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Balázs Z, Balermpas P, Ivanković I, Willmann J, Gitchev T, Bryant A, Guckenberger M, Krauthammer M, Andratschke N. Longitudinal cell-free DNA characterization by low-coverage whole-genome sequencing in patients undergoing high-dose radiotherapy. Radiother Oncol 2024; 197:110364. [PMID: 38834154 DOI: 10.1016/j.radonc.2024.110364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND AND PURPOSE Current radiotherapy guidelines rely heavily on imaging-based monitoring. Liquid biopsy monitoring promises to complement imaging by providing frequent systemic information about the tumor. In particular, cell-free DNA (cfDNA) sequencing offers a tumor-agnostic approach, which lends itself to monitoring heterogeneous cohorts of cancer patients. METHODS We collected plasma cfDNA from oligometastatic patients (OMD) and head-and-neck cancer patients (SCCHN) at six time points before, during, and after radiotherapy, and compared them to the plasma samples of healthy and polymetastatic volunteers. We performed low-pass (on average 7x) whole-genome sequencing on 93 plasma cfDNA samples and correlated copy number alterations and fragment length distributions to clinical and imaging findings. RESULTS We observed copy number alterations in 4/7 polymetastatic cancer patients, 1/7 OMD and 1/7 SCCHN patients, these patients' imaging showed progression following radiotherapy. Using unsupervised learning, we identified cancer-specific fragment length features that showed a strong correlation with copy number-based tumor fraction estimates. In 4/4 HPV-positive SCCHN patient samples, we detected viral DNA that enabled the monitoring of very low tumor fraction samples. CONCLUSIONS Our results indicate that an elevated tumor fraction is associated with tumor aggressiveness and systemic tumor spread. This information may be used to adapt treatment strategies. Further, we show that by detecting specific sequences such as viral DNA, the sensitivity of detecting cancer from cell-free DNA sequencing data can be greatly increased.
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Affiliation(s)
- Zsolt Balázs
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Panagiotis Balermpas
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Ivna Ivanković
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Jonas Willmann
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Todor Gitchev
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Asher Bryant
- Center for Cancer Research, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Matthias Guckenberger
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland
| | - Michael Krauthammer
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland; Department of Biomedical Informatics, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
| | - Nicolaus Andratschke
- Department of Radiation Oncology, University Hospital of Zurich, University of Zurich, Zurich, Switzerland.
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Hashimoto T, Nakamura Y, Oki E, Kobayashi S, Yuda J, Shibuki T, Bando H, Yoshino T. Bridging horizons beyond CIRCULATE-Japan: a new paradigm in molecular residual disease detection via whole genome sequencing-based circulating tumor DNA assay. Int J Clin Oncol 2024; 29:495-511. [PMID: 38551727 PMCID: PMC11043144 DOI: 10.1007/s10147-024-02493-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 02/16/2024] [Indexed: 04/26/2024]
Abstract
Circulating tumor DNA (ctDNA) is the fraction of cell-free DNA in patient blood that originates from a tumor. Advances in DNA sequencing technologies and our understanding of the molecular biology of tumors have increased interest in exploiting ctDNA to facilitate detection of molecular residual disease (MRD). Analysis of ctDNA as a promising MRD biomarker of solid malignancies has a central role in precision medicine initiatives exemplified by our CIRCULATE-Japan project involving patients with resectable colorectal cancer. Notably, the project underscores the prognostic significance of the ctDNA status at 4 weeks post-surgery and its correlation to adjuvant therapy efficacy at interim analysis. This substantiates the hypothesis that MRD is a critical prognostic indicator of relapse in patients with colorectal cancer. Despite remarkable advancements, challenges endure, primarily attributable to the exceedingly low ctDNA concentration in peripheral blood, particularly in scenarios involving low tumor shedding and the intrinsic error rates of current sequencing technologies. These complications necessitate more sensitive and sophisticated assays to verify the clinical utility of MRD across all solid tumors. Whole genome sequencing (WGS)-based tumor-informed MRD assays have recently demonstrated the ability to detect ctDNA in the parts-per-million range. This review delineates the current landscape of MRD assays, highlighting WGS-based approaches as the forefront technique in ctDNA analysis. Additionally, it introduces our upcoming endeavor, WGS-based pan-cancer MRD detection via ctDNA, in our forthcoming project, SCRUM-Japan MONSTAR-SCREEN-3.
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Affiliation(s)
- Tadayoshi Hashimoto
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Yoshiaki Nakamura
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shin Kobayashi
- Department of Hepatobiliary and Pancreatic Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Junichiro Yuda
- Department of Hematology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Taro Shibuki
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hideaki Bando
- Translational Research Support Office, National Cancer Center Hospital East, Kashiwa, Japan
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, 6-5-1 Kashiwanoha, Kashiwa, Chiba, 277-8577, Japan.
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3
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Daban A, Beaussire-Trouvay L, Lévêque É, Alexandru C, Tennevet I, Langlois O, Veresezan O, Marguet F, Clatot F, Di Fiore F, Sarafan-Vasseur N, Fontanilles M. Prognostic value of circulating short-length DNA fragments in unresected glioblastoma patients. Transl Oncol 2024; 42:101897. [PMID: 38340682 PMCID: PMC10867437 DOI: 10.1016/j.tranon.2024.101897] [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: 11/09/2023] [Revised: 01/08/2024] [Accepted: 01/28/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Liquid biopsy application is still challenging in glioblastoma patients and the usefulness of short-length DNA (slDNA) fragments is not established. The aim was to investigate slDNA concentration as a prognostic marker in unresected glioblastoma patients. METHODS Patients with unresected glioblastoma and treated by radiochemotherapy (RT/TMZ) were included. Plasmas were prospectively collected at three times: before (pre-) RT, after (post-) RT and at the time of progression. Primary objective was to investigate the impact on survival of slDNA concentration [slDNA] variation during RT/TMZ. Secondary objectives were to explore the association between tumor volume, corticosteroid exposition and [slDNA]; and the impact of slDNA detection at pre-RT on survival. RESULTS Thirty-six patients were analyzed: 11 patients (30.6 %) experienced [slDNA] decrease during RT/TMZ, 22 patients (61.1 %) experienced increase and 3 patients (8.3 %) had stability. Decrease of [slDNA] during RT/TMZ was associated with better outcome compared to increase or stability: median OS, since end of RT, of 13.2 months [11.4 - NA] vs 10.1 months [7.8 - 12.6] and 6.8 months [4.5 - NA], p = 0.015, respectively. slDNA detection at pre-RT time was associated with improved OS: 11.7 months in the slDNA(+) group versus 8.8 months in the slDNA(-) group, p = 0.004. [slDNA] was not associated with corticosteroids exposition or tumor volume. No influence on survival was observed for both whole cfDNA concentration or slDNA peak size. CONCLUSION [slDNA] decrease during radiochemotherapy phase is a favorable prognostic marker on OS for unresected glioblastoma patients. Larger and independent cohorts are now required. TRIAL REGISTRATION ClinicalTrial, NCT02617745. Registered 1 December 2015, https://clinicaltrials.gov/ct2/show/NCT02617745?term=glioplak&draw=2&rank=1.
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Affiliation(s)
- Arthur Daban
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, 76038, Rouen, France
| | | | - Émilie Lévêque
- Clinical Research Unit, Cancer Centre Henri Becquerel, Rue d'Amiens, 76038, Rouen, France
| | - Cristina Alexandru
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, 76038, Rouen, France
| | - Isabelle Tennevet
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, 76038, Rouen, France
| | - Olivier Langlois
- Department of Neurosurgery, Rouen University Hospital, F-76031, 1 Rue de Germont, Rouen, CEDEX 76031, France
| | - Ovidiu Veresezan
- Department of Radiation Oncology, Henri Becquerel Cancer Center, 76038, Rouen, France
| | - Florent Marguet
- Univ Rouen Normandy, INSERM unit U1245 Brain and Cancer Genomics, Rouen, 76000 France; Department of Pathology, Rouen University Hospital, 1 Rue de Germont, Rouen, CEDEX 76031, France
| | - Florian Clatot
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, 76038, Rouen, France; Univ Rouen Normandy, INSERM unit U1245 Brain and Cancer Genomics, Rouen, 76000 France
| | - Frédéric Di Fiore
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, 76038, Rouen, France; Univ Rouen Normandy, INSERM unit U1245 Brain and Cancer Genomics, Rouen, 76000 France
| | | | - Maxime Fontanilles
- Department of Medical Oncology, Cancer Centre Henri Becquerel, Rue d'Amiens, 76038, Rouen, France; Univ Rouen Normandy, INSERM unit U1245 Brain and Cancer Genomics, Rouen, 76000 France.
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Andersson D, Kebede FT, Escobar M, Österlund T, Ståhlberg A. Principles of digital sequencing using unique molecular identifiers. Mol Aspects Med 2024; 96:101253. [PMID: 38367531 DOI: 10.1016/j.mam.2024.101253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 02/19/2024]
Abstract
Massively parallel sequencing technologies have long been used in both basic research and clinical routine. The recent introduction of digital sequencing has made previously challenging applications possible by significantly improving sensitivity and specificity to now allow detection of rare sequence variants, even at single molecule level. Digital sequencing utilizes unique molecular identifiers (UMIs) to minimize sequencing-induced errors and quantification biases. Here, we discuss the principles of UMIs and how they are used in digital sequencing. We outline the properties of different UMI types and the consequences of various UMI approaches in relation to experimental protocols and bioinformatics. Finally, we describe how digital sequencing can be applied in specific research fields, focusing on cancer management where it can be used in screening of asymptomatic individuals, diagnosis, treatment prediction, prognostication, monitoring treatment efficacy and early detection of treatment resistance as well as relapse.
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Affiliation(s)
- Daniel Andersson
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Firaol Tamiru Kebede
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Mandy Escobar
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden
| | - Tobias Österlund
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden
| | - Anders Ståhlberg
- Sahlgrenska Center for Cancer Research, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 413 90, Gothenburg, Sweden; Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 413 90, Gothenburg, Sweden; Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, 413 45, Gothenburg, Sweden.
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5
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Souza SS, Stephens EM, Bourdillon AT, Bhethanabotla R, Farzal Z, Plonowska-Hirschfeld K, Qualliotine JR, Heaton CM, Ha PK, Ryan WR. Circulating tumor HPV DNA assessments after surgery for human papilloma virus-associated oropharynx carcinoma. Am J Otolaryngol 2024; 45:104184. [PMID: 38101135 DOI: 10.1016/j.amjoto.2023.104184] [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: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/17/2023]
Abstract
PURPOSE To understand the utility of circulating tumor human papillomavirus DNA (ctHPVDNA) blood testing for HPV-associated oropharynx squamous cell carcinoma (HPV + OPSCC) after definitive surgery. MATERIALS AND METHODS Prospective cohort study of HPV(+)OPSCC patients with ctHPVDNA test data to assess its accuracy in detecting biopsy-confirmed disease at various post-treatment time points. Eligible patients had p16(+)/HPV(+) OPSCC and ctHPVDNA testing performed at any time pre-operatively and/or postoperatively. In cases of recurrence, patients were excluded from analysis if ctHPVDNA testing was not performed within 6 months of biopsy. RESULTS 196 all-treatment-type patients had at least one PT ctHPVDNA test. The initial post-treatment (PT) ctHPVDNA sensitivity, specificity, PPV, and NPV were 69.2 % (9/13), 96.7 % (177/183), 60.0 % (9/15), and 97.8 % (177/181). 61 surgery alone (SA) patients underwent 128 PT tests. The initial PT SA ctHPVDNA sensitivity, specificity, PPV, and NPV were 100 % (2/2), 96.0 % (48/50), 50 % (2/4), and 100 % (48/48). 35 of 61 (57.4 %) SA patients had NCCN-based histopathologic indications for adjuvant (chemo)radiation but declined. 3 of 35 (8.57 %) had a positive PT ctHPVDNA test of which 1 of 3 (33 %) had biopsy-proven recurrence. Prospectively, ten patients had a PreT positive ctHPVDNA, underwent SA, refused adjuvant treatment, had an undetectable ctHPVDNA within 2 weeks of SA, and remained free of disease (mean 10.3 months). CONCLUSION The high specificity and NPV of ctHPVDNA after SA suggest ctHPVDNA may have a role in determining the omission of PT adjuvant (chemo)radiation in select patients.
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Affiliation(s)
- Spenser S Souza
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, United States of America
| | - Erika M Stephens
- School of Medicine, University of California-San Francisco, United States of America
| | - Alexandra T Bourdillon
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, United States of America
| | | | - Zainab Farzal
- Division of Head and Neck Oncologic and Endocrine Surgery, Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, United States of America
| | - Karolina Plonowska-Hirschfeld
- Department of Otolaryngology-Head and Neck Surgery, University of California-San Francisco, United States of America
| | - Jesse R Qualliotine
- Division of Head and Neck Oncologic Surgery, Department of Otolaryngology-Head and Neck Surgery, University of California-San Diego, United States of America
| | - Chase M Heaton
- Division of Head and Neck Oncologic Surgery, Department of Otolaryngology-Head and Neck Surgery, University of California-San Diego, United States of America
| | - Patrick K Ha
- Division of Head and Neck Oncologic Surgery, Department of Otolaryngology-Head and Neck Surgery, University of California-San Diego, United States of America
| | - William R Ryan
- Division of Head and Neck Oncologic Surgery, Department of Otolaryngology-Head and Neck Surgery, University of California-San Diego, United States of America.
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6
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Iseas S, Mariano G, Gros L, Baba-Hamed N, De Parades V, Adam J, Raymond E, Abba MC. Unraveling Emerging Anal Cancer Clinical Biomarkers from Current Immuno-Oncogenomics Advances. Mol Diagn Ther 2024; 28:201-214. [PMID: 38267771 PMCID: PMC10925578 DOI: 10.1007/s40291-023-00692-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
Anal squamous cell carcinoma (ASCC) is a rare gastrointestinal malignancy associated with high-risk human papillomavirus (HPV) and is currently one of the fastest-growing causes of cancer incidence and mortality in developed countries. Although next-generation sequencing technologies (NGS) have revolutionized cancer and immuno-genomic research in various tumor types, a limited amount of clinical research has been developed to investigate the expression and the functional characterization of genomic data in ASCC. Herein, we comprehensively assess recent advancements in "omics" research, including a systematic analysis of genome-based studies, aiming to identify the most relevant ASCC cancer driver gene expressions and their associated signaling pathways. We also highlight the most significant biomarkers associated with anal cancer progression, gene expression of potential diagnostic biomarkers, expression of therapeutic drug targets, and emerging treatment opportunities. This review stresses the urgent need for developing target-specific therapies in ASCC. By illuminating the molecular characteristics and drug-target expression in ASCC, this study aims to provide insights for the development of precision medicine in anal cancer.
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Affiliation(s)
- Soledad Iseas
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France.
| | - Golubicki Mariano
- Oncology Unit, Gastroenterology Hospital "Dr. Carlos Bonorino Udaondo", Av. Caseros 2061, C1264, Ciudad Autónoma de Buenos Aires, Argentina
| | - Louis Gros
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Nabil Baba-Hamed
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Vincent De Parades
- Proctology Unit, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Julien Adam
- Pathology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Eric Raymond
- Medical Oncology Department, Paris-St Joseph Hospital, 185 rue Raymond Losserand, 75014, Paris, France
| | - Martin Carlos Abba
- Basic and Applied Immunological Research Center (CINIBA), School of Medical Sciences, NationalUniversity of La Plata, Calle 60 y 120, C1900, La Plata, Argentina.
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Naegele S, Ruiz-Torres DA, Zhao Y, Goss D, Faden DL. Comparing the Diagnostic Performance of Quantitative PCR, Digital Droplet PCR, and Next-Generation Sequencing Liquid Biopsies for Human Papillomavirus-Associated Cancers. J Mol Diagn 2024; 26:179-190. [PMID: 38103593 PMCID: PMC10918646 DOI: 10.1016/j.jmoldx.2023.11.007] [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: 04/28/2023] [Revised: 08/29/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Human papillomavirus (HPV)-associated cancers, including oropharyngeal squamous cell carcinoma (HPV + OPSCC), cervical cancer, and squamous cell carcinoma of the anus (HPV + SCCA), release circulating tumor HPV DNA (ctHPVDNA) into the blood. The diagnostic performance of ctHPVDNA detection depends on the approaches used and the individual assay metrics. A comparison of these approaches has not been systematically performed to inform expected performance, which in turn affects clinical interpretation. A meta-analysis was performed using Ovid MEDLINE, Embase, and Web of Science Core Collection databases to assess the diagnostic accuracy of ctHPVDNA detection across cancer anatomic sites, detection platforms, and blood components. The population included patients with HPV + OPSCC, HPV-associated cervical cancer, and HPV + SCCA with pretreatment samples analyzed by quantitative PCR (qPCR), digital droplet PCR (ddPCR), or next-generation sequencing (NGS). Thirty-six studies involving 2986 patients met the inclusion criteria. The sensitivity, specificity, and quality of each study were assessed and pooled for each analysis. The sensitivity of ctHPVDNA detection was greatest with NGS, followed by ddPCR and then qPCR when pooling all studies, whereas specificity was similar (sensitivity: ddPCR > qPCR, P < 0.001; NGS > ddPCR, P = 0.014). ctHPVDNA from OPSCC was more easily detected compared with cervical cancer and SCCA, overall (P = 0.044). In conclusion, detection platform, anatomic site of the cancer, and blood component used affects ctHPVDNA detection and must be considered when interpreting results. Plasma NGS-based testing may be the most sensitive approach for ctHPVDNA overall.
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Affiliation(s)
- Saskia Naegele
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Daniel A Ruiz-Torres
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Yan Zhao
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Deborah Goss
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts
| | - Daniel L Faden
- Department of Otolaryngology-Head and Neck Surgery, Massachusetts Eye and Ear, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts; Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
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Agelaki S, Boukovinas I, Athanasiadis I, Trimis G, Dimitriadis I, Poughias L, Morais E, Sabale U, Bencina G, Athanasopoulos C. A systematic literature review of the human papillomavirus prevalence in locally and regionally advanced and recurrent/metastatic head and neck cancers through the last decade: The "ALARM" study. Cancer Med 2024; 13:e6916. [PMID: 38247106 PMCID: PMC10905345 DOI: 10.1002/cam4.6916] [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: 07/18/2023] [Revised: 11/29/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024] Open
Abstract
AIMS The aim of this systematic literature review was to provide updated information on human papillomavirus (HPV) prevalence in locally and regionally advanced (LA) and recurrent/metastatic (RM) head and neck cancer (HNC) worldwide. METHODS Electronic searches were conducted on clinicaltrials.gov, MEDLINE/PubMed, Embase, and ASCO/ESMO journals of congresses for interventional studies (IS; Phase I-III trials) as well as MEDLINE and Embase for non-interventional studies (NIS) of LA/RM HNC published between January 01, 2010 and December 31, 2020. Criteria for study selection included: availability of HPV prevalence data for LA/RM HNC patients, patient enrollment from January 01, 2010 onward, and oropharyngeal cancer (OPC) included among HNC types. HPV prevalence per study was calculated as proportion of HPV+ over total number of enrolled patients. For overall HPV prevalence across studies, mean of reported HPV prevalence rates across studies and pooled estimate (sum of all HPV+ patients over sum of all patients enrolled) were assessed. RESULTS Eighty-one studies (62 IS; 19 NIS) were included, representing 9607 LA/RM HNC cases, with an overall mean (pooled) HPV prevalence of 32.6% (25.1%). HPV prevalence was 44.7% (44.0%) in LA and 24.3% (18.6%) in RM. Among 2714 LA/RM OPC patients from 52 studies with available data, mean (pooled) value was 55.8% (50.7%). The majority of data were derived from Northern America and Europe, with overall HPV prevalence of 46.0% (42.1%) and 24.7% (25.3%) across studies conducted exclusively in these geographic regions, respectively (Northern Europe: 31.9% [63.1%]). A "p16-based" assay was the most frequently reported HPV detection methodology (58.0%). CONCLUSION Over the last decade, at least one quarter of LA/RM HNC and half of OPC cases studied in IS and NIS were HPV+. This alarming burden is consistent with a potential implication of HPV in the pathogenesis of at least a subgroup of HNC, underscoring the relevance of HPV testing and prophylaxis to HNC prevention and management.
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Affiliation(s)
- Sofia Agelaki
- Laboratory of Translational Oncology, School of MedicineUniversity of CreteHerakleionGreece
- Department of Medical OncologyUniversity General Hospital of HerakleionHerakleionGreece
| | | | | | | | | | | | - Edith Morais
- MSD, Center for Observational and Real‐World Evidence (CORE)LyonFrance
| | - Ugne Sabale
- MSD, Center for Observational and Real‐World Evidence (CORE)StockholmSweden
| | - Goran Bencina
- MSD, Center for Observational and Real‐World Evidence (CORE)MadridSpain
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9
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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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10
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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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11
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Hoerres D, Dai Q, Elmore S, Sheth S, Gupta GP, Kumar S, Gulley ML. Calibration of cell-free DNA measurements by next-generation sequencing. Am J Clin Pathol 2023; 160:314-321. [PMID: 37244060 PMCID: PMC10472744 DOI: 10.1093/ajcp/aqad055] [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: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/29/2023] Open
Abstract
OBJECTIVES Accurate monitoring of disease burden depends on accurate disease marker quantification. Although next-generation sequencing (NGS) is a promising technology for noninvasive monitoring, plasma cell-free DNA levels are often reported in misleading units that are confounded by non-disease-related factors. We proposed a novel strategy for calibrating NGS assays using spiked normalizers to improve precision and to promote standardization and harmonization of analyte concentrations. METHODS In this study, we refined our NGS protocol to calculate absolute analyte concentrations to (1) adjust for assay efficiency, as judged by recovery of spiked synthetic normalizer DNAs, and (2) calibrate NGS values against droplet digital polymerase chain reaction (ddPCR). As a model target, we chose the Epstein-Barr virus (EBV) genome. In patient (n = 12) and mock (n = 12) plasmas, NGS and 2 EBV ddPCR assays were used to report EBV load in copies per mL of plasma. RESULTS Next-generation sequencing was equally sensitive to ddPCR, with improved linearity when NGS values were normalized for spiked DNA read counts (R2 = 0.95 for normalized vs 0.91 for raw read concentrations). Linearity permitted NGS calibration to each ddPCR assay, achieving equivalent concentrations (copies/mL). CONCLUSIONS Our novel strategy for calibrating NGS assays suggests potential for a universal reference material to overcome biological and preanalytical variables hindering traditional NGS strategies for quantifying disease burden.
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Affiliation(s)
- Derek Hoerres
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Qunsheng Dai
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Sandra Elmore
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
| | - Siddharth Sheth
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Division of Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Sunil Kumar
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
| | - Margaret L Gulley
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, US
- Lineberger Comprehensive Cancer Center, Chapel Hill, NC, US
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12
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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: 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: 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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13
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Ginzac A, Ferreira MC, Cayre A, Bouvet C, Biau J, Molnar I, Saroul N, Pham-Dang N, Durando X, Bernadach M. Prediction of residual disease using circulating DNA detection after potentiated radiotherapy for locally advanced head and neck cancer (NeckTAR): a study protocol for a prospective, multicentre trial. BMC Cancer 2023; 23:621. [PMID: 37400806 DOI: 10.1186/s12885-023-11136-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023] Open
Abstract
BACKGROUND Sensitive and reproducible detection of residual disease after treatment is a major challenge for patients with locally advanced head and neck cancer. Indeed, the current imaging techniques are not always reliable enough to determine the presence of residual disease. The aim of the NeckTAR trial is to assess the ability of circulating DNA (cDNA), both tumoral and viral, at three months post-treatment, to predict residual disease, at the time of the neck dissection, among patients with partial cervical lymph node response on PET-CT, after potentiated radiotherapy. METHODS This will be an interventional, multicentre, single-arm, open-label, prospective study. A blood sample will be screened for cDNA before potentiated radiotherapy and after 3 months if adenomegaly persists on the CT scan 3 months after the end of treatment. Patients will be enrolled in 4 sites in France. Evaluable patients, i.e. those with presence of cDNA at inclusion, an indication for neck dissection, and a blood sample at M3, will be followed for 30 months. Thirty-two evaluable patients are expected to be recruited in the study. DISCUSSION The decision to perform neck dissection in case of persistent cervical adenopathy after radio-chemotherapy for locally advanced head and neck cancer is not always straightforward. Although studies have shown that circulating tumour DNA is detectable in a large proportion of patients with head and neck cancer, enabling the monitoring of response, the current data is insufficient to allow routine use of this marker. Our study could lead to better identification of patients who do not have residual lymph node disease in order to avoid neck dissection and preserve their quality-of-life while maintaining their prospects of survival. TRIAL REGISTRATION Clinicaltrials.gov: NCT05710679, registered on 02/02/2023, https://clinicaltrials.gov/ct2/show/ . Identifier with the French National Agency for the Safety of Medicines and Health Products (ANSM): N°ID RCB 2022-A01668-35, registered on July 15th, 2022.
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Affiliation(s)
- Angeline Ginzac
- Division de Recherche Clinique, Clermont Auvergne University, INSERM, U1240, Molecular Imaging and Theranostic Strategies, Jean PERRIN Center, 58, Rue Montalembert, 63011, Clermont-Ferrand, France.
- Clinical Investigation Center, UMR501, 63011, Clermont-Ferrand, France.
- Clinical Research Division, Delegation for Clinical Research and Innovation, Jean PERRIN Center, 63011, Clermont-Ferrand, France.
| | - Marie-Céleste Ferreira
- OncoGènAuvergne Laboratory, Pathology Unit, Jean PERRIN Center, Clermont-Ferrand, 63011, France
| | - Anne Cayre
- OncoGènAuvergne Laboratory, Pathology Unit, Jean PERRIN Center, Clermont-Ferrand, 63011, France
| | - Clément Bouvet
- Nuclear Medicine Department, Jean Perrin Center, Clermont Ferrand, 63011, France
| | - Julian Biau
- Radiotherapy department, Jean PERRIN Center, 63011, Clermont-Ferrand, France
| | - Ioana Molnar
- Division de Recherche Clinique, Clermont Auvergne University, INSERM, U1240, Molecular Imaging and Theranostic Strategies, Jean PERRIN Center, 58, Rue Montalembert, 63011, Clermont-Ferrand, France
- Clinical Investigation Center, UMR501, 63011, Clermont-Ferrand, France
- Clinical Research Division, Delegation for Clinical Research and Innovation, Jean PERRIN Center, 63011, Clermont-Ferrand, France
| | - Nicolas Saroul
- Department of Otorhinolaryngology - Head and Neck Surgery, Gabriel Montpied University Hospital Center, 63000, Clermont-Ferrand, France
| | - Nathalie Pham-Dang
- Department of Maxillofacial and Plastic Surgery, Estaing University Hospital Center Clermont-Ferrand, 63000, Clermont-Ferrand, France
| | - Xavier Durando
- Division de Recherche Clinique, Clermont Auvergne University, INSERM, U1240, Molecular Imaging and Theranostic Strategies, Jean PERRIN Center, 58, Rue Montalembert, 63011, Clermont-Ferrand, France
- Clinical Investigation Center, UMR501, 63011, Clermont-Ferrand, France
- Clinical Research Division, Delegation for Clinical Research and Innovation, Jean PERRIN Center, 63011, Clermont-Ferrand, France
- Medical Oncology Department, Jean PERRIN Center, 63011, Clermont-Ferrand, France
| | - Maureen Bernadach
- Clinical Research Division, Delegation for Clinical Research and Innovation, Jean PERRIN Center, 63011, Clermont-Ferrand, France
- Medical Oncology Department, Jean PERRIN Center, 63011, Clermont-Ferrand, France
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14
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Mittelstadt S, Kelemen O, Admard J, Gschwind A, Koch A, Wörz S, Oberlechner E, Engler T, Bonzheim I, Staebler A, Weidner N, Stubenrauch F, Iftner T, Riess O, Schroeder C, Kommoss S, Ossowski S. Detection of circulating cell-free HPV DNA of 13 HPV types for patients with cervical cancer as potential biomarker to monitor therapy response and to detect relapse. Br J Cancer 2023; 128:2097-2103. [PMID: 36973448 DOI: 10.1038/s41416-023-02233-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/27/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND HPV-related cervical cancer (CC) is the fourth most frequent cancer in women worldwide. Cell-free tumour DNA is a potent biomarker to detect treatment response, residual disease, and relapse. We investigated the potential use of cell-free circulating HPV-DNA (cfHPV-DNA) in plasma of patients with CC. METHODS cfHPV-DNA levels were measured using a highly sensitive next-generation sequencing-based approach targeting a panel of 13 high-risk HPV types. RESULTS Sequencing was performed in 69 blood samples collected from 35 patients, of which 26 were treatment-naive when the first liquid biopsy sample was retrieved. cfHPV-DNA was successfully detected in 22/26 (85%) cases. A significant correlation between tumour burden and cfHPV-DNA levels was observed: cfHPV-DNA was detectable in all treatment-naive patients with advanced-stage disease (17/17, FIGO IB3-IVB) and in 5/9 patients with early-stage disease (FIGO IA-IB2). Sequential samples revealed a decrease of cfHPV-DNA levels in 7 patients corresponding treatment response and an increase in a patient with relapse. CONCLUSIONS In this proof-of-concept study we demonstrated the potential of cfHPV-DNA as a biomarker for therapy monitoring in patients with primary and recurrent CC. Our findings facilitate the development of a sensitive and precise, non-invasive, inexpensive, and easily accessible tool in CC diagnosis, therapy monitoring and follow-up.
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Affiliation(s)
- Suzana Mittelstadt
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany.
| | - Olga Kelemen
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Jakob Admard
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
| | - Axel Gschwind
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - André Koch
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Sarah Wörz
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Ernst Oberlechner
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Tobias Engler
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Irina Bonzheim
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Annette Staebler
- Institute of Pathology and Neuropathology, University Hospital Tübingen, Tübingen, Germany
| | - Nicola Weidner
- Department of Radiooncology, University Hospital Tübingen, Tübingen, Germany
| | - Frank Stubenrauch
- Institute for Medical Virology and Epidemiology of Viral Disease, University Hospital Tübingen, Tübingen, Germany
| | - Thomas Iftner
- Institute for Medical Virology and Epidemiology of Viral Disease, University Hospital Tübingen, Tübingen, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), partner site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Kommoss
- Department of Women's Health, University Hospital Tübingen, Tübingen, Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
- NGS Competence Center Tübingen (NCCT), University of Tübingen, Tübingen, Germany
- German Cancer Consortium (DKTK), partner site Tübingen and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
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15
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Lin G, Li J. Circulating HPV DNA in HPV-associated cancers. Clin Chim Acta 2023; 542:117269. [PMID: 36841427 DOI: 10.1016/j.cca.2023.117269] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 02/26/2023]
Abstract
Human papillomavirus (HPV) infections are the primary cause of almost all cervical cancers, anal cancers, and a variable proportion of other anogenital tumors, as well as head and neck cancers. Circulating HPV DNA (cHPV-DNA) is emerging as a biomarker with extensive potential in the management of HPV-driven malignancies. There has been a rapid advancement in the development of techniques for analyzing cHPV-DNA for the detection, characterization, and monitoring of HPV-associated cancers. As clinical evidence accumulates, it is becoming evident that cHPV-DNA can be used as a diagnostic tool. By conducting clinical trials assessing the clinical utility of cHPV-DNA, the full potential of cHPV-DNA for the screening, diagnosis, and treatment of HPV-related malignancies can be corroborated. In this review, we examine the current landscape of applications for cHPV-DNA liquid biopsies throughout the cancer care continuum, highlighting future opportunities for research and integration into clinical practice.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, PR China.
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16
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Mack M, Broche J, George S, Hajjari Z, Janke F, Ranganathan L, Ashouri M, Bleul S, Desuki A, Engels C, Fliedner SM, Hartmann N, Hummel M, Janning M, Kiel A, Köhler T, Koschade S, Lablans M, Lambarki M, Loges S, Lueong S, Meyer S, Ossowski S, Scherer F, Schroeder C, Skowronek P, Thiede C, Uhl B, Vehreschild JJ, von Bubnoff N, Wagner S, Werner TV, Westphalen CB, Fresser P, Sültmann H, Tinhofer I, Winter C. The DKTK EXLIQUID consortium – exploiting liquid biopsies to advance cancer precision medicine for molecular tumor board patients. J LAB MED 2022. [DOI: 10.1515/labmed-2022-0071] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
Abstract
Testing for genetic alterations in tumor tissue allows clinicians to identify patients who most likely will benefit from molecular targeted treatment. EXLIQUID – exploiting liquid biopsies to advance cancer precision medicine – investigates the potential of additional non-invasive tools for guiding therapy decisions and monitoring of advanced cancer patients. The term “liquid biopsy” (LB) refers to non-invasive analysis of tumor-derived circulating material such as cell-free DNA in blood samples from cancer patients. Although recent technological advances allow sensitive and specific detection of LB biomarkers, only few LB assays have entered clinical routine to date. EXLIQUID is a German Cancer Consortium (DKTK)-wide joint funding project that aims at establishing LBs as a minimally-invasive tool to analyze molecular changes in circulating tumor DNA (ctDNA). Here, we present the structure, clinical aim, and methodical approach of the new DKTK EXLIQUID consortium. Within EXLIQUID, we will set up a multicenter repository of high-quality LB samples from patients participating in DKTK MASTER and local molecular tumor boards, which use molecular profiles of tumor tissues to guide targeted therapies. We will develop LB assays for monitoring of therapy efficacy by the analysis of tumor mutant variants and tumor-specific DNA methylation patterns in ctDNA from these patients. By bringing together LB experts from all DKTK partner sites and exploiting the diversity of their particular expertise, complementary skills and technologies, the EXLIQUID consortium addresses the challenges of translating LBs into the clinic. The DKTK structure provides EXLIQUID a unique position for the identification of liquid biomarkers even in less common tumor types, thereby extending the group of patients benefitting from non-invasive LB testing. Besides its scientific aims, EXLIQUID is building a valuable precision oncology cohort and LB platform which will be available for future collaborative research studies within the DKTK and beyond.
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Affiliation(s)
- Matthias Mack
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Julian Broche
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephen George
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Zahra Hajjari
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Janke
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Lavanya Ranganathan
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohammadreza Ashouri
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sabine Bleul
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Alexander Desuki
- University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg-University Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Cecilia Engels
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephanie M.J. Fliedner
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Nils Hartmann
- Institute of Pathology, University Medical Center JGU Mainz , Mainz , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Michael Hummel
- Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Melanie Janning
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Alexander Kiel
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Thomas Köhler
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sebastian Koschade
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Martin Lablans
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Mohamed Lambarki
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sonja Loges
- DKFZ-Hector Cancer Institute at the University Medical Center Mannheim , Mannheim , Germany
- Division of Personalized Medical Oncology (A420) , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Personalized Oncology, Medical Faculty Mannheim , University Hospital Mannheim, University of Heidelberg , Mannheim , Germany
| | - Smiths Lueong
- West German Cancer Center , Bridge Institute of Experimental Tumor Therapy, University Hospital Essen , Essen , Germany
- German Cancer Consortium (DKTK), Partner Site Essen/Düsseldorf , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Sandra Meyer
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Florian Scherer
- Department of Medicine I , Medical Center – University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen , Tübingen , Germany
- German Cancer Consortium (DKTK), Partner Site Tübingen , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrick Skowronek
- Complex Data Processing in Medical Informatics , University Medical Center Mannheim , Mannheim , Germany
- German Cancer Consortium (DKTK); and Federated Information Systems , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christian Thiede
- Department of Medicine I , University Hospital Carl Gustav Carus , Dresden , Germany
- German Cancer Consortium (DKTK), Partner Site Dresden , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Barbara Uhl
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Jörg Janne Vehreschild
- University Hospital Frankfurt , Frankfurt , Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Nikolas von Bubnoff
- University Cancer Center Schleswig-Holstein, University Medical Center Schleswig-Holstein , Kiel/Lübeck , Germany
| | - Sebastian Wagner
- German Cancer Consortium (DKTK), Partner Site Frankfurt/Mainz , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- Department of Medicine, Hematology/Oncology , Goethe University , Frankfurt , Germany
| | - Tamara V. Werner
- Medical Center, Medical Faculty , Institute for Surgical Pathology, University of Freiburg , Freiburg , Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - C. Benedikt Westphalen
- Comprehensive Cancer Center Munich & Department of Medicine III , Ludwig Maximilian University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Patrizia Fresser
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Holger Sültmann
- Division of Cancer Genome Research , German Cancer Research Center (DKFZ) , Heidelberg , Germany
- German Cancer Consortium (DKTK) , Heidelberg , Germay
| | - Ingeborg Tinhofer
- Department of Radiooncology and Radiotherapy , Charité University Hospital Berlin , Berlin , Germany
- German Cancer Consortium (DKTK), Partner Site Berlin , German Cancer Research Center (DKFZ) , Heidelberg , Germany
| | - Christof Winter
- School of Medicine , Institute of Clinical Chemistry and Pathobiochemistry, Technical University of Munich , Munich , Germany
- German Cancer Consortium (DKTK), Partner Site Munich , German Cancer Research Center (DKFZ) , Heidelberg , Germany
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17
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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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18
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Paramasivam A. Plasma circulating tumor DNA as a molecular marker for oral cancer. Oral Oncol 2022; 130:105926. [PMID: 35596978 DOI: 10.1016/j.oraloncology.2022.105926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 05/10/2022] [Indexed: 12/12/2022]
Affiliation(s)
- Arumugam Paramasivam
- Centre for Cellular and Molecular Research, Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Chennai, India.
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19
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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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20
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Emerging precision diagnostics in advanced cutaneous squamous cell carcinoma. NPJ Precis Oncol 2022; 6:17. [PMID: 35322182 PMCID: PMC8943023 DOI: 10.1038/s41698-022-00261-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 02/11/2022] [Indexed: 12/14/2022] Open
Abstract
Advanced cutaneous squamous cell carcinoma (cSCC) encompasses unresectable and metastatic disease. Although immune checkpoint inhibition has been approved for this entity recently, a considerable proportion of cases is associated with significant morbidity and mortality. Clinical, histopathological, and radiological criteria are used for current diagnostics, classification, and therapeutic decision-making. The identification of complex molecular biomarkers to accurately stratify patients is a not yet accomplished requirement to further shift current diagnostics and care to a personalized precision medicine. This article highlights new insights into the mutational profile of cSCC, summarizes current diagnostic and therapeutic standards, and discusses emerging diagnostic approaches with emphasis on liquid biopsy and tumor tissue-based analyses.
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21
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Haring CT, Dermody SM, Yalamanchi P, Kang SY, Old MO, Chad Brenner J, Spector ME, Rocco JW. The future of circulating tumor DNA as a biomarker in HPV related oropharyngeal squamous cell carcinoma. Oral Oncol 2022; 126:105776. [DOI: 10.1016/j.oraloncology.2022.105776] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/02/2022] [Accepted: 02/13/2022] [Indexed: 12/30/2022]
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22
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Mishra V, Singh A, Chen X, Rosenberg AJ, Pearson AT, Zhavoronkov A, Savage PA, Lingen MW, Agrawal N, Izumchenko E. Application of liquid biopsy as multi-functional biomarkers in head and neck cancer. Br J Cancer 2022; 126:361-370. [PMID: 34876674 PMCID: PMC8810877 DOI: 10.1038/s41416-021-01626-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a molecularly heterogeneous disease, with a 5-year survival rate that still hovers at ~60% despite recent advancements. The advanced stage upon diagnosis, limited success with effective targeted therapy and lack of reliable biomarkers are among the key factors underlying the marginally improved survival rates over the decades. Prevention, early detection and biomarker-driven treatment adaptation are crucial for timely interventions and improved clinical outcomes. Liquid biopsy, analysis of tumour-specific biomarkers circulating in bodily fluids, is a rapidly evolving field that may play a striking role in optimising patient care. In recent years, significant progress has been made towards advancing liquid biopsies for non-invasive early cancer detection, prognosis, treatment adaptation, monitoring of residual disease and surveillance of recurrence. While these emerging technologies have immense potential to improve patient survival, numerous methodological and biological limitations must be overcome before their implementation into clinical practice. This review outlines the current state of knowledge on various types of liquid biopsies in HNSCC, and their potential applications for diagnosis, prognosis, grading treatment response and post-treatment surveillance. It also discusses challenges associated with the clinical applicability of liquid biopsies and prospects of the optimised approaches in the management of HNSCC.
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Affiliation(s)
- Vasudha Mishra
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Alka Singh
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Xiangying Chen
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Ari J Rosenberg
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Alexander T Pearson
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | | | - Peter A Savage
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Mark W Lingen
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Nishant Agrawal
- Department of Surgery, Section of Otolaryngology-Head and Neck Surgery, University of Chicago, Chicago, IL, USA.
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA.
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23
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Serial ctDNA analysis predicts clinical progression in patients with advanced urothelial carcinoma. Br J Cancer 2022; 126:430-439. [PMID: 35046520 PMCID: PMC8810988 DOI: 10.1038/s41416-021-01648-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 10/28/2021] [Accepted: 11/22/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Targeted sequencing of circulating tumour DNA (ctDNA) is a promising tool to monitor dynamic changes in the variant allele frequencies (VAF) of genomic alterations and predict clinical outcomes in patients with advanced urothelial carcinoma (UC). METHODS We performed targeted sequencing of 182 serial ctDNA samples from 53 patients with advanced UC. RESULTS Serial ctDNA-derived metrics predicted the clinical outcomes in patients with advanced UC. Combining serial ctDNA aggregate VAF (aVAF) values with clinical factors, including age, sex, and liver metastasis, improved the performance of prognostic models. An increase of the ctDNA aVAF by ≥1 in serial ctDNA samples predicted disease progression within 6 months in 90% of patients. The majority of patients with aVAFs ≤0.7 in three consecutive ctDNA samples achieved durable clinical responses (≥6 months). CONCLUSIONS Serial ctDNA analysis predicts disease progression and enables dynamic monitoring to guide precision medicine in patients with advanced UC.
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24
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Boniface CT, Spellman PT. Blood, Toil, and Taxoteres: Biological Determinates of Treatment-Induce ctDNA Dynamics for Interpreting Tumor Response. Pathol Oncol Res 2022; 28:1610103. [PMID: 35665409 PMCID: PMC9160182 DOI: 10.3389/pore.2022.1610103] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022]
Abstract
Collection and analysis of circulating tumor DNA (ctDNA) is one of the few methods of liquid biopsy that measures generalizable and tumor specific molecules, and is one of the most promising approaches in assessing the effectiveness of cancer care. Clinical assays that utilize ctDNA are commercially available for the identification of actionable mutations prior to treatment and to assess minimal residual disease after treatment. There is currently no clinical ctDNA assay specifically intended to monitor disease response during treatment, partially due to the complex challenge of understanding the biological sources of ctDNA and the underlying principles that govern its release. Although studies have shown pre- and post-treatment ctDNA levels can be prognostic, there is evidence that early, on-treatment changes in ctDNA levels are more accurate in predicting response. Yet, these results also vary widely among cohorts, cancer type, and treatment, likely due to the driving biology of tumor cell proliferation, cell death, and ctDNA clearance kinetics. To realize the full potential of ctDNA monitoring in cancer care, we may need to reorient our thinking toward the fundamental biological underpinnings of ctDNA release and dissemination from merely seeking convenient clinical correlates.
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Affiliation(s)
- Christopher T. Boniface
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
| | - Paul T. Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
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25
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Honoré N, Galot R, van Marcke C, Limaye N, Machiels JP. Liquid Biopsy to Detect Minimal Residual Disease: Methodology and Impact. Cancers (Basel) 2021; 13:5364. [PMID: 34771526 PMCID: PMC8582541 DOI: 10.3390/cancers13215364] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
One reason why some patients experience recurrent disease after a curative-intent treatment might be the persistence of residual tumor cells, called minimal residual disease (MRD). MRD cannot be identified by standard radiological exams or clinical evaluation. Tumor-specific alterations found in the blood indirectly diagnose the presence of MRD. Liquid biopsies thus have the potential to detect MRD, allowing, among other things, the detection of circulating tumor DNA (ctDNA), circulating tumor cells (CTC), or tumor-specific microRNA. Although liquid biopsy is increasingly studied, several technical issues still limit its clinical applicability: low sensitivity, poor standardization or reproducibility, and lack of randomized trials demonstrating its clinical benefit. Being able to detect MRD could give clinicians a more comprehensive view of the risk of relapse of their patients and could select patients requiring treatment escalation with the goal of improving cancer survival. In this review, we are discussing the different methodologies used and investigated to detect MRD in solid cancers, their respective potentials and issues, and the clinical impacts that MRD detection will have on the management of cancer patients.
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Affiliation(s)
- Natasha Honoré
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
| | - Rachel Galot
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Cédric van Marcke
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Nisha Limaye
- Genetics of Autoimmune Diseases and Cancer, de Duve Institute, Université Catholique de Louvain (UCLouvain), 1200 Brussels, Belgium;
| | - Jean-Pascal Machiels
- Institute for Experimental and Clinical Research (IREC, Pôle MIRO), Université Catholique de Louvain (UCLouvain) ,1200 Brussels, Belgium; (R.G.); (C.v.M.)
- Department of Medical Oncology, Institut Roi Albert II, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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26
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Thompson MK, Gale D, Brenton JD. Circulating tumour DNA for clinicians: current and future clinical applications. Clin Radiol 2021; 76:737-747. [PMID: 34389159 DOI: 10.1016/j.crad.2021.07.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 07/20/2021] [Indexed: 12/12/2022]
Abstract
This review introduces clinicians to the basic concepts of the biology of circulating tumour DNA (ctDNA), which is required to understand clinical use of ctDNA technology. We provide an overview of how new technology has improved the sensitivity of ctDNA detection over the last decade and the available techniques for ctDNA analysis including whole-genome sequencing (WGS), targeted cancer-associated gene panels, and methylation analysis. We discuss the most recent evidence from clinical trials for ctDNA in patient care including precision treatment of advanced cancers, disease monitoring, improving adjuvant treatment, and screening for early detection of cancer. Finally, we outline how ctDNA is likely to directly impact radiologists, and identify further research required for ctDNA to progress into routine clinical application.
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Affiliation(s)
- M K Thompson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK.
| | - D Gale
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
| | - J D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, UK; Department of Oncology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, CB2 0QQ, UK; Cancer Research UK Cambridge Centre, University of Cambridge, Cambridge, CB2 0RE, UK
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27
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Campo F, Zocchi J, Moretto S, Mazzola F, Petruzzi G, Donà MG, Benevolo M, Iocca O, De Virgilio A, Pichi B, Manciocco V, Pellini R. Cell-Free Human Papillomavirus-DNA for Monitoring Treatment Response of Head and Neck Squamous Cell Carcinoma: Systematic Review and Meta-Analysis. Laryngoscope 2021; 132:560-568. [PMID: 34236084 DOI: 10.1002/lary.29739] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 06/22/2021] [Accepted: 06/26/2021] [Indexed: 11/09/2022]
Abstract
OBJECTIVES/HYPOTHESIS The aim of this study was to assess the value of cell-free human papillomavirus-DNA (cfHPV-DNA) as a diagnostic test for the post-treatment surveillance of patients with HPV-positive head and neck squamous cell carcinoma (HNSCC) through a systematic review and meta-analysis. STUDY DESIGN Systematic review and meta-analysis. METHODS A literature search was conducted in three databases (MEDLINE, Embase, and Scopus) in January 2021. The population included patients with HPV-positive HNSCC. The intervention was the use of the repeated liquid biopsy with circulating HPV-DNA detection during follow-up. The outcome was to establish the value of cfHPV-DNA as a diagnostic test for the post-treatment surveillance of patients with HPV-positive HNSCC. RESULTS Ten studies included in the meta-analysis provided a total of 457 patients with HPV-positive HNSCC. The meta-analytic study estimated the diagnostic performance of cfHPV-DNA as follows: pooled sensitivity and specificity of 0.65 (95% confidence interval [CI]: 0.40-0.84) and 0.99 (99% CI: 0.96-0.99), respectively; positive and negative likelihood ratios of 62.5 (99% CI: 22.9-170.2) and 0.05 (99% CI: 0.013-0.24), respectively; and pooled diagnostic odds ratio of 371.66 (99% CI: 60.4-2286.7). CONCLUSION Currently, the follow-up protocol for HNSCC patients includes routine clinical evaluation and radiological imaging. Biomarkers to monitor this disease are not established. Considering its high specificity, cfHPV-DNA represents a potential confirmatory test in the case of positive positron emission tomography and computed tomography. In the near future, cfHPV-DNA could be used as a biomarker for monitoring the treatment response during the clinical trials of de-escalation therapy or immunotherapy. Larger sample sizes and the homologation of study protocols and methodology are needed to better establish its utility in the clinical practice. Laryngoscope, 2021.
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Affiliation(s)
- Flaminia Campo
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy.,Department of Sense Organs, Sapienza University of Rome, Rome, Italy
| | - Jacopo Zocchi
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Silvia Moretto
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Francesco Mazzola
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Gerardo Petruzzi
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Maria G Donà
- STI/HIV Unit, San Gallicano Dermatological Institute IRCCS, Rome, Italy
| | - Maria Benevolo
- Department of Pathology, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Oreste Iocca
- Division of Maxillofacial Surgery, Surgical Science Department, University of Torino, Torino, Italy
| | - Armando De Virgilio
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,Otorhinolaryngology Unit, IRCCS Humanitas Research Hospital, Milan, Italy
| | - Barbara Pichi
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Valentina Manciocco
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy
| | - Raul Pellini
- Department of Otolaryngology-Head and Neck Surgery, Regina Elena National Cancer Institute IRCCS, Rome, Italy
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28
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Human Papillomavirus Detection by Whole-Genome Next-Generation Sequencing: Importance of Validation and Quality Assurance Procedures. Viruses 2021; 13:v13071323. [PMID: 34372528 PMCID: PMC8310033 DOI: 10.3390/v13071323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/04/2021] [Accepted: 06/18/2021] [Indexed: 12/27/2022] Open
Abstract
Next-generation sequencing (NGS) yields powerful opportunities for studying human papillomavirus (HPV) genomics for applications in epidemiology, public health, and clinical diagnostics. HPV genotypes, variants, and point mutations can be investigated in clinical materials and described in previously unprecedented detail. However, both the NGS laboratory analysis and bioinformatical approach require numerous steps and checks to ensure robust interpretation of results. Here, we provide a step-by-step review of recommendations for validation and quality assurance procedures of each step in the typical NGS workflow, with a focus on whole-genome sequencing approaches. The use of directed pilots and protocols to ensure optimization of sequencing data yield, followed by curated bioinformatical procedures, is particularly emphasized. Finally, the storage and sharing of data sets are discussed. The development of international standards for quality assurance should be a goal for the HPV NGS community, similar to what has been developed for other areas of sequencing efforts including microbiology and molecular pathology. We thus propose that it is time for NGS to be included in the global efforts on quality assurance and improvement of HPV-based testing and diagnostics.
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Dermody SM, Haring CT, Bhambhani C, Tewari M, Brenner JC, Swiecicki PL. Surveillance and Monitoring Techniques for HPV-Related Head and Neck Squamous Cell Carcinoma: Circulating Tumor DNA. Curr Treat Options Oncol 2021; 22:21. [PMID: 33559043 DOI: 10.1007/s11864-021-00821-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/11/2021] [Indexed: 12/11/2022]
Abstract
OPINION STATEMENT Human papilloma virus (HPV) related head and neck cancer is rising in prevalence, preferentially affecting young patients and imparting long term toxicities. Despite this, there are no screening tests or clinical biomarkers for treatment monitoring. HPV circulating tumor DNA (HPV ctDNA) represents a novel circulating biomarker which may provide real-time assessment of tumor response to therapy and recurrence. Early work suggests the promise of this assay as a predictive biomarker in numerous clinical settings, namely risk of recurrence after chemoradiation in locally advanced disease. Advancement of these findings to the clinic will require a collaborative effort in the field, including technical harmonization of assay testing characteristics, understanding of the normal kinetics in patients being treated with standard of care therapies, and appropriately designed phase III trials prior to implementation in the clinic. If successful, HPV ctDNA has the potential to revolutionize clinical trial treatment paradigms and transform patient care.
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Affiliation(s)
- Sarah M Dermody
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, USA
| | - Catherine T Haring
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, USA
| | - Chandan Bhambhani
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Hematology/Oncology, Ann Arbor Veterans Affairs Medical Center, Ann Arbor, MI, USA
| | - J Chad Brenner
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, USA
| | - Paul L Swiecicki
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, USA.
- Department of Internal Medicine, Division of Hematology/Oncology, Ann Arbor Veterans Affairs Medical Center, Ann Arbor, MI, USA.
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Knebel FH, Barber LJ, Newey A, Kleftogiannis D, Woolston A, Griffiths B, Fenwick K, Bettoni F, Ribeiro MFSA, da Fonseca L, Costa F, Capareli FC, Hoff PM, Sabbaga J, Camargo AA, Gerlinger M. Circulating Tumour DNA Sequencing Identifies a Genetic Resistance-Gap in Colorectal Cancers with Acquired Resistance to EGFR-Antibodies and Chemotherapy. Cancers (Basel) 2020; 12:E3736. [PMID: 33322618 PMCID: PMC7764102 DOI: 10.3390/cancers12123736] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/07/2020] [Indexed: 02/05/2023] Open
Abstract
Epidermal growth factor receptor antibodies (EGFR-Abs) confer a survival benefit in patients with RAS wild-type metastatic colorectal cancer (mCRC), but resistance invariably occurs. Previous data showed that only a minority of cancer cells harboured known genetic resistance drivers when clinical resistance to single-agent EGFR-Abs had evolved, supporting the activity of non-genetic resistance mechanisms. Here, we used error-corrected ctDNA-sequencing (ctDNA-Seq) of 40 cancer genes to identify drivers of resistance and whether a genetic resistance-gap (a lack of detectable genetic resistance mechanisms in a large fraction of the cancer cell population) also occurs in RAS wild-type mCRCs treated with a combination of EGFR-Abs and chemotherapy. We detected one MAP2K1/MEK1 mutation and one ERBB2 amplification in 2/3 patients with primary resistance and KRAS, NRAS, MAP2K1/MEK1 mutations and ERBB2 aberrations in 6/7 patients with acquired resistance. In vitro testing identified MAP2K1/MEK1 P124S as a novel driver of EGFR-Ab resistance. Mutation subclonality analyses confirmed a genetic resistance-gap in mCRCs treated with EGFR-Abs and chemotherapy, with only 13.42% of cancer cells harboring identifiable resistance drivers. Our results support the utility of ctDNA-Seq to guide treatment allocation for patients with resistance and the importance of investigating further non-canonical EGFR-Ab resistance mechanisms, such as microenvironmentally-mediated resistance. The detection of MAP2K1 mutations could inform trials of MEK-inhibitors in these tumours.
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Affiliation(s)
- Franciele H. Knebel
- Translational Oncogenomics Lab, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (F.H.K.); (L.J.B.); (A.N.); (A.W.); (B.G.)
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Louise J. Barber
- Translational Oncogenomics Lab, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (F.H.K.); (L.J.B.); (A.N.); (A.W.); (B.G.)
| | - Alice Newey
- Translational Oncogenomics Lab, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (F.H.K.); (L.J.B.); (A.N.); (A.W.); (B.G.)
| | - Dimitrios Kleftogiannis
- Centre for Evolution and Cancer, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK;
| | - Andrew Woolston
- Translational Oncogenomics Lab, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (F.H.K.); (L.J.B.); (A.N.); (A.W.); (B.G.)
| | - Beatrice Griffiths
- Translational Oncogenomics Lab, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (F.H.K.); (L.J.B.); (A.N.); (A.W.); (B.G.)
| | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK;
| | - Fabiana Bettoni
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Maurício Fernando Silva Almeida Ribeiro
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Leonardo da Fonseca
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Frederico Costa
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Fernanda Cunha Capareli
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Paulo M. Hoff
- Instituto D’Or de Pesquisa e Ensino, IDOR, Oncologia D’Or, Avenida República do Líbano 611, São Paulo 04.502-001, SP, Brazil;
| | - Jorge Sabbaga
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Anamaria A. Camargo
- Sociedade Beneficiente de Senhoras Hospital Sírio Libanês, SBSHSL, Rua Dona Adma Jafet 91, São Paulo 01308-050, SP, Brazil; (F.B.); (M.F.S.A.R.); (L.d.F.); (F.C.); (F.C.C.); (J.S.); (A.A.C.)
| | - Marco Gerlinger
- Translational Oncogenomics Lab, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, UK; (F.H.K.); (L.J.B.); (A.N.); (A.W.); (B.G.)
- GI Cancer Unit, The Royal Marsden Hospital, 203 Fulham Road, London SW3 6JJ, UK
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