy, the landscape of postoperative adjuvant treatment has been changing. In this review, we discuss some key issues regarding choice of adjuvant treatment after complete resection in NSCLC, and provide further updates on recent advances in treatment modalities.
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Affiliation(s)
- Jeong Uk Lim
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Yeouido St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, South Korea
| | - Chang Dong Yeo
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Eunpyeong St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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44
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Moding EJ, Nabet BY, Alizadeh AA, Diehn M. Detecting Liquid Remnants of Solid Tumors: Circulating Tumor DNA Minimal Residual Disease. Cancer Discov 2021; 11:2968-2986. [PMID: 34785539 PMCID: PMC8976700 DOI: 10.1158/2159-8290.cd-21-0634] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022]
Abstract
Growing evidence demonstrates that circulating tumor DNA (ctDNA) minimal residual disease (MRD) following treatment for solid tumors predicts relapse. These results suggest that ctDNA MRD could identify candidates for adjuvant therapy and measure response to such treatment. Importantly, factors such as assay type, amount of ctDNA release, and technical and biological background can affect ctDNA MRD results. Furthermore, the clinical utility of ctDNA MRD for treatment personalization remains to be fully established. Here, we review the evidence supporting the value of ctDNA MRD in solid cancers and highlight key considerations in the application of this potentially transformative biomarker. SIGNIFICANCE ctDNA analysis enables detection of MRD and predicts relapse after definitive treatment for solid cancers, thereby promising to revolutionize personalization of adjuvant and consolidation therapies.
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Affiliation(s)
- Everett J. Moding
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Barzin Y. Nabet
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Current address: Department of Oncology Biomarker Development, Genentech, South San Francisco, CA 94080, USA
| | - Ash A. Alizadeh
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, California, USA
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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45
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Blomain ES, Moding EJ. Liquid Biopsies for Molecular Biology-Based Radiotherapy. Int J Mol Sci 2021; 22:11267. [PMID: 34681925 PMCID: PMC8538046 DOI: 10.3390/ijms222011267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 11/29/2022] Open
Abstract
Molecular alterations drive cancer initiation and evolution during development and in response to therapy. Radiotherapy is one of the most commonly employed cancer treatment modalities, but radiobiologic approaches for personalizing therapy based on tumor biology and individual risks remain to be defined. In recent years, analysis of circulating nucleic acids has emerged as a non-invasive approach to leverage tumor molecular abnormalities as biomarkers of prognosis and treatment response. Here, we evaluate the roles of circulating tumor DNA and related analyses as powerful tools for precision radiotherapy. We highlight emerging work advancing liquid biopsies beyond biomarker studies into translational research investigating tumor clonal evolution and acquired resistance.
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Affiliation(s)
- Erik S. Blomain
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA;
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA;
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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