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Kumar S, Poria R, Kala D, Nagraik R, Dhir Y, Dhir S, Singh B, Kaushik NK, Noorani MS, Kumar D, Gupta S, Kaushal A. Recent advances in ctDNA detection using electrochemical biosensor for cancer. Discov Oncol 2024; 15:517. [PMID: 39356360 PMCID: PMC11448507 DOI: 10.1007/s12672-024-01365-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/18/2024] [Indexed: 10/03/2024] Open
Abstract
In the quest for early cancer diagnosis, early identification and treatment are paramount. Recently, ctDNA detection has emerged as a viable avenue for early screening of cancer. The examination of ctDNA in fluid biopsies has gained substantial attention in tumor diagnosis and therapy. Both the scientific community and industry are actively exploring this field. However, developing cost-effective, portable, and real-time ctDNA measurement methods using conventional gene detection equipment poses a significant challenge. This challenge has led to the exploration of alternative approaches. Electrochemical biosensors, distinguished by their heightened sensitivity, remarkable specificity, affordability, and excellent portability, have emerged as a promising avenue for ctDNA detection. This review is dedicated to the specific focus on ctDNA detection, highlighting recent advancements in this evolving detection technology. We aimed to reference previous studies related to ctDNA-targeted cancer detection using electrochemical biosensors to advocate the utilization of electrochemical biosensors in healthcare diagnostics. Further research is imperative for the effective integration of ctDNA analysis into point-of-care cancer testing. Innovative approaches utilizing multiple markers need to be explored to advance this technology and make substantial contributions to societal well-being.
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Affiliation(s)
- Sahil Kumar
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Renu Poria
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Deepak Kala
- NL-11 Centera Tetrahertz Laboratory, Institute of High Pressure Physics, Polish Academy of Sciences, 29/37 Sokolowska Street, Warsaw, 01142, Poland
| | - Rupak Nagraik
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Yashika Dhir
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Sunny Dhir
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Bharat Singh
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India
| | - Naveen Kumar Kaushik
- Department of Industrial Biotechnology, College of Biotechnology, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Md Salik Noorani
- Department of Botany, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, 110062, India
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical Sciences, Shoolini University, Solan, 173229, Himachal Pradesh, India.
| | - Shagun Gupta
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India.
| | - Ankur Kaushal
- Department of Bio-Sciences and Technology, Maharishi Markandeshwar (Deemed to Be) University, Mullana, 133203, Ambala, India.
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Piana D, Iavarone F, De Paolis E, Daniele G, Parisella F, Minucci A, Greco V, Urbani A. Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges. Int J Mol Sci 2024; 25:8830. [PMID: 39201516 PMCID: PMC11354793 DOI: 10.3390/ijms25168830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Tumor heterogeneity refers to the diversity observed among tumor cells: both between different tumors (inter-tumor heterogeneity) and within a single tumor (intra-tumor heterogeneity). These cells can display distinct morphological and phenotypic characteristics, including variations in cellular morphology, metastatic potential and variability treatment responses among patients. Therefore, a comprehensive understanding of such heterogeneity is necessary for deciphering tumor-specific mechanisms that may be diagnostically and therapeutically valuable. Innovative and multidisciplinary approaches are needed to understand this complex feature. In this context, proteogenomics has been emerging as a significant resource for integrating omics fields such as genomics and proteomics. By combining data obtained from both Next-Generation Sequencing (NGS) technologies and mass spectrometry (MS) analyses, proteogenomics aims to provide a comprehensive view of tumor heterogeneity. This approach reveals molecular alterations and phenotypic features related to tumor subtypes, potentially identifying therapeutic biomarkers. Many achievements have been made; however, despite continuous advances in proteogenomics-based methodologies, several challenges remain: in particular the limitations in sensitivity and specificity and the lack of optimal study models. This review highlights the impact of proteogenomics on characterizing tumor phenotypes, focusing on the critical challenges and current limitations of its use in different clinical and preclinical models for tumor phenotypic characterization.
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Affiliation(s)
- Diletta Piana
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
| | - Federica Iavarone
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
| | - Elisa De Paolis
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
- Departmental Unit of Molecular and Genomic Diagnostics, Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Gennaro Daniele
- Phase 1 Unit, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy;
| | - Federico Parisella
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
| | - Angelo Minucci
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
- Departmental Unit of Molecular and Genomic Diagnostics, Genomics Core Facility, Gemelli Science and Technology Park (G-STeP), Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Viviana Greco
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
| | - Andrea Urbani
- Department of Basic Biotechnological Sciences, Intensivological and Perioperative Clinics, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (D.P.); (F.I.); (F.P.)
- Departmen Unity of Chemistry, Biochemistry and Clinical Molecular Biology, Department of Diagnostic and Laboratory Medicine, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy; (E.D.P.); (A.M.)
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Li A, Lou E, Leder K, Foo J. Early ctDNA kinetics as a dynamic biomarker of cancer treatment response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.01.601508. [PMID: 39005329 PMCID: PMC11244961 DOI: 10.1101/2024.07.01.601508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Circulating tumor DNA assays are promising tools for the prediction of cancer treatment response. Here, we build a framework for the design of ctDNA biomarkers of therapy response that incorporate variations in ctDNA dynamics driven by specific treatment mechanisms. We develop mathematical models of ctDNA kinetics driven by tumor response to several therapy classes, and utilize them to simulate randomized virtual patient cohorts to test candidate biomarkers. Using this approach, we propose specific biomarkers, based on ctDNA longitudinal features, for targeted therapy, chemotherapy and radiation therapy. We evaluate and demonstrate the efficacy of these biomarkers in predicting treatment response within a randomized virtual patient cohort dataset. These biomarkers are based on novel proposals for ctDNA sampling protocols, consisting of frequent sampling within a compact time window surrounding therapy initiation - which we hypothesize to hold valuable prognostic information on longer-term treatment response. This study highlights a need for tailoring ctDNA sampling protocols and interpretation methodology to specific biological mechanisms of therapy response, and it provides a novel modeling and simulation framework for doing so. In addition, it highlights the potential of ctDNA assays for making early, rapid predictions of treatment response within the first days or weeks of treatment, and generates hypotheses for further clinical testing.
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Affiliation(s)
- Aaron Li
- School of Mathematics, University of Minnesota, Twin Cities, MN, USA
| | - Emil Lou
- Masonic Cancer Center, University of Minnesota, Twin Cities, MN, USA
- Division of Hematology, Oncology, and Transplantation, Department of Medicine, University of Minnesota, MN, USA
| | - Kevin Leder
- Department of Industrial and Systems Engineering, University of Minnesota, Twin Cities, MN, USA
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Twin Cities, MN, USA
- Masonic Cancer Center, University of Minnesota, Twin Cities, MN, USA
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Pathak PS, Chan G, Deming DA, Chee CE. State-of-the-Art Management of Colorectal Cancer: Treatment Advances and Innovation. Am Soc Clin Oncol Educ Book 2024; 44:e438466. [PMID: 38768405 DOI: 10.1200/edbk_438466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Colorectal cancer (CRC) remains a significant global health challenge, ranking among the leading causes of cancer-related morbidity and mortality worldwide. Recent advancements in molecular characterization have revolutionized our understanding of the heterogeneity within colorectal tumors, particularly in the context of tumor sidedness. Tumor sidedness, referring to the location of the primary tumor in either the right or left colon, has emerged as a critical factor influencing prognosis and treatment responses in metastatic CRC. Molecular underpinnings of CRC, the impact of tumor sidedness, and how this knowledge guides therapeutic decisions in the era of precision medicine have led to improved outcomes and better quality of life in patients. The emergence of circulating tumor DNA as a prognostic and predictive tool in CRC heralds promising advancements in the diagnosis and monitoring of the disease. This innovation facilitates better patient selection for exploration of additional treatment options. As the field progresses, with investigational agents demonstrating potential as future treatments for refractory metastatic CRC, new avenues for enhancing outcomes in this challenging disease are emerging.
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Affiliation(s)
- Priyadarshini S Pathak
- Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Gloria Chan
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore
| | - Dustin A Deming
- Division of Hematology, Medical Oncology, and Palliative Care, Department of Medicine, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
- University of Wisconsin Carbone Cancer Center, Madison, WI
- McArdle Laboratory for Cancer Research, Department of Oncology, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI
| | - Cheng Ean Chee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore, National University Health System, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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5
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Xu Y, Wang Z, Pei B, Wang J, Xue Y, Zhao G. DNA methylation markers in esophageal cancer. Front Genet 2024; 15:1354195. [PMID: 38774285 PMCID: PMC11106492 DOI: 10.3389/fgene.2024.1354195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/19/2024] [Indexed: 05/24/2024] Open
Abstract
Background Esophageal cancer (EC) is a prevalent malignancy characterized by a low 5-year survival rate, primarily attributed to delayed diagnosis and limited therapeutic options. Currently, early detection of EC heavily relies on endoscopy and pathological examination, which pose challenges due to their invasiveness and high costs, leading to low patient compliance. The detection of DNA methylation offers a non-endoscopic, cost-effective, and secure approach that holds promising prospects for early EC detection. Methods To identify improved methylation markers for early EC detection, we conducted a comprehensive review of relevant literature, summarized the performance of DNA methylation markers based on different input samples and analytical methods in EC early detection and screening. Findings This review reveals that blood cell free DNA methylation-based method is an effective non-invasive method for early detection of EC, although there is still a need to improve its sensitivity and specificity. Another highly sensitive and specific non-endoscopic approach for early detection of EC is the esophageal exfoliated cells based-DNA methylation analysis. However, while there are substantial studies in esophageal adenocarcinoma, further more validation is required in esophageal squamous cell carcinoma. Conclusion In conclusion, DNA methylation detection holds significant potential as an early detection and screening technology for EC.
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Affiliation(s)
- Yongle Xu
- Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Suzhou, China
| | - Zhenzhen Wang
- Department of Laboratory Medicine, Affiliated Xuzhou Maternity and Child Healthcare Hospital of Xuzhou Medical University, Xuzhou, China
| | - Bing Pei
- Department of Clinical Laboratory, The Affiliated Suqian First People’s Hospital of Nanjing Medical University, Suqian, China
| | - Jie Wang
- Department of Spleen and Stomach Diseases, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
| | - Ying Xue
- Suzhou Municipal Hospital, Gusu School, The Affiliated Suzhou Hospital of Nanjing Medical University, Nanjing Medical University, Suzhou, China
| | - Guodong Zhao
- Department of Spleen and Stomach Diseases, Kunshan Hospital of Traditional Chinese Medicine, Kunshan, China
- Zhejiang University of Technology, Hangzhou, China
- ZJUT Yinhu Research Institute of Innovation and Entrepreneurship, Hangzhou, China
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Wever BMM, Steenbergen RDM. Unlocking the potential of tumor-derived DNA in urine for cancer detection: methodological challenges and opportunities. Mol Oncol 2024. [PMID: 38462745 DOI: 10.1002/1878-0261.13628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/20/2023] [Accepted: 01/27/2024] [Indexed: 03/12/2024] Open
Abstract
High cancer mortality rates and the rising cancer burden worldwide drive the development of innovative methods in order to advance cancer diagnostics. Urine contains a viable source of tumor material and allows for self-collection from home. Biomarker testing in this liquid biopsy represents a novel approach that is convenient for patients and can be effective in detecting cancer at a curable stage. Here, we set out to provide a detailed overview of the rationale behind urine-based cancer detection, with a focus on non-urological cancers, and its potential for cancer diagnostics. Moreover, evolving methodological challenges and untapped opportunities for urine biomarker testing are discussed, particularly emphasizing DNA methylation of tumor-derived cell-free DNA. We also provide future recommendations for technical advancements in urine-based cancer detection and elaborate on potential mechanisms involved in the transrenal transport of cell-free DNA.
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Affiliation(s)
- Birgit M M Wever
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
| | - Renske D M Steenbergen
- Department of Pathology, Amsterdam UMC, location Vrije Universiteit Amsterdam, The Netherlands
- Imaging and Biomarkers, Cancer Center Amsterdam, The Netherlands
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Gouda MA, Janku F, Wahida A, Buschhorn L, Schneeweiss A, Abdel Karim N, De Miguel Perez D, Del Re M, Russo A, Curigliano G, Rolfo C, Subbiah V. Liquid Biopsy Response Evaluation Criteria in Solid Tumors (LB-RECIST). Ann Oncol 2024; 35:267-275. [PMID: 38145866 DOI: 10.1016/j.annonc.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/17/2023] [Accepted: 12/09/2023] [Indexed: 12/27/2023] Open
Abstract
Current evaluation of treatment response in solid tumors depends on dynamic changes in tumor diameters as measured by imaging. However, these changes can only be detected when there are enough macroscopic changes in tumor volume, which limits the usability of radiological response criteria in evaluating earlier stages of disease response and necessitates much time to lapse for gross changes to be notable. One promising approach is to incorporate dynamic changes in circulating tumor DNA (ctDNA), which occur early in the course of therapy and can predict tumor responses weeks before gross size changes manifest. However, several issues need to be addressed before recommending the implementation of ctDNA response criteria in daily clinical practice such as clinical, biological, and regulatory challenges and, most importantly, the need to standardize/harmonize detection methods and ways to define ctDNA response and/or progression for precision oncology. Herein, we review the use of liquid biopsy (LB) to evaluate response in solid tumors and propose a plan toward standardization of LB-RECIST.
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Affiliation(s)
- M A Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston
| | - F Janku
- Monte Rosa Therapeutics, Boston, USA
| | - A Wahida
- Division of Gynecological Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - L Buschhorn
- Division of Gynecological Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - A Schneeweiss
- Division of Gynecological Oncology, National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - N Abdel Karim
- Inova Schar Cancer Institute, Fairfax, (5)University of Virginia, Charlottesville
| | - D De Miguel Perez
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - M Del Re
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - A Russo
- Medical Oncology Unit, Papardo Civil Hospital and Department of Human Pathology, University of Messina, Messina
| | - G Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milano; Division of Early Drug Development for Innovative Therapies, European Institute of Oncology, IRCCS, Milano, Italy
| | - C Rolfo
- Center for Thoracic Oncology, Icahn School of Medicine at Mount Sinai, New York, USA
| | - V Subbiah
- Sarah Cannon Research Institute, Nashville, USA.
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Bhambhani C, Kang Q, Hovelson DH, Sandford E, Olesnavich M, Dermody SM, Wolfgang J, Tuck KL, Brummel C, Bhangale AD, He K, Gutierrez MG, Lindstrom RH, Liu CJ, Tuck M, Kandarpa M, Mierzwa M, Casper K, Prince ME, Krauss JC, Talpaz M, Henry NL, Giraldez MD, Ramnath N, Tomlins SA, Swiecicki PL, Brenner JC, Tewari M. ctDNA transiting into urine is ultrashort and facilitates noninvasive liquid biopsy of HPV+ oropharyngeal cancer. JCI Insight 2024; 9:e177759. [PMID: 38516891 PMCID: PMC11018327 DOI: 10.1172/jci.insight.177759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/02/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUNDTransrenal cell-free tumor DNA (TR-ctDNA), which transits from the bloodstream into urine, has the potential to enable noninvasive cancer detection for a wide variety of nonurologic cancer types.MethodsUsing whole-genome sequencing, we discovered that urine TR-ctDNA fragments across multiple cancer types are predominantly ultrashort (<50 bp) and, therefore, likely to be missed by conventional ctDNA assays. We developed an ultrashort droplet digital PCR assay to detect TR-ctDNA originating from HPV-associated oropharyngeal squamous cell carcinoma (HPV+ OPSCC) and confirmed that assaying ultrashort DNA is critical for sensitive cancer detection from urine samples.ResultsTR-ctDNA was concordant with plasma ctDNA for cancer detection in patients with HPV+ OPSCC. As proof of concept for using urine TR-ctDNA for posttreatment surveillance, in a small longitudinal case series, TR-ctDNA showed promise for noninvasive detection of recurrence of HPV+ OPSCC.ConclusionOur data indicate that focusing on ultrashort fragments of TR-ctDNA will be important for realizing the full potential of urine-based cancer diagnostics. This has implications for urine-based detection of a wide variety of cancer types and for facilitating access to care through at-home specimen collections.FundingNIH grants R33 CA229023, R21 CA225493; NIH/National Cancer Institute grants U01 CA183848, R01 CA184153, and P30CA046592; American Cancer Society RSG-18-062-01-TBG; American Cancer Society Mission Boost grant MBGI-22-056-01-MBG; and the A. Alfred Taubman Medical Research Institute.
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Affiliation(s)
| | - Qing Kang
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Daniel H. Hovelson
- Michigan Center for Translational Pathology
- Department of Computational Medicine & Bioinformatics
| | - Erin Sandford
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Mary Olesnavich
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | - Jenny Wolfgang
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Kirsten L. Tuck
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | | | - Kuang He
- Department of Internal Medicine, Division of Hematology/Oncology
| | | | | | - Chia-Jen Liu
- Michigan Center for Translational Pathology
- Department of Pathology
| | - Melissa Tuck
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Malathi Kandarpa
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Michelle Mierzwa
- Department of Radiation Oncology, and
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Keith Casper
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Mark E. Prince
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - John C. Krauss
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Moshe Talpaz
- Department of Internal Medicine, Division of Hematology/Oncology
| | - N. Lynn Henry
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Maria D. Giraldez
- Department of Internal Medicine, Division of Hematology/Oncology
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, Consejo Superior de Investigaciones Científicas, University of Seville, Seville, Spain
| | - Nithya Ramnath
- Department of Internal Medicine, Division of Hematology/Oncology
| | - Scott A. Tomlins
- Michigan Center for Translational Pathology
- Department of Pathology
- Department of Urology
| | - Paul L. Swiecicki
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
| | - J. Chad Brenner
- Department of Otolaryngology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pharmacology
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Engineering, and
- Center for Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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Arhant G, Lachkar S, Thiebaut PA, Marguet F, Lamy A, Thiberville L, Salaün M, Guisier F, Sabourin JC, Piton N. Detection of Tumor DNA in Bronchoscopic Fluids in Peripheral NSCLC: A Proof-of-Concept Study. JTO Clin Res Rep 2024; 5:100596. [PMID: 38328474 PMCID: PMC10847031 DOI: 10.1016/j.jtocrr.2023.100596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/07/2023] [Accepted: 10/14/2023] [Indexed: 02/09/2024] Open
Abstract
Introduction DNA genotyping from plasma is a useful tool for molecular characterization of NSCLC. Nevertheless, the false-negative rate justifies the development of methods with higher sensitivity, especially in difficult-to-reach peripheral lung tumors. Methods We aimed at comparing molecular analysis from the supernatant of guide sheath flush fluid collected during radial-EndoBronchial UltraSound (r-EBUS) bronchoscopy with plasma sampling and tumor biopsies in patients with peripheral NSCLC. The DNA was genotyped using high-throughput sequencing or the COBAS mutation test. There were 65 patients with peripheral lung tumors subjected to concomitant sampling of guide sheath flush supernatant, plasma tumor DNA, and tumor biopsy and cytology using r-EBUS. There were 33 patients (including 24 newly diagnosed with having NSCLC) with an identifiable tumor mutation in the primary lesion selected for the comparative analysis. Results Guide sheath flush-based genotyping yielded a mutation detection rate of 61.8% (17 of 24 mutated EGFR, one of two ERBB2, one of one KRAS, one of one MAP2K, one of four MET, and zero of one STK11), compared with 33% in plasma-based genotyping (p = 0.0151). Furthermore, in eight of 34 r-EBUS without tumor cells on microscopic examination, we were able to detect the mutation in four paired guide sheath flush supernatant, compared with only two in paired plasma. Conclusion The detection of tumor DNA in the supernatant of guide sheath flush fluid collected during r-EBUS bronchoscopy represents a sensitive and complementary method for genotyping NSCLC.
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Affiliation(s)
- Gwenaëlle Arhant
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Samy Lachkar
- Department of Pneumology, CHU Rouen, Rouen, France
| | - Pierre-Alain Thiebaut
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Florent Marguet
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Aude Lamy
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Luc Thiberville
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Mathieu Salaün
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Florian Guisier
- Department of Pneumology, CHU Rouen, Rouen, France
- Department of Pneumology, Normandie Univ, UNIROUEN, LITIS Lab QuantIF team EA4108, CHU Rouen, and Institut national de la santé et de la recherche médicale (INSERM) CIC-CRB 1404, Rouen, France
| | - Jean-Christophe Sabourin
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
| | - Nicolas Piton
- Department of Pathology, Normandie Univ, UNIROUEN, Institut national de la santé et de la recherche médicale (INSERM) U1245, CHU Rouen, Rouen, France
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10
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Lockwood CM, Borsu L, Cankovic M, Earle JSL, Gocke CD, Hameed M, Jordan D, Lopategui JR, Pullambhatla M, Reuther J, Rumilla KM, Tafe LJ, Temple-Smolkin RL, Terraf P, Tsimberidou AM. Recommendations for Cell-Free DNA Assay Validations: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 2023; 25:876-897. [PMID: 37806433 DOI: 10.1016/j.jmoldx.2023.09.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
Diagnosing, selecting therapy for, and monitoring cancer in patients using a minimally invasive blood test represents a significant advance in precision medicine. Wide variability exists in how circulating tumor DNA (ctDNA) assays are developed, validated, and reported in the literature, which hinders clinical adoption and may negatively impact patient care. Standardization is needed for factors affecting ctDNA assay performance and reporting, including pre-analytical variables, analytical considerations, and elements of laboratory assay reporting. The Association for Molecular Pathology Clinical Practice Committee's Liquid Biopsy Working Group (LBxWG), including organizational representation from the American Society of Clinical Oncology and the College of American Pathologists, has undertaken a full-text data extraction of 1228 ctDNA publications that describe assays performed in patients with lymphoma and solid tumor malignancies. With an emphasis on clinical assay validation, the LBxWG has developed a set of 13 best practice consensus recommendations for validating, reporting, and publishing clinical ctDNA assays. Recommendations include reporting key pre-analytical considerations and assay performance metrics; this analysis demonstrates these elements are inconsistently included in publications. The LBxWG recommendations are intended to assist clinical laboratories with validating and reporting ctDNA assays and to ensure high-quality data are included in publications. It is expected that these recommendations will need to be updated as the body of literature continues to mature.
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Affiliation(s)
- Christina M Lockwood
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington; Brotman Baty Institute for Precision Medicine, Seattle, Washington.
| | - Laetitia Borsu
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Milena Cankovic
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Henry Ford Hospital, Detroit, Michigan
| | - Jonathan S L Earle
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Hartford Hospital, Hartford, Connecticut; Hartford Pathology Associates, Hartford, Connecticut
| | - Christopher D Gocke
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Meera Hameed
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jean R Lopategui
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Jacquelyn Reuther
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Invitae, San Francisco, California
| | - Kandelaria M Rumilla
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Laura J Tafe
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Panieh Terraf
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Apostolia M Tsimberidou
- Liquid Biopsy Working Group of the Clinical Practice Committee, Association for Molecular Pathology, Rockville, Maryland; Department of Investigational Cancer Therapeutics, Unit 455, The University of Texas MD Anderson Cancer Center, Houston, Texas
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11
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Wang J, Zhu J, Hu J, Wang Z, Wang X, Pan J, Chu Y, Li Z, Jiang W, Liang C, Hou J, Guo J, Dang Y, Jiang S. A novel in vitro prognostic model of bladder cancer based on urine-derived living tumor cells. Genes Dis 2023; 10:2586-2596. [PMID: 37554182 PMCID: PMC10405094 DOI: 10.1016/j.gendis.2022.10.022] [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: 05/17/2022] [Revised: 08/28/2022] [Accepted: 10/22/2022] [Indexed: 11/27/2022] Open
Abstract
Bladder cancer (BLCA) remains a difficult malignancy to manage because of its high recurrence, intense follow-up, and invasive diagnostic and treatment techniques. Immune checkpoint inhibitors (ICIs) have forged a new direction for the treatment of BLCA, but it is currently challenging to predict whether an individual patient will be sensitive to ICIs. We collected 43 urine/tumor samples from BLCA patients for primary bladder cancer cells (BCCs) culturing using our previously reported BCC culture platform. We used flow cytometry (FCM) to measure the expression levels of Programmed Death-Ligand 1 (PD-L1) on BCCs before and after interferon-gamma (IFN-γ) treatment and found that PD-L1 expression and the sensitivities to IFN-γ varied among patients. RNA-sequencing, western blotting, and programmed death-1 (PD-1) binding assays confirmed that the BCC FCM-based PD-L1 detection platform (BC-PD-L1) was reliable and was not hindered by the glycosylation of PD-L1. In the subsequent retrospective study, we found that IFN-γ-stimulated PD-L1 (sPD-L1) expression on BCCs detected by BC-PD-L1 could predict the prognosis of BLCA patients. Importantly, the prognostic value was similar or even better in urine-derived BC-PD-L1 (UBC-PD-L1). Transcriptome analysis showed that BCCs with high sPD-L1 tended to enrich genes associated with the collagen-containing extracellular matrix, cell-cell adhesion, and positive regulation of the immune system. In addition, the UBC-PD-L1 also exhibited predictive value for ICI response in BLCA patients. In conclusion, as a novel personalized urine-detection method, UBC-PD-L1 may provide a rapid, accurate, and non-invasive tool for monitoring tumor progression, predicting therapeutic responses, and helping improve BLCA clinical treatment in future.
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Affiliation(s)
- Jiaqi Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jiying Zhu
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Laboratory of Tumor Immunology, Department of Anatomy, Histology, and Embryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Junchi Hu
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, Chongqing 400016, China
| | - Ziruoyu Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaobo Wang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianbo Pan
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, Chongqing 400016, China
| | - Yiwei Chu
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Zengxia Li
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Wei Jiang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Chunmin Liang
- Laboratory of Tumor Immunology, Department of Anatomy, Histology, and Embryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jun Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jianming Guo
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Yongjun Dang
- Key Laboratory of Metabolism and Molecular Medicine, Ministry of Education and Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Center for Novel Target and Therapeutic Intervention, Chongqing Medical University, Chongqing 400016, China
| | - Shuai Jiang
- Department of Urology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Urology, Zhongshan Hospital Wusong Branch, Fudan University, Shanghai 200940, China
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12
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Costas L, Onieva I, Pelegrina B, Marin F, Carmona Á, López-Querol M, Frias-Gomez J, Peremiquel-Trillas P, Martínez JM, Dorca E, Brunet J, Pineda M, Ponce J, Matias-Guiu X, de Sanjosé S, Bosch FX, Alemany L, Paytubi S. Evaluation of Somatic Mutations in Urine Samples as a Noninvasive Method for the Detection and Molecular Classification of Endometrial Cancer. Clin Cancer Res 2023; 29:3681-3690. [PMID: 37439797 DOI: 10.1158/1078-0432.ccr-23-0367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/19/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
PURPOSE Current diagnostic methods for endometrial cancer lack specificity, leading to many women undergoing invasive procedures. The aim of this study was to evaluate somatic mutations in urine to accurately discriminate patients with endometrial cancer from controls. EXPERIMENTAL DESIGN Overall, 72 samples were analyzed using next-generation sequencing (NGS) with molecular identifiers targeting 47 genes. We evaluated urine supernatant samples from women with endometrial cancer (n = 19) and age-matched controls (n = 20). Cell pellets from urine and plasma samples from seven cases were sequenced; further, we also evaluated paired tumor samples from all cases. Finally, immunohistochemical markers for molecular profiling were evaluated in all tumor samples. RESULTS Overall, we were able to identify mutations in DNA from urine supernatant samples in 100% of endometrial cancers. In contrast, only one control (5%) showed variants at a variant allele frequency (VAF) ≥ 2% in the urine supernatant samples. The molecular classification obtained by using tumor samples and urine samples showed good agreement. Analyses in paired samples revealed a higher number of mutations and VAF in urine supernatants than in urine cell pellets and blood samples. CONCLUSIONS Evaluation of somatic mutations using urine samples may offer a user-friendly and reliable tool for endometrial cancer detection and molecular classification. The diagnostic performance for endometrial cancer detection was very high, and cases could be molecularly classified using these noninvasive and self-collected samples. Additional multicenter evaluations using larger sample sizes are needed to validate the results and understand the potential of urine samples for the early detection and prognosis of endometrial cancer.
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Affiliation(s)
- Laura Costas
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Madrid, Spain
| | - Irene Onieva
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Beatriz Pelegrina
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Madrid, Spain
| | - Fátima Marin
- Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | | | - Marta López-Querol
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Jon Frias-Gomez
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Madrid, Spain
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Paula Peremiquel-Trillas
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Madrid, Spain
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - José Manuel Martínez
- Faculty of Medicine, University of Barcelona, Barcelona, Spain
- Department of Gynecology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Eduard Dorca
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Joan Brunet
- Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGI, Girona, Spain
- Medical Oncology Department, Catalan Institute of Oncology, Doctor Josep Trueta Girona University Hospital, Girona, Spain
| | - Marta Pineda
- Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Madrid, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, ONCOBELL Program, L'Hospitalet, Barcelona, Spain
| | - Jordi Ponce
- Department of Gynecology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Matias-Guiu
- Consortium for Biomedical Research in Cancer - CIBERONC, Carlos III Institute of Health, Madrid, Spain
- Department of Pathology, Hospital Universitari de Bellvitge, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | | | - Francesc Xavier Bosch
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Madrid, Spain
- Universitat Oberta de Catalunya, Barcelona, Spain
| | - Laia Alemany
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Madrid, Spain
| | - Sonia Paytubi
- Cancer Epidemiology Research Programme, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health - CIBERESP, Carlos III Institute of Health, Madrid, Spain
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13
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Ferrier ST, Tsering T, Sadeghi N, Zeitouni A, Burnier JV. Blood and saliva-derived ctDNA is a marker of residual disease after treatment and correlates with recurrence in human papillomavirus-associated head and neck cancer. Cancer Med 2023; 12:15777-15787. [PMID: 37526056 PMCID: PMC10469655 DOI: 10.1002/cam4.6191] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 05/15/2023] [Accepted: 05/21/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND There is an alarming increase in human papillomavirus-associated head and neck cancer (HNC), reaching epidemic levels. While patient prognosis is generally good, off-target treatment effects are associated with decreased quality of life. Thus, non-invasive strategies to predict treatment response and risk of recurrence could help de-escalate treatment. In this study, we tested circulating tumor (ct)DNA in liquid biopsies (blood/saliva) of HPV-positive HNC patients to assess treatment response and disease progression. METHODS A total of 235 blood and saliva samples were collected from 60 HPV-positive and 17 HPV-negative HNC patients (control group) before and/or after treatment. Samples were analyzed using ddPCR for HPV16/18/31/33/35/45 and correlated with imaging and pathological examination. RESULTS HPV-ctDNA detection was significantly higher prior to treatment (91%) than after treatment (8.0%) (χ2 p < 0.00001), with high concordance between saliva and blood (93%). In matched samples, all patients positive for ctDNA before treatment showed significant reductions in ctDNA levels post treatment (p < 0.0001). All but one patient with persistent ctDNA after treatment showed residual tumor and subsequent recurrence. Finally, fragmentomic analysis revealed shifts in cell-free DNA fragment size after treatment, suggesting a complementary biomarker for treatment response. CONCLUSIONS Blood and saliva were found to be good sources of HPV-ctDNA. The presence of ctDNA strongly correlated with treatment response, demonstrating clinical utility as a non-invasive biomarker to monitor tumor progression in HPV-positive HNC. Liquid biopsy based ctDNA testing could be an effective approach to predict recurrence and stratify patients for de-escalation of treatment, thereby improving quality of life.
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Affiliation(s)
- Sarah Tadhg Ferrier
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealCanada
- Department of PathologyMcGill UniversityMontrealCanada
| | - Thupten Tsering
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealCanada
- Department of PathologyMcGill UniversityMontrealCanada
| | - Nader Sadeghi
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealCanada
- Department of Otolaryngology – Head and Neck SurgeryMcGill UniversityMontrealCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealCanada
| | - Anthony Zeitouni
- Department of Otolaryngology – Head and Neck SurgeryMcGill UniversityMontrealCanada
| | - Julia V. Burnier
- Cancer Research ProgramResearch Institute of the McGill University Health CentreMontrealCanada
- Department of PathologyMcGill UniversityMontrealCanada
- Gerald Bronfman Department of OncologyMcGill UniversityMontrealCanada
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14
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Telekes A, Horváth A. The Role of Cell-Free DNA in Cancer Treatment Decision Making. Cancers (Basel) 2022; 14:6115. [PMID: 36551600 PMCID: PMC9776613 DOI: 10.3390/cancers14246115] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to evaluate the present status of the use of cell-free DNA and its fraction of circulating tumor DNA (ctDNA) because this year July 2022, an ESMO guideline was published regarding the application of ctDNA in patient care. This review is for clinical oncologists to explain the concept, the terms used, the pros and cons of ctDNA; thus, the technical aspects of the different platforms are not reviewed in detail, but we try to help in navigating the current knowledge in liquid biopsy. Since the validated and adequately sensitive ctDNA assays have utility in identifying actionable mutations to direct targeted therapy, ctDNA may be used for this soon in routine clinical practice and in other different areas as well. The cfDNA fragments can be obtained by liquid biopsy and can be used for diagnosis, prognosis, and selecting among treatment options in cancer patients. A great proportion of cfDNA comes from normal cells of the body or from food uptake. Only a small part (<1%) of it is related to tumors, originating from primary tumors, metastatic sites, or circulating tumor cells (CTCs). Soon the data obtained from ctDNA may routinely be used for finding minimal residual disease, detecting relapse, and determining the sites of metastases. It might also be used for deciding appropriate therapy, and/or emerging resistance to the therapy and the data analysis of ctDNA may be combined with imaging or other markers. However, to achieve this goal, further clinical validations are inevitable. As a result, clinicians should be aware of the limitations of the assays. Of course, several open questions are still under research and because of it cfDNA and ctDNA testing are not part of routine care yet.
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Affiliation(s)
- András Telekes
- Omnimed-Etosz, Ltd., 81 Széher Rd., 1021 Budapest, Hungary
- Semmelweis University, 26. Üllői Rd., 1085 Budapest, Hungary
| | - Anna Horváth
- Department of Internal Medicine and Haematology, Semmelweis University, 46. Szentkirályi Rd., 1088 Budapest, Hungary
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15
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Salfer B, Li F, Wong DT, Zhang L. Urinary Cell-Free DNA in Liquid Biopsy and Cancer Management. Clin Chem 2022; 68:1493-1501. [PMID: 36213956 PMCID: PMC10423312 DOI: 10.1093/clinchem/hvac122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/30/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND The current methodology used to detect, diagnose, and monitor many types of cancers requires invasive tissue biopsy testing. Recently, liquid biopsy using blood, plasma, urine, saliva, and various other bodily fluids has shown utility to solve many issues associated with tissue biopsy. Blood/plasma has received most of the attention within the liquid biopsy field, however, obtaining blood samples from patients is still somewhat invasive and requires trained professionals. Using urine to detect cell-free DNA cancer biomarkers offers a truly non-invasive sampling method that can be easily and reproducibly conducted by patients. CONTENT Novel technologies and approaches have made the detection of small quantities of cell-free tumor DNA of varying lengths possible. Recent studies using urine circulating tumor DNA to detect cancer mutations and other biomarkers have shown sensitivity comparable to blood/plasma cell-free DNA liquid biopsy for many cancer types. Thus, urine cell-free DNA liquid biopsy may replace or provide supplementary information to tissue/blood biopsies. Further investigation with larger patient cohorts and standardization of pre-analytical factors is necessary to determine the utility of urine cell-free DNA liquid biopsy for cancer detection, diagnosis, and monitoring in a clinical setting. SUMMARY In this mini-review we discuss the biological aspects of cell-free DNA in urine, numerous studies using urine cell-free DNA to detect urological cancers, and recent studies using urine cell-free DNA to detect and monitor non-urological cancers including lung, breast, colorectal, and other cancers.
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Affiliation(s)
- Blake Salfer
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Feng Li
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - David T.W. Wong
- School of Dentistry, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Liying Zhang
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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16
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Endogenous cell-free DNA in fetal bovine serum introduces artifacts to in vitro cell-free DNA models. Biotechniques 2022; 73:219-226. [DOI: 10.2144/btn-2022-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Cell-free DNA (cfDNA) is of growing clinical and research significance. In vitro cfDNA models are a useful tool in cfDNA research; however, artifacts in these models may have implications for the interpretation of new and published data. This report aimed to establish how endogenous cfDNA in fetal bovine serum (FBS) may influence in vitro cfDNA measurements. Three commercial cell culture media, supplemented with 10% FBS, were analyzed for the presence of cfDNA, with and without culture with ovarian cancer cell lines. cfDNA from FBS was identified with all three commercial media and contributed a major portion of 167-bp cfDNA. Future studies should account for bovine cfDNA in FBS-supplemented media when conducting in vitro cfDNA research.
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17
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Nikanjam M, Kato S, Kurzrock R. Liquid biopsy: current technology and clinical applications. J Hematol Oncol 2022; 15:131. [PMID: 36096847 PMCID: PMC9465933 DOI: 10.1186/s13045-022-01351-y] [Citation(s) in RCA: 270] [Impact Index Per Article: 135.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
Liquid biopsies are increasingly used for cancer molecular profiling that enables a precision oncology approach. Circulating extracellular nucleic acids (cell-free DNA; cfDNA), circulating tumor DNA (ctDNA), and circulating tumor cells (CTCs) can be isolated from the blood and other body fluids. This review will focus on current technologies and clinical applications for liquid biopsies. ctDNA/cfDNA has been isolated and analyzed using many techniques, e.g., droplet digital polymerase chain reaction, beads, emulsion, amplification, and magnetics (BEAMing), tagged-amplicon deep sequencing (TAm-Seq), cancer personalized profiling by deep sequencing (CAPP-Seq), whole genome bisulfite sequencing (WGBS-Seq), whole exome sequencing (WES), and whole genome sequencing (WGS). CTCs have been isolated using biomarker-based cell capture, and positive or negative enrichment based on biophysical and other properties. ctDNA/cfDNA and CTCs are being exploited in a variety of clinical applications: differentiating unique immune checkpoint blockade response patterns using serial samples; predicting immune checkpoint blockade response based on baseline liquid biopsy characteristics; predicting response and resistance to targeted therapy and chemotherapy as well as immunotherapy, including CAR-T cells, based on serial sampling; assessing shed DNA from multiple metastatic sites; assessing potentially actionable alterations; analyzing prognosis and tumor burden, including after surgery; interrogating difficult-to biopsy tumors; and detecting cancer at early stages. The latter can be limited by the small amounts of tumor-derived components shed into the circulation; furthermore, cfDNA assessment in all cancers can be confounded by clonal hematopoeisis of indeterminate potential, especially in the elderly. CTCs can be technically more difficult to isolate that cfDNA, but permit functional assays, as well as evaluation of CTC-derived DNA, RNA and proteins, including single-cell analysis. Blood biopsies are less invasive than tissue biopsies and hence amenable to serial collection, which can provide critical molecular information in real time. In conclusion, liquid biopsy is a powerful tool, and remarkable advances in this technology have impacted multiple aspects of precision oncology, from early diagnosis to management of refractory metastatic disease. Future research may focus on fluids beyond blood, such as ascites, effusions, urine, and cerebrospinal fluid, as well as methylation patterns and elements such as exosomes.
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Affiliation(s)
- Mina Nikanjam
- Division of Hematology-Oncology, University of California San Diego, La Jolla, 1200 Garden View Road, Encinitas, CA, 92024, USA.
| | - Shumei Kato
- Division of Hematology-Oncology, University of California San Diego, La Jolla, 1200 Garden View Road, Encinitas, CA, 92024, USA
| | - Razelle Kurzrock
- Medical College of Wisconsin Cancer Center, Milwaukee, WI, USA.,WIN Consortium, Paris, France
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18
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Liu Z, Han Y, Dang Q, Xu H, Zhang Y, Duo M, Lv J, Li H, Kong Y, Han X. Roles of circulating tumor DNA in PD-1/PD-L1 immune checkpoint Inhibitors: Current evidence and future directions. Int Immunopharmacol 2022; 111:109173. [PMID: 35998502 DOI: 10.1016/j.intimp.2022.109173] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 12/18/2022]
Abstract
Circulating tumor DNA (ctDNA) sequencing holds considerable promise for early diagnosis and detection of surveillance and minimal residual disease. Blood ctDNA monitors specific cancers by detecting the alterations found in cancer cells, such as apoptosis and necrosis. Due to the short half-life, ctDNA reflects the actual burden of other treatments on tumors. In addition, ctDNA might be preferable to monitor tumor development and treatment compared with invasive tissue biopsy. ctDNA-based liquid biopsy brings remarkable strength to targeted therapy and precision medicine. Notably, multiple ctDNA analysis platforms have been broadly applied in clinical immunotherapy. Through targeted sequencing, early variations in ctDNA could predict response to immune checkpoint inhibitor (ICI). Several studies have demonstrated a correlation between ctDNA kinetics and anti-PD1 antibodies. The need for further research and development remains, although this biomarker holds significant prospects for early cancer detection. This review focuses on describing the basis of ctDNA and its current utilities in oncology and immunotherapy, either for clinical management or early detection, highlighting its advantages and inherent limitations.
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Affiliation(s)
- Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
| | - Yilin Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qin Dang
- Department of Colorectal Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Hui Xu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Mengjie Duo
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Huanyun Li
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ying Kong
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China; Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China.
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19
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Pesta M, Shetti D, Kulda V, Knizkova T, Houfkova K, Bagheri MS, Svaton M, Polivka J. Applications of Liquid Biopsies in Non-Small-Cell Lung Cancer. Diagnostics (Basel) 2022; 12:1799. [PMID: 35892510 PMCID: PMC9330570 DOI: 10.3390/diagnostics12081799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
The concept of liquid biopsy as an analysis tool for non-solid tissue carried out for the purpose of providing information about solid tumors was introduced approximately 20 years ago. Additional to the detection of circulating tumor cells (CTCs), the liquid biopsy approach quickly included the analysis of circulating tumor DNA (ctDNA) and other tumor-derived markers such as circulating cell-free RNA or extracellular vesicles. Liquid biopsy is a non-invasive technique for detecting multiple cancer-associated biomarkers that is easy to obtain and can reflect the characteristics of the entire tumor mass. Currently, ctDNA is the key component of the liquid biopsy approach from the point of view of the prognosis assessment, prediction, and monitoring of the treatment of non-small-cell lung cancer (NSCLC) patients. ctDNA in NSCLC patients carries variants or rearrangements that drive carcinogenesis, such as those in EGFR, KRAS, ALK, or ROS1. Due to advances in pharmacology, these variants are the subject of targeted therapy. Therefore, the detection of these variants has gained attention in clinical medicine. Recently, methods based on qPCR (ddPCR, BEAMing) and next-generation sequencing (NGS) are the most effective approaches for ctDNA analysis. This review addresses various aspects of the use of liquid biopsy with an emphasis on ctDNA as a biomarker in NSCLC patients.
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Affiliation(s)
- Martin Pesta
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Dattatrya Shetti
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Vlastimil Kulda
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic;
| | - Tereza Knizkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Katerina Houfkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Mahyar Sharif Bagheri
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
| | - Martin Svaton
- Department of Pneumology and Phthisiology, Faculty of Medicine in Pilsen, Charles University, University Hospital in Pilsen, E. Benese 13, 301 00 Plzen, Czech Republic;
| | - Jiri Polivka
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
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20
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Gouda MA, Huang HJ, Piha-Paul SA, Call SG, Karp DD, Fu S, Naing A, Subbiah V, Pant S, Dustin DJ, Tsimberidou AM, Hong DS, Rodon J, Meric-Bernstam F, Janku F. Longitudinal Monitoring of Circulating Tumor DNA to Predict Treatment Outcomes in Advanced Cancers. JCO Precis Oncol 2022; 6:e2100512. [PMID: 35834760 PMCID: PMC9307306 DOI: 10.1200/po.21.00512] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/24/2022] [Accepted: 05/31/2022] [Indexed: 12/22/2022] Open
Abstract
PURPOSE The response to cancer therapies is typically assessed with radiologic imaging 6-10 weeks after treatment initiation. Circulating tumor DNA (ctDNA), however, has a short half-life, and dynamic changes in ctDNA quantity may allow for earlier assessment of the therapeutic response. METHODS Patients with advanced solid tumors referred to the Department of Investigational Cancer Therapeutics at The University of Texas MD Anderson Cancer Center were invited to participate in a liquid biopsy protocol for which serial blood samples were collected before, during, and after systemic therapy. We isolated ctDNA from serially collected plasma samples at baseline, mid-treatment, and first restaging. Genomically informed droplet digital polymerase chain reaction (ddPCR) was performed, and ctDNA quantities were reported as aggregate variant allele frequencies for all detected molecular aberrations. RESULTS We included 204 patients receiving 260 systemic therapies. The ctDNA detection rate was higher in progressors (patients with progressive disease) compared with nonprogressors (patients with stable disease, partial responses, or complete responses) at all time points (P < .009). Moreover, ctDNA detection was associated with a shorter median time-to-treatment failure (P ≤ .001). Positive delta and slope values for changes in ctDNA quantity were more frequent in progressors (P ≤ .03 and P < .001, respectively) and were associated with a shorter median time-to-treatment failure (P ≤ .014 and P < .001, respectively). Increasing ctDNA quantity was predictive of clinical and/or radiologic progressive disease in 73% of patients (median lead time, 23 days). CONCLUSION Detection of ctDNA and early dynamic changes in its quantity can predict the clinical outcomes of systemic therapies in patients with advanced solid tumors.
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Affiliation(s)
- Mohamed A. Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Clinical Oncology, Faculty of Medicine, Menoufia University. Shebin Al-Kom, Egypt
| | - Helen J. Huang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sarina A. Piha-Paul
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S. Greg Call
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Daniel D. Karp
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Aung Naing
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shubham Pant
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Derek J. Dustin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Apostolia M. Tsimberidou
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David S. Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jordi Rodon
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
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21
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Abstract
Cancer cells shed naked DNA molecules into the circulation. This circulating tumor DNA (ctDNA) has become the predominant analyte for liquid biopsies to understand the mutational landscape of cancer. Coupled with next-generation sequencing, ctDNA can serve as an alternative substrate to tumor tissues for mutation detection and companion diagnostic purposes. In fact, recent advances in precision medicine have rapidly enabled the use of ctDNA to guide treatment decisions for predicting response and resistance to targeted therapies and immunotherapies. An advantage of using ctDNA over conventional tissue biopsies is the relatively noninvasive approach of obtaining peripheral blood, allowing for simple repeated and serial assessments. Most current clinical practice using ctDNA has endeavored to identify druggable and resistance mutations for guiding systemic therapy decisions, albeit mostly in metastatic disease. However, newer research is evaluating potential for ctDNA as a marker of minimal residual disease in the curative setting and as a useful screening tool to detect cancer in the general population. Here we review the history of ctDNA and liquid biopsies, technologies to detect ctDNA, and some of the current challenges and limitations in using ctDNA as a marker of minimal residual disease and as a general blood-based cancer screening tool. We also discuss the need to develop rigorous clinical studies to prove the clinical utility of ctDNA for future applications in oncology.
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22
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Kim AK, Hamilton JP, Lin SY, Chang TT, Hann HW, Hu CT, Lou Y, Lin YJ, Gade TP, Park G, Luu H, Lee TJ, Wang J, Chen D, Goggins MG, Jain S, Song W, Su YH. Urine DNA biomarkers for hepatocellular carcinoma screening. Br J Cancer 2022; 126:1432-1438. [PMID: 35046521 PMCID: PMC9091244 DOI: 10.1038/s41416-022-01706-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/20/2021] [Accepted: 01/07/2022] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) occurs in a well-defined high-risk patient population, but better screening tests are needed to improve sensitivity and efficacy. Therefore, we investigated the use of urine circulating tumour DNA (ctDNA) as a screening test. METHODS Candidate markers in urine were selected from HCC and controls. We then enrolled 609 patients from five medical centres to test the selected urine panel. A two-stage model was developed to combine AFP and urine panel as a screening test. RESULTS Mutated TP53, and methylated RASSF1a, and GSTP1 were selected as the urine panel markers. Serum AFP outperformed the urine panel among all cases of HCC, but the urine panel identified 49% of HCC cases with low AFP < 20 ng/ml. Using the two-stage model, the combined AFP and urine panel identified 148 of the 186 HCC cases (79.6% sensitivity at 90% specificity), which was 30% more than the cases detected with serum AFP alone. It also increased early-stage HCC detection from 62% to 92% (BCLC stage 0), and 40% to 77% (BCLC stage A). CONCLUSION Urine ctDNA has promising diagnostic utility in patients in HCC, especially in those with low AFP and can be used as a potential non-invasive HCC screening test.
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Affiliation(s)
- Amy K Kim
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James P Hamilton
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Ting-Tsung Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hie-Won Hann
- Department of Medicine, Division of Gastroenterology and Hepatology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - Chi-Tan Hu
- Division of Gastroenterology, Department of Internal Medicine, Hualien Tzu-Chi Hospital, Buddhist Tzu-Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Yue Lou
- The Baruch S. Blumberg Institute, Doylestown, PA, USA
| | - Yih-Jyh Lin
- Department of Surgery, National Cheng Kung University Medical College and Hospital, Tainan, Taiwan, Republic of China
| | - Terence P Gade
- Department of Radiology, University of Pennsylvania College of Medicine, Philadelphia, PA, USA
| | - Grace Park
- Department of Medicine, Division of Gastroenterology and Hepatology, Thomas Jefferson University Hospital, Philadelphia, PA, USA
| | - Harry Luu
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Tai-Jung Lee
- The Baruch S. Blumberg Institute, Doylestown, PA, USA
| | | | - Dion Chen
- ClinPharma Consulting, Inc, Phoenixville, PA, USA
| | - Michael G Goggins
- Division of Gastroenterology and Hepatology, Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University, Baltimore, MD, USA
| | | | - Wei Song
- JBS Science, Inc., Doylestown, PA, USA
| | - Ying-Hsiu Su
- The Baruch S. Blumberg Institute, Doylestown, PA, USA.
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23
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Wever B, Bach S, Tibbesma M, ter Braak T, Wajon D, Dickhoff C, Lissenberg-Witte B, Hulbert A, Kazemier G, Bahce I, Steenbergen R. Detection of non-metastatic non-small-cell lung cancer in urine by methylation-specific PCR analysis: a feasibility study. Lung Cancer 2022; 170:156-164. [DOI: 10.1016/j.lungcan.2022.06.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/27/2022] [Accepted: 06/20/2022] [Indexed: 12/25/2022]
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24
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You J, Park C, Jang K, Park J, Na S. Novel Detection Method for Circulating EGFR Tumor DNA Using Gravitationally Condensed Gold Nanoparticles and Catalytic Walker DNA. MATERIALS (BASEL, SWITZERLAND) 2022; 15:3301. [PMID: 35591635 PMCID: PMC9101948 DOI: 10.3390/ma15093301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/25/2022] [Accepted: 04/29/2022] [Indexed: 01/27/2023]
Abstract
The detection of circulating tumor DNA is a major challenge in liquid biopsies for cancer. Conventionally, quantitative polymerase chain reactions or next-generation sequencing are used to detect circulating tumor DNA; however, these techniques require significant expertise, and are expensive. Owing to the increasing demand for a simple diagnostic method and constant monitoring of cancer, a cost-effective detection technique that can be conducted by non-experts is required. The aim of this study was to detect the circulating tumor DNA containing the epidermal growth factor receptor (EGFR) exon 19 deletion, which frequently occurs in lung cancer. By applying walker DNA to a catalytic hairpin assembly and using the differential dispersibility of gold nanoparticles, we detected EGFR exon 19 deletion mutant #2 DNA associated with lung cancer. Our sensing platform exhibited a limit of detection of 38.5 aM and a selectivity of 0.1% for EGFR exon 19 wild-type DNA. Moreover, we tested and compared EGFR exon 19 deletion mutants #1 and #3 to evaluate the effect of base pair mismatches on the performance of the said technique.
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Affiliation(s)
- Juneseok You
- Department of Mechanical Engineering, Korea University, Seoul 02841, Korea;
| | - Chanho Park
- Division of Foundry, Samsung Electronics, Hwaseong-si 18448, Korea;
| | - Kuewhan Jang
- School of Mechanical Engineering, Hoseo University, Asan 31499, Korea;
| | - Jinsung Park
- Department of Biomechatronics Engineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Suwon 16419, Korea
| | - Sungsoo Na
- Department of Mechanical Engineering, Korea University, Seoul 02841, Korea;
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25
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Malla M, Parikh AR. Evolving Role of Circulating Tumor DNA and Emerging Targeted Therapy in Colorectal Cancer. Hematol Oncol Clin North Am 2022; 36:583-601. [DOI: 10.1016/j.hoc.2022.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Dermody SM, Bhambhani C, Swiecicki PL, Brenner JC, Tewari M. Trans-Renal Cell-Free Tumor DNA for Urine-Based Liquid Biopsy of Cancer. Front Genet 2022; 13:879108. [PMID: 35571046 PMCID: PMC9091346 DOI: 10.3389/fgene.2022.879108] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Cancer biomarkers are a promising tool for cancer detection, personalization of therapy, and monitoring of treatment response or recurrence. “Liquid biopsy” commonly refers to minimally invasive or non-invasive sampling of a bodily fluid (i.e., blood, urine, saliva) for detection of cancer biomarkers such as circulating tumor cells or cell-free tumor DNA (ctDNA). These methods offer a means to collect frequent tumor assessments without needing surgical biopsies. Despite much progress with blood-based liquid biopsy approaches, there are limitations—including the limited amount of blood that can be drawn from a person and challenges with collecting blood samples at frequent intervals to capture ctDNA biomarker kinetics. These limitations are important because ctDNA is present at extremely low levels in plasma and there is evidence that measuring ctDNA biomarker kinetics over time can be useful for clinical prediction. Additionally, blood-based assays require access to trained phlebotomists and often a trip to a healthcare facility. In contrast, urine is a body fluid that can be self-collected from a patient’s home, at frequent intervals, and mailed to a laboratory for analysis. Multiple reports indicate that fragments of ctDNA pass from the bloodstream through the kidney’s glomerular filtration system into the urine, where they are known as trans-renal ctDNA (TR-ctDNA). Accumulating studies indicate that the limitations of blood based ctDNA approaches for cancer can be overcome by measuring TR-ctDNA. Here, we review current knowledge about TR-ctDNA in urine as a cancer biomarker approach, and discuss its clinical potential and open questions in this research field.
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Affiliation(s)
- Sarah M. Dermody
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, United States
| | - Chandan Bhambhani
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Paul L. Swiecicki
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, United States
- Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, United States
| | - J. Chad Brenner
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, MI, United States
| | - Muneesh Tewari
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI, United States
- Veterans Affairs Ann Arbor Healthcare System, Ann Arbor, MI, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, United States
- Center for Computational Biology and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Muneesh Tewari,
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27
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Lu C, Zhang YC, Chen ZH, Zhou Q, Wu YL. Applications of Circulating Tumor DNA in Immune Checkpoint Inhibition: Emerging Roles and Future Perspectives. Front Oncol 2022; 12:836891. [PMID: 35359372 PMCID: PMC8963952 DOI: 10.3389/fonc.2022.836891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/11/2022] [Indexed: 11/13/2022] Open
Abstract
Immune checkpoint inhibitors (ICIs), especially anti-programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) antibodies, have made dramatic progress in the treatment of lung cancer, especially for patients with cancers not driven by oncogenes. However, responses are limited to a subset of patients, and which subset of patients will optimally benefit from ICI remains unknown. With the advantage of being minimally invasive and dynamic, noninvasive biomarkers are promising candidates to predict response, monitor resistance, and track the evolution of lung cancer during ICI treatment. In this review, we focus on the application of circulating tumor DNA (ctDNA) in plasma in immunotherapy. We examine the potential of pre- and on-treatment features of ctDNA as biomarkers, and following multiparameter analysis, we determine the potential clinical value of integrating predictive liquid biomarkers of ICIs to optimize patient management. We further discuss the role of ctDNA in monitoring treatment resistance, as well as challenges in clinical translation.
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Affiliation(s)
- Chang Lu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi-Chen Zhang
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhi-Hong Chen
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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28
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Kato S, Li B, Adashek JJ, Cha SW, Bianchi-Frias D, Qian D, Kim L, so TW, Mitchell M, Kamei N, Hoiness R, Hoo J, Gray PN, Iyama T, Kashiwagi M, Lu HM, Kurzrock R. Serial changes in liquid biopsy-derived variant allele frequency predict immune checkpoint inhibitor responsiveness in the pan-cancer setting. Oncoimmunology 2022; 11:2052410. [PMID: 35371621 PMCID: PMC8966985 DOI: 10.1080/2162402x.2022.2052410] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Major immunotherapy challenges include a limited number of predictive biomarkers and the unusual imaging features post-therapy, such as pseudo-progression, which denote immune infiltrate-mediated tumor enlargement. Such phenomena confound clinical decision-making, since the cancer may eventually regress, and the patient should stay on treatment. We prospectively evaluated serial, blood-derived cell-free DNA (cfDNA) (baseline and 2–3 weeks post-immune checkpoint inhibitors [ICIs]) for variant allele frequency (VAF) and blood tumor mutation burden (bTMB) changes (next-generation sequencing) (N = 84 evaluable patients, diverse cancers). Low vs. high cfDNA-derived average adjusted ΔVAF (calculated by a machine-learning model) was an independent predictor of higher clinical benefit rate (stable disease ≥6 months/complete/partial response) (69.2% vs. 22.5%), and longer median progression-free (10.1 vs. 2.25 months) and overall survival (not reached vs. 6.1 months) (all P < .001, multivariate). bTMB changes did not correlate with outcomes. Therefore, early dynamic changes in cfDNA-derived VAF were a powerful predictor of pan-cancer immunotherapy outcomes. Liquid biopsy to predict immunotherapy response.
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Affiliation(s)
- Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Bing Li
- Ambry Genetics, Aliso Viejo, CA, USA
| | - Jacob J. Adashek
- Department of Internal Medicine, University of South Florida, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | | | | | | | - Lisa Kim
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Tiffany W so
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Marcus Mitchell
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Naoki Kamei
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc, Tokyo, Japan
| | | | - Jayne Hoo
- Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Teruaki Iyama
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc, Tokyo, Japan
| | - Masahide Kashiwagi
- Bio Advanced Technology Division, Corporate R&D Headquarters, Konica Minolta, Inc, Tokyo, Japan
| | | | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, CA, USA
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29
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Lone SN, Nisar S, Masoodi T, Singh M, Rizwan A, Hashem S, El-Rifai W, Bedognetti D, Batra SK, Haris M, Bhat AA, Macha MA. Liquid biopsy: a step closer to transform diagnosis, prognosis and future of cancer treatments. Mol Cancer 2022; 21:79. [PMID: 35303879 PMCID: PMC8932066 DOI: 10.1186/s12943-022-01543-7] [Citation(s) in RCA: 294] [Impact Index Per Article: 147.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 02/21/2022] [Indexed: 02/07/2023] Open
Abstract
Over the past decade, invasive techniques for diagnosing and monitoring cancers are slowly being replaced by non-invasive methods such as liquid biopsy. Liquid biopsies have drastically revolutionized the field of clinical oncology, offering ease in tumor sampling, continuous monitoring by repeated sampling, devising personalized therapeutic regimens, and screening for therapeutic resistance. Liquid biopsies consist of isolating tumor-derived entities like circulating tumor cells, circulating tumor DNA, tumor extracellular vesicles, etc., present in the body fluids of patients with cancer, followed by an analysis of genomic and proteomic data contained within them. Methods for isolation and analysis of liquid biopsies have rapidly evolved over the past few years as described in the review, thus providing greater details about tumor characteristics such as tumor progression, tumor staging, heterogeneity, gene mutations, and clonal evolution, etc. Liquid biopsies from cancer patients have opened up newer avenues in detection and continuous monitoring, treatment based on precision medicine, and screening of markers for therapeutic resistance. Though the technology of liquid biopsies is still evolving, its non-invasive nature promises to open new eras in clinical oncology. The purpose of this review is to provide an overview of the current methodologies involved in liquid biopsies and their application in isolating tumor markers for detection, prognosis, and monitoring cancer treatment outcomes.
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Affiliation(s)
- Saife N Lone
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, Jammu & Kashmir, India
| | - Sabah Nisar
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Tariq Masoodi
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Mayank Singh
- Department of Medical Oncology, Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Arshi Rizwan
- Department of Nephrology, All India Institute of Medical Sciences, New Delhi, India
| | - Sheema Hashem
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
| | - Wael El-Rifai
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL, USA
- Department of Veterans Affairs, Miami Healthcare System, Miami, FL, USA
| | - Davide Bedognetti
- Cancer Research Department, Research Branch, Sidra Medicince, Doha, Qatar
- Department of Internal Medicine and Medical Specialities, University of Genova, Genova, Italy
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Surinder K Batra
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, NE 68198, Omaha, USA
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center , Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, University of Nebraska Medical Center, NE 68198, Omaha, USA
| | - Mohammad Haris
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar
- Laboratory Animal Research Center, Qatar University, Doha, Qatar
- Center for Advanced Metabolic Imaging in Precision Medicine, Department of Radiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | - Ajaz A Bhat
- Laboratory of Molecular and Metabolic Imaging, Cancer Research Department, Sidra Medicine, PO BOX 26999, Doha, Qatar.
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, (IUST), 192122, Awantipora, Jammu & Kashmir, India.
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Breadner DA, Vincent MD, Correa R, Black M, Warner A, Sanatani M, Bhat V, Morris C, Jones G, Allan A, Palma DA, Raphael J. Exploitation of treatment induced tumor lysis to enhance the sensitivity of ctDNA analysis: A first-in-human pilot study. Lung Cancer 2022; 165:145-151. [PMID: 35124411 DOI: 10.1016/j.lungcan.2022.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/30/2021] [Accepted: 01/19/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Blood-based liquid biopsies examining circulating tumour DNA (ctDNA) have increasing applications in non-small cell lung cancer (NSCLC). Limitations in sensitivity remain a barrier to ctDNA replacing tissue-based testing. We hypothesized that testing immediately after starting treatment would yield an increased abundance of ctDNA in plasma because of tumor lysis, allowing for the detection of genetic alterations that were occult in baseline testing. METHODS Three prospective cohorts of patients with stage III/IV NSCLC were enrolled. Cohort 1 (C1) contained patients starting platinum doublet chemoradiation (n = 10) and cohort 2 (C2) initiating platinum doublet cytotoxic chemotherapy ± immunotherapy (n = 10). Cohort 3 (C3) contained patients receiving palliative radiation. Two baseline samples were collected. In C1 and C2, subsequent samples were collected 3, 6, 24 and 48 h post initiation of chemotherapy. Patients in C3 had samples collected immediately prior to the next three radiotherapy fractions. Samples were analyzed for ctDNA using the 36-gene amplicon-based NGS Inivata InVisionFirst®-Lung assay. RESULTS A total of 40 patients were enrolled. Detectable ctDNA was present at baseline in 32 patients (80%), 4 additional patients (50%) had detectable ctDNA in post-treatment samples. Seven patients with detectable ctDNA at baseline (23%) had new genetic alterations detected in post-treatment samples. Mutant molecule numbers increased with treatment in 24 of 31 (77%) pts with detectable ctDNA. ctDNA levels peaked a median of 7 h (IQR:2-26 h) after the initiation of chemotherapy and a median of 2 days (IQR:1-3 days) after radiation was commenced. CONCLUSION ctDNA levels increase in the hours to days after starting treatment. ctDNA testing in the acute post-treatment phase can yield results that were not evident in pre-treatment testing. Application of this principle could improve ctDNA utility as an alternate to tissue-based testing and improve sensitivity for the detection of treatment-resistant clones.(NCT03986463).
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Affiliation(s)
- Daniel A Breadner
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada.
| | - Mark D Vincent
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Rohann Correa
- Division of Radiation Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Morgan Black
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Andrew Warner
- Division of Radiation Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Michael Sanatani
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Vasudeva Bhat
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, 1151 Richmond St, N6A 5C1 London, Ontario, Canada
| | - Clive Morris
- Inivata Inc., 7020 Kit Creek Road, Suite 140, Research Triangle Park, 27560, NC, United States
| | - Greg Jones
- Inivata Inc., 7020 Kit Creek Road, Suite 140, Research Triangle Park, 27560, NC, United States
| | - Alison Allan
- Department of Anatomy and Cell Biology, Schulich School of Medicine and Dentistry, 1151 Richmond St, N6A 5C1 London, Ontario, Canada
| | - David A Palma
- Division of Radiation Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
| | - Jacques Raphael
- Division of Medical Oncology, London Regional Cancer Program, 800 Commissioners Road East, N6A5W9 London, Ontario, Canada
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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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Moiseyenko FV, Kuligina ES, Zhabina AS, Belukhin SA, Laidus TA, Martianov AS, Zagorodnev KA, Sokolova TN, Chuinyshena SA, Kholmatov MM, Artemieva EV, Stepanova EO, Shuginova TN, Volkov NM, Yanus GA, Imyanitov EN. Changes in the concentration of EGFR-mutated plasma DNA in the first hours of targeted therapy allow the prediction of tumor response in patients with EGFR-driven lung cancer. Int J Clin Oncol 2022; 27:850-862. [PMID: 35171360 PMCID: PMC8853017 DOI: 10.1007/s10147-022-02128-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/23/2022] [Indexed: 11/25/2022]
Abstract
PURPOSE This study aimed to analyze changes in the plasma concentration of EGFR-mutated circulating tumor DNA (ctDNA) occurring immediately after the start of therapy with EGFR tyrosine kinase inhibitors (TKIs). METHODS Serial plasma samples were collected from 30 patients with EGFR-driven non-small cell lung cancer before intake of the first tablet and at 0.5, 1, 2, 3, 6, 12, 24, 36 and 48 h after the start of the therapy. The content of EGFR alleles (exon 19 deletions or L858R) in ctDNA was measured by ddPCR. RESULTS ctDNA was detected at base-line in 25/30 (83%) subjects. Twelve (50%) out of 24 informative patients showed > 25% reduction of the ctDNA content at 48 h time point; all these patients demonstrated disease control after 4 and 8-12 weeks of therapy. The remaining 12 individuals showed either stable content of EGFR-mutated ctDNA (n = 5) or the elevation of ctDNA concentration (n = 7). 10 of 12 patients with elevated or stable ctDNA level achieved an objective response at 4 weeks, but only 5 of 10 evaluable patients still demonstrated disease control at 8-12 weeks (p = 0.032, when compared to the group with ctDNA decrease). The decline of the amount of circulating EGFR mutant copies at 48 h also correlated with longer progression-free survival (14.7 months vs. 8.5 months, p = 0.013). CONCLUSION Comparison of concentration of EGFR-mutated ctDNA at base-line and at 48 h after the start of therapy is predictive for the duration of TKI efficacy.
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Affiliation(s)
- Fedor V. Moiseyenko
- City Cancer Center, 68A Leningradskaya street, Pesochny, Saint Petersburg, 197758 Russia
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
| | - Ekaterina S. Kuligina
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
- St.-Petersburg Pediatric Medical University, 2 Litovskaya street, Saint Petersburg, 194100 Russia
| | - Albina S. Zhabina
- City Cancer Center, 68A Leningradskaya street, Pesochny, Saint Petersburg, 197758 Russia
| | - Sergey A. Belukhin
- City Cancer Center, 68A Leningradskaya street, Pesochny, Saint Petersburg, 197758 Russia
| | - Tatiana A. Laidus
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
- St.-Petersburg Pediatric Medical University, 2 Litovskaya street, Saint Petersburg, 194100 Russia
| | - Aleksandr S. Martianov
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
- St.-Petersburg Pediatric Medical University, 2 Litovskaya street, Saint Petersburg, 194100 Russia
| | - Kirill A. Zagorodnev
- St.-Petersburg Pediatric Medical University, 2 Litovskaya street, Saint Petersburg, 194100 Russia
| | - Tatyana N. Sokolova
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
| | - Svetlana A. Chuinyshena
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
- St.-Petersburg Pediatric Medical University, 2 Litovskaya street, Saint Petersburg, 194100 Russia
| | - Maxim M. Kholmatov
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
| | - Elizaveta V. Artemieva
- City Cancer Center, 68A Leningradskaya street, Pesochny, Saint Petersburg, 197758 Russia
| | - Ekaterina O. Stepanova
- City Cancer Center, 68A Leningradskaya street, Pesochny, Saint Petersburg, 197758 Russia
| | - Tatiana N. Shuginova
- City Cancer Center, 68A Leningradskaya street, Pesochny, Saint Petersburg, 197758 Russia
| | - Nikita M. Volkov
- City Cancer Center, 68A Leningradskaya street, Pesochny, Saint Petersburg, 197758 Russia
| | - Grigoriy A. Yanus
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
- St.-Petersburg Pediatric Medical University, 2 Litovskaya street, Saint Petersburg, 194100 Russia
| | - Evgeny N. Imyanitov
- Laboratory of Molecular Oncology, Department of Tumor Biology, N.N. Petrov Institute of Oncology, 68 Leningradskaya street, Pesochny-2, St.-Petersburg, 197758 Russia
- St.-Petersburg Pediatric Medical University, 2 Litovskaya street, Saint Petersburg, 194100 Russia
- I.I. Mechnikov North-Western Medical University, 41 Kirochnaya street, Saint Petersburg, 191015 Russia
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Abstract
PURPOSE OF REVIEW Liquid biopsies have emerged as a noninvasive alternative to tissue biopsy with potential applications during all stages of pediatric oncology care. The purpose of this review is to provide a survey of pediatric cell-free DNA (cfDNA) studies, illustrate their potential applications in pediatric oncology, and to discuss technological challenges and approaches to overcome these hurdles. RECENT FINDINGS Recent literature has demonstrated liquid biopsies' ability to inform treatment selection at diagnosis, monitor clonal evolution during treatment, sensitively detect minimum residual disease following local control, and provide sensitive posttherapy surveillance. Advantages include reduced procedural anesthesia, molecular profiling unbiased by tissue heterogeneity, and ability to track clonal evolution. Challenges to wider implementation in pediatric oncology, however, include blood volume restrictions and relatively low mutational burden in childhood cancers. Multiomic approaches address challenges presented by low-mutational burden, and novel bioinformatic analyses allow a single assay to yield increasing amounts of information, reducing blood volume requirements. SUMMARY Liquid biopsies hold tremendous promise in pediatric oncology, enabling noninvasive serial surveillance with adaptive care. Already integrated into adult care, recent advances in technologies and bioinformatics have improved applicability to the pediatric cancer landscape.
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Affiliation(s)
- R Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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Sanz-Garcia E, Zhao E, Bratman SV, Siu LL. Monitoring and adapting cancer treatment using circulating tumor DNA kinetics: Current research, opportunities, and challenges. SCIENCE ADVANCES 2022; 8:eabi8618. [PMID: 35080978 PMCID: PMC8791609 DOI: 10.1126/sciadv.abi8618] [Citation(s) in RCA: 74] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Circulating tumor DNA (ctDNA) has emerged as a biomarker with wide-ranging applications in cancer management. While its role in guiding precision medicine in certain tumors via noninvasive detection of susceptibility and resistance alterations is now well established, recent evidence has pointed to more generalizable use in treatment monitoring. Quantitative changes in ctDNA levels over time (i.e., ctDNA kinetics) have shown potential as an early indicator of therapeutic efficacy and could enable treatment adaptation. However, ctDNA kinetics are complex and heterogeneous, affected by tumor biology, host physiology, and treatment factors. This review outlines the current preclinical and clinical knowledge of ctDNA kinetics in cancer and how early on-treatment changes in ctDNA levels could be applied in clinical research to collect evidence to support implementation in daily practice.
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Affiliation(s)
- Enrique Sanz-Garcia
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Eric Zhao
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Scott V. Bratman
- Department of Radiation Oncology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
- Corresponding author.
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Alborelli I, Jermann PM. Preanalytical Variables and Sample Quality Control for Clinical Variant Analysis. Methods Mol Biol 2022; 2493:331-351. [PMID: 35751825 DOI: 10.1007/978-1-0716-2293-3_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Broad molecular profiling by next-generation sequencing of solid tumors has become a critical tool for clinical decision-making in the era of precision oncology. In addition to many already approved targeted therapies, more than half of ongoing oncology-related clinical trials are biomarker-driven. Therefore, accurate and reliable assays are needed to assess the genetic make-up of tumor cells and guide clinicians in the therapy decision process. In order to obtain high-quality NGS data for variant detection, certain preanalytical steps and quality metrics should be followed. These include assessment of sample types, choice of extraction method, library preparation technology, sequencing platform, and finally sequencing quality control. Each of these steps has certain challenges and pitfalls that need to be addressed and overcome, respectively. In this chapter, we address the preanalytical quality control and how each of the involved steps may influence the final result. Following these guidelines and QC metrics may help in obtaining optimal results that will allow the precise and robust assessment of genetic variants in a clinical setting.
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Affiliation(s)
- Ilaria Alborelli
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland
| | - Philip M Jermann
- Institute of Medical Genetics and Pathology, University Hospital Basel, Basel, Switzerland.
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Goodman AM, Holden KA, Jeong AR, Kim L, Fitzgerald KD, Almasri E, McLennan G, Eisenberg M, Jahromi AH, Hoh C, Hurley M, Mulroney C, Tzachanis D, Ball ED, Jensen TJ, Kurzrock R. Assessing CAR T-Cell Therapy Response Using Genome-Wide Sequencing of Cell-Free DNA in Patients With B-Cell Lymphomas. Transplant Cell Ther 2021; 28:30.e1-30.e7. [PMID: 34655803 DOI: 10.1016/j.jtct.2021.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/09/2021] [Accepted: 10/06/2021] [Indexed: 10/20/2022]
Abstract
Methods that enable monitoring of therapeutic efficacy of autologous chimeric antigen receptor (CAR) T-cell therapy will be clinically useful. The aim of this study is to demonstrate the feasibility of blood-derived cell-free DNA (cfDNA) to predict CAR T-cell therapy response in patients with refractory B-cell lymphomas. Whole blood was collected before and throughout CAR T-cell therapy until day 154. Low-coverage (∼0.4×), genome-wide cfDNA sequencing, similar to that established for noninvasive prenatal testing, was performed. The genomic instability number (GIN) was used to quantify plasma copy number alteration level. Twelve patients were enrolled. Seven (58%) patients achieved a complete response (CR); 2 (25%), a partial response. Median progression-free survival was 99 days; median overall survival was not reached (median follow-up, 247 days). Altogether, 127 blood samples were analyzed (median, 10 samples/patient [range 8-13]). All 5 patients who remained in CR at the time of last measurement had GIN <170 (threshold). Two patients who attained CR, but later relapsed, and all but one patient who had best response other than CR had last GIN measurement of >170. In 5 of 6 patients with relapsed or progressive disease, increasing GIN was observed before the diagnosis by imaging. The abundance of CAR T-cell construct (absolute number of construct copies relative to the number of human genome equivalents) also showed a trend to correlate with outcome (day 10, P = .052). These data describe a proof-of-concept for the use of multiple liquid biopsy technologies to monitor therapeutic response in B-cell lymphoma patients receiving CAR T-cell therapy.
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Affiliation(s)
- Aaron M Goodman
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California.
| | | | - Ah-Reum Jeong
- Department of Medicine, Division of Hematology/Oncology, University of California San Diego, La Jolla, California
| | - Lisa Kim
- Laboratory Corporation of America, San Diego, California
| | | | - Eyad Almasri
- Laboratory Corporation of America, San Diego, California
| | | | | | - Amin H Jahromi
- Department of Radiology, University of California San Diego, La Jolla, California
| | - Carl Hoh
- Department of Radiology, University of California San Diego, La Jolla, California
| | - Michael Hurley
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Carolyn Mulroney
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Dimitrios Tzachanis
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Edward D Ball
- Department of Medicine, Division of Blood and Marrow Transplantation, University of California San Diego, La Jolla, California
| | - Taylor J Jensen
- Laboratory Corporation of America, San Diego, California; Laboratory Corporation of America, Durham, North Carolina
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Abdayem P, Planchard D. Update on molecular pathology and role of liquid biopsy in nonsmall cell lung cancer. Eur Respir Rev 2021; 30:200294. [PMID: 34289984 PMCID: PMC9489045 DOI: 10.1183/16000617.0294-2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/26/2020] [Indexed: 02/03/2023] Open
Abstract
Personalised medicine, an essential component of modern thoracic oncology, has been evolving continuously ever since the discovery of the epidermal growth factor receptor and its tyrosine kinase inhibitors. Today, screening for driver alterations in patients with advanced lung adenocarcinoma as well as those with squamous cell carcinoma and no/little history of smoking is mandatory. Multiplex molecular platforms are preferred to sequential molecular testing since they are less time- and tissue-consuming. In this review, we present the latest updates on the nine most common actionable driver alterations in nonsmall cell lung cancer. Liquid biopsy, a simple noninvasive technique that uses different analytes, mostly circulating tumour DNA, is an appealing tool that is used in thoracic oncology to identify driver alterations including resistance mutations. Additional roles are being evaluated in clinical trials and include monitoring the response to treatment, screening for lung cancer in high-risk patients and early detection of relapse in the adjuvant setting. In addition, liquid biopsy is being tested in immune-oncology as a prognostic, predictive and pharmacodynamic tool. The major limitation of plasma-based assays remains their low sensitivity when compared to tissue-based assays. Ensuring the clinical validity and utility of liquid biopsy will definitely optimise cancer care.
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Affiliation(s)
- Pamela Abdayem
- Dept of Cancer Medicine, Thoracic Group, Gustave Roussy Cancer Campus, Villejuif, France
| | - David Planchard
- Dept of Cancer Medicine, Thoracic Group, Gustave Roussy Cancer Campus, Villejuif, France
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Shah P, Sands J, Normanno N. The expanding capability and clinical relevance of molecular diagnostic technology to identify and evaluate EGFR mutations in advanced/metastatic NSCLC. Lung Cancer 2021; 160:118-126. [PMID: 34500194 DOI: 10.1016/j.lungcan.2021.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/30/2021] [Accepted: 08/01/2021] [Indexed: 11/25/2022]
Abstract
Epidermal growth factor receptor (EGFR) mutation testing in advanced non-small-cell lung cancer (NSCLC) has evolved rapidly over the past decade, largely triggered by the introduction of the targeted EGFR tyrosine kinase inhibitors (TKIs). Initially used to detect common EGFR mutations and determine the most appropriate first-line therapy at diagnosis, testing methodologies have expanded to test for multiple mutations at multiple time points throughout the disease course. Here we review the current mutation testing approaches, including types of biopsies, and the available assays commonly used in the clinic. Specific application of these approaches in advanced NSCLC, including current guideline recommendations, and potential future developments are discussed.
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Affiliation(s)
- Parth Shah
- Dartmouth-Hitchcock Medical Centre, 1 Medical Center Dr, Lebanon, NH 03766, USA.
| | - Jacob Sands
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA 02215, USA.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, Via Mariano Semmola 52, 80131 Naples, Italy.
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Li Z, Lu J, Pang Q, You J. Construction of a near-infrared fluorescent probe for ratiometric imaging of peroxynitrite during tumor progression. Analyst 2021; 146:5204-5211. [PMID: 34312630 DOI: 10.1039/d1an00980j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Malignant tumors are one of the main causes for human death and are tightly associated with overexpression of reactive oxygen species (ROS) in pathological processes. Therefore, in vivo monitoring of ROS, especially ONOO-, remains of great significance for diagnosis and therapy of tumors to improve the survival rate. Herein, we designed and constructed a reliable near-infrared (NIR) ratiometric fluorescent biosensor CDMS for monitoring the fluctuations of ONOO- in the process of tumor progression. CDMS featured outstanding stability to photoirradiation, substantial quantum yields, rapid response (<5 s), high selectivity and excellent biocompatibility. Moreover, CDMS exhibited distinct ratiometric fluorescence signal changes after reacting with ONOO-. Fluorescence imaging in immune stimulated cells indicated that CDMS was competent to determine the levels of ONOO- in the cellular level. Remarkably, CDMS was further applied in monitoring the expression of ONOO- in a peritonitis mouse model and tumor-bearing mouse model. Based on the excellent properties of CDMS, the probe exhibited the potential for noninvasive in vivo visualization of ONOO- in the occurrence and process of tumor development. It is envisioned that CDMS can be employed as a promising tool for monitoring the ONOO- fluxes in tumor pathological progression, especially for tumor diagnosis and therapy.
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Affiliation(s)
- Zan Li
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P.R. China.
| | - Jiao Lu
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P.R. China.
| | - Qing Pang
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P.R. China.
| | - Jinmao You
- Key Laboratory of Life-Organic Analysis of Shandong Province, School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu 273165, P.R. China.
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Mouliere F, Smith CG, Heider K, Su J, van der Pol Y, Thompson M, Morris J, Wan JCM, Chandrananda D, Hadfield J, Grzelak M, Hudecova I, Couturier D, Cooper W, Zhao H, Gale D, Eldridge M, Watts C, Brindle K, Rosenfeld N, Mair R. Fragmentation patterns and personalized sequencing of cell-free DNA in urine and plasma of glioma patients. EMBO Mol Med 2021; 13:e12881. [PMID: 34291583 PMCID: PMC8350897 DOI: 10.15252/emmm.202012881] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 12/11/2022] Open
Abstract
Glioma-derived cell-free DNA (cfDNA) is challenging to detect using liquid biopsy because quantities in body fluids are low. We determined the glioma-derived DNA fraction in cerebrospinal fluid (CSF), plasma, and urine samples from patients using sequencing of personalized capture panels guided by analysis of matched tumor biopsies. By sequencing cfDNA across thousands of mutations, identified individually in each patient's tumor, we detected tumor-derived DNA in the majority of CSF (7/8), plasma (10/12), and urine samples (10/16), with a median tumor fraction of 6.4 × 10-3 , 3.1 × 10-5 , and 4.7 × 10-5 , respectively. We identified a shift in the size distribution of tumor-derived cfDNA fragments in these body fluids. We further analyzed cfDNA fragment sizes using whole-genome sequencing, in urine samples from 35 glioma patients, 27 individuals with non-malignant brain disorders, and 26 healthy individuals. cfDNA in urine of glioma patients was significantly more fragmented compared to urine from patients with non-malignant brain disorders (P = 1.7 × 10-2 ) and healthy individuals (P = 5.2 × 10-9 ). Machine learning models integrating fragment length could differentiate urine samples from glioma patients (AUC = 0.80-0.91) suggesting possibilities for truly non-invasive cancer detection.
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Wang H, Zhou F, Qiao M, Li X, Zhao C, Cheng L, Chen X, Zhou C. The Role of Circulating Tumor DNA in Advanced Non-Small Cell Lung Cancer Patients Treated With Immune Checkpoint Inhibitors: A Systematic Review and Meta-Analysis. Front Oncol 2021; 11:671874. [PMID: 34367957 PMCID: PMC8335591 DOI: 10.3389/fonc.2021.671874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/02/2021] [Indexed: 12/30/2022] Open
Abstract
Background The use of circulating tumor DNA (ctDNA) to reflect clinical benefits of advanced non-small cell lung cancer (NSCLC) patients during immune checkpoint inhibitor (ICI) therapy remains controversial. This study aimed to determine the association of pre-treatment and early dynamic changes of ctDNA with clinical outcomes in advanced NSCLC patients treated with ICIs. Methods Electronic databases (PubMed, Embase, Web of Science, and Cochrane) were systematically searched to include relevant studies published in English up to November 2020. The primary outcomes were overall survival (OS) and progression-free survival (PFS) and the secondary outcome was objective response rate (ORR) with RECIST criteria. Results A total of 1017 patients from 10 studies were identified. The baseline ctDNA levels (detected versus not detected) showed no significant association with clinical outcomes regarding OS (hazard ratio [HR], 1.18; 95% confidence interval [CI], 0.93-1.51), PFS (HR, 0.98; 95% CI, 0.80-1.21), and ORR (odds ratio [OR], 0.89; 95% CI, 0.54-1.46). Interestingly, when taken early longitudinal assessment of ctDNA into consideration, the early reduction of the concentration of ctDNA was associated with significant improvements of OS (HR, 0.19; 95% CI, 0.10-0.35), PFS (HR, 0.30; 95% CI, 0.22-0.41) and ORR (OR, 0.07; 95% CI, 0.03-0.18). Further subgroup analyses revealed that the reduction magnitude did not significantly impact the association between ctDNA and clinical outcomes, suggesting that both patients with decreased ctDNA or a ≥50% reduction of ctDNA was associated with improved OS, PFS and ORR. Conclusion Early reduction of ctDNA was associated with improved OS, PFS and ORR in advanced NSCLC patients treated with ICIs. Systematic Review Registration https://www.crd.york.ac.uk/PROSPERO, CRD42021226255.
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Affiliation(s)
- Haowei Wang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fei Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Meng Qiao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xuefei Li
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Chao Zhao
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lei Cheng
- Department of Lung Cancer and Immunology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xiaoxia Chen
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Caicun Zhou
- Department of Medical Oncology, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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Adashek JJ, Janku F, Kurzrock R. Signed in Blood: Circulating Tumor DNA in Cancer Diagnosis, Treatment and Screening. Cancers (Basel) 2021; 13:3600. [PMID: 34298813 PMCID: PMC8306582 DOI: 10.3390/cancers13143600] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/23/2021] [Accepted: 07/13/2021] [Indexed: 12/18/2022] Open
Abstract
With the addition of molecular testing to the oncologist's diagnostic toolbox, patients have benefitted from the successes of gene- and immune-directed therapies. These therapies are often most effective when administered to the subset of malignancies harboring the target identified by molecular testing. An important advance in the application of molecular testing is the liquid biopsy, wherein circulating tumor DNA (ctDNA) is analyzed for point mutations, copy number alterations, and amplifications by polymerase chain reaction (PCR) and/or next-generation sequencing (NGS). The advantages of evaluating ctDNA over tissue DNA include (i) ctDNA requires only a tube of blood, rather than an invasive biopsy, (ii) ctDNA can plausibly reflect DNA shedding from multiple metastatic sites while tissue DNA reflects only the piece of tissue biopsied, and (iii) dynamic changes in ctDNA during therapy can be easily followed with repeat blood draws. Tissue biopsies allow comprehensive assessment of DNA, RNA, and protein expression in the tumor and its microenvironment as well as functional assays; however, tumor tissue acquisition is costly with a risk of complications. Herein, we review the ways in which ctDNA assessment can be leveraged to understand the dynamic changes of molecular landscape in cancers.
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Affiliation(s)
- Jacob J. Adashek
- Department of Internal Medicine, University of South Florida, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33606, USA
| | - Filip Janku
- Department of Investigational Cancer Therapeutics (Phase 1 Clinical Trials Program), Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
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Muller M, Hoogendoorn R, Moritz RJG, van der Noort V, Lanfermeijer M, Korse CM, van den Broek D, Ten Hoeve JJ, Baas P, van Rossum HH, van den Heuvel MM. Validation of a clinical blood-based decision aid to guide immunotherapy treatment in patients with non-small cell lung cancer. Tumour Biol 2021; 43:115-127. [PMID: 34219680 DOI: 10.3233/tub-211504] [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] [Indexed: 11/15/2022] Open
Abstract
BACKGROUND The widespread introduction of immunotherapy in patients with advanced non-small cell lung cancer (NSCLC) has led to durable responses but still many patients fail and are treated beyond progression. OBJECTIVE This study investigated whether readily available blood-based tumor biomarkers allow accurate detection of early non-responsiveness, allowing a timely switch of therapy and cost reduction. METHODS In a prospective, observational study in patients with NSCLC treated with nivolumab or pembrolizumab, five serum tumor markers were measured at baseline and every other week. Six months disease control as determined by RECIST was used as a measure of clinical response. Patients with a disease control < 6 months were deemed non-responsive. For every separate tumor marker a criterion for predicting of non-response was developed. Each marker test was defined as positive (predictive of non-response) if the value of that tumor marker increased at least 50% from the value at baseline and above a marker dependent minimum value to be determined. Also, tests based on combination of multiple markers were designed. Specificity and sensitivity for predicting non-response was calculated and results were validated in an independent cohort. The target specificity of the test for detecting non-response was set at > 95%, in order to allow its safe use for treatment decisions. RESULTS A total of 376 patients (training cohort: 180, validation cohort: 196) were included in our analysis. Results for the specificity of the single marker tests in the validation set were CEA: 98·3% (95% CI: 90·9-100%), NSE: 96·5% (95% CI: 87·9-99·6%), SCC: 96·5% (95% CI: 88·1-99·6%), Cyfra21·1 : 91.8% (95% CI: 81·9-97·3%), and CA125 : 86·0% (95% CI: 74·2-93·7%). A test based on the combination of Cyfra21.1, CEA and NSE accurately predicted non-response in 32.3% (95% CI 22.6-43.1%) of patients 6 weeks after start of immunotherapy. Survival analysis showed a significant difference between predicted responders (Median PFS: 237 days (95% CI 184-289 days)) and non-responders (Median PFS: 58 days (95% CI 46-70 days)) (p < 0.001). CONCLUSIONS Serum tumor marker based tests can be used for accurate detection of non-response in NSCLC, thereby allowing early and safe discontinuation of immunotherapy in a significant subset of patients.
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Affiliation(s)
- Mirte Muller
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roland Hoogendoorn
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ruben J G Moritz
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Vincent van der Noort
- Department of Biometrics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mirthe Lanfermeijer
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Catharina M Korse
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Daan van den Broek
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jelle J Ten Hoeve
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Paul Baas
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Huub H van Rossum
- Department of Laboratory Medicine, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Michel M van den Heuvel
- Department of Thoracic Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Respiratory Diseases, Radboud Medical Center, Nijmegen, The Netherlands
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Haring CT, Bhambhani C, Brummel C, Jewell B, Bellile E, Heft Neal ME, Sandford E, Spengler RM, Bhangale A, Spector ME, McHugh J, Prince ME, Mierzwa M, Worden FP, Tewari M, Swiecicki PL, Brenner JC. Human papilloma virus circulating tumor DNA assay predicts treatment response in recurrent/metastatic head and neck squamous cell carcinoma. Oncotarget 2021; 12:1214-1229. [PMID: 34194620 PMCID: PMC8238244 DOI: 10.18632/oncotarget.27992] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/02/2021] [Indexed: 11/25/2022] Open
Abstract
Despite the rising incidence of human papillomavirus related (HPV+) oropharyngeal squamous cell carcinoma (OPSCC), treatment of metastatic disease remains palliative. Even with new treatments such as immunotherapy, response rates are low and can be delayed, while even mild tumor progression in the face of an ineffective therapy can lead to rapid death. Real-time biomarkers of response to therapy could improve outcomes by guiding early change of therapy in the metastatic setting. Herein, we developed and analytically validated a new droplet digital PCR (ddPCR)-based assay for HPV16 circulating tumor DNA (ctDNA) and evaluated plasma HPV16 ctDNA for predicting treatment response in metastatic HPV+ OPSCC. We found that longitudinal changes HPV16 ctDNA correlate with treatment response and that ctDNA responses are observed earlier than conventional imaging (average 70 days, range: 35-166). With additional validation in multi-site studies, this assay may enable early identification of treatment failure, allowing patients to be directed promptly toward clinical trials or alternative therapies.
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Affiliation(s)
- Catherine T. Haring
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
- Co-First Authors
| | - Chandan Bhambhani
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, Ann Arbor, MI 48109, USA
- Co-First Authors
| | - Collin Brummel
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
| | - Brittany Jewell
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
| | - Emily Bellile
- University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA
| | - Molly E. Heft Neal
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
| | - Erin Sandford
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, Ann Arbor, MI 48109, USA
| | - Ryan M. Spengler
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, Ann Arbor, MI 48109, USA
| | - Apurva Bhangale
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
| | - Matthew E. Spector
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
- University of Michigan, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Jonathan McHugh
- University of Michigan, Rogel Cancer Center, Ann Arbor, MI 48109, USA
- University of Michigan, Department of Pathology, Ann Arbor, MI 48109, USA
| | - Mark E. Prince
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
| | - Michelle Mierzwa
- University of Michigan, Rogel Cancer Center, Ann Arbor, MI 48109, USA
- University of Michigan, Department of Radiation Oncology, Ann Arbor, MI 48109, USA
| | - Francis P. Worden
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, Ann Arbor, MI 48109, USA
- University of Michigan, Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Muneesh Tewari
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, Ann Arbor, MI 48109, USA
- University of Michigan, Rogel Cancer Center, Ann Arbor, MI 48109, USA
- University of Michigan, Department of Biomedical Engineering, Ann Arbor, MI 48109, USA
- University of Michigan, Center for Computational Medicine and Bioinformatics, Ann Arbor, MI 48109, USA
- Co-Senior Authors
| | - Paul L. Swiecicki
- University of Michigan, Department of Internal Medicine, Division of Hematology and Oncology, Ann Arbor, MI 48109, USA
- University of Michigan, Rogel Cancer Center, Ann Arbor, MI 48109, USA
- Co-Senior Authors
| | - J. Chad Brenner
- University of Michigan, Department of Otolaryngology-Head and Neck Surgery, Ann Arbor, MI 48109, USA
- University of Michigan, Rogel Cancer Center, Ann Arbor, MI 48109, USA
- University of Michigan, Department of Pharmacology, Ann Arbor, MI 48109, USA
- Co-Senior Authors
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Patel A, Hissong E, Rosado L, Burkhardt R, Cong L, Alperstein SA, Siddiqui MT, Park HJ, Song W, Velu PD, Rennert H, Heymann JJ. Next-Generation Sequencing of Cell-Free DNA Extracted From Pleural Effusion Supernatant: Applications and Challenges. Front Med (Lausanne) 2021; 8:662312. [PMID: 34195208 PMCID: PMC8236629 DOI: 10.3389/fmed.2021.662312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/10/2021] [Indexed: 12/11/2022] Open
Abstract
Cell-free DNA (cfDNA) extracted from diverse specimen types has emerged as a high quality substrate for molecular tumor profiling. Analytical and pre-analytical challenges in the utilization of cfDNA extracted from pleural effusion supernatant (PES) are herein characterized in patients with metastatic non-small cell lung carcinoma (NSCLC). Pleural effusion specimens containing metastatic NSCLC were collected prospectively. After ThinPrep® (TP) and cell block (CB) preparation, DNA was extracted from residual PES and analyzed by gel electrophoresis for quality and quantity. Libraries were prepared and sequenced with a targeted next-generation sequencing (NGS) platform and panel clinically validated for plasma specimens. Results were compared with DNA extracted from corresponding FFPE samples that were sequenced using institutional targeted NGS assays clinically validated for solid tumor FFPE samples. Tumor (TC) and overall cellularity (OC) were evaluated. Fourteen specimens were collected from 13 patients. Median specimen volume was 180 mL (range, 35–1,400 mL). Median TC and OC on TP slides and CB sections were comparable. Median extracted DNA concentration was 7.4 ng/μL (range, 0.1–58.0 ng/μL), with >5 ng/μL DNA extracted from 10/14 specimens (71%). Mutations were identified in 10/14 specimens, including 1/3 specimens with median molecular coverage <1,000 reads. The minimal detected allelic fraction was 0.6%. NGS was falsely negative for the presence of one driver mutation. No correlation was identified between sample volume or OC, quality or quantity of extracted DNA, or mutation detection. Despite analytical and pre-analytical challenges, PES represents a robust source of DNA for NGS.
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Affiliation(s)
- Ami Patel
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Erika Hissong
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Lucelina Rosado
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Robert Burkhardt
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Lin Cong
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Susan A Alperstein
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Momin T Siddiqui
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Hyeon Jin Park
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Wei Song
- Clinical Genomics Laboratory, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Priya D Velu
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Hanna Rennert
- Division of Molecular and Genomic Pathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
| | - Jonas J Heymann
- Division of Cytopathology, Department of Pathology and Laboratory Medicine, New York-Presbyterian Hospital-Weill Cornell Medical College, New York, NY, United States
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Urine as a Source of Liquid Biopsy for Cancer. Cancers (Basel) 2021; 13:cancers13112652. [PMID: 34071230 PMCID: PMC8199052 DOI: 10.3390/cancers13112652] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/20/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022] Open
Abstract
Simple Summary Tissue biopsy is essential for diagnosis and characterization of a tumor. Recently circulating tumor cells and other tumor-derived nucleic acid can be detected from blood, which is called liquid biopsy. Now this concept has been expanded to many other body fluids including urine. Urine is the least invasive method to obtain a liquid biopsy and can be done anywhere, which allows longitudinal repeated sampling. Here, we review the latest update on urine liquid biopsy in urological and non-urological cancers. Abstract Tissue biopsy is the gold standard for diagnosis and morphological and immunohistochemical analyses to characterize cancer. However, tissue biopsy usually requires an invasive procedure, and it can be challenging depending on the condition of the patient and the location of the tumor. Even liquid biopsy analysis of body fluids such as blood, saliva, gastric juice, sweat, tears and cerebrospinal fluid may require invasive procedures to obtain samples. Liquid biopsy can be applied to circulating tumor cells (CTCs) or nucleic acids (NAs) in blood. Recently, urine has gained popularity due to its less invasive sampling, ability to easily repeat samples, and ability to follow tumor evolution in real-time, making it a powerful tool for diagnosis and treatment monitoring in cancer patients. With the development and advancements in extraction methods of urinary substances, urinary NAs have been found to be closely related to carcinogenesis, metastasis, and therapeutic response, not only in urological cancers but also in non-urological cancers. This review mainly highlights the components of urine liquid biopsy and their utility and limitations in oncology, especially in non-urological cancers.
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Rostami A, Lambie M, Yu CW, Stambolic V, Waldron JN, Bratman SV. Senescence, Necrosis, and Apoptosis Govern Circulating Cell-free DNA Release Kinetics. Cell Rep 2021; 31:107830. [PMID: 32610131 DOI: 10.1016/j.celrep.2020.107830] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 02/22/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022] Open
Abstract
The kinetics of circulating cell-free DNA (cfDNA) release may provide a real-time assessment of induced cell death. However, there is a limited understanding of the underlying biological rationale for cfDNA release following distinct treatments and cell death mechanisms. Here, we uncover a complex interplay between apoptosis, necrosis, and senescence in determining cfDNA release kinetics. Utilizing multiple in vitro and in vivo preclinical models, we show how cfDNA release is modulated through a combination of apoptotic and senescent triggers and inhibitors. Interestingly, we identify treatment-induced senescence as a previously unrecognized determinant of cfDNA kinetics that can counteract its release. Necrosis is the predominant cell death mechanism that consistently contributes to cfDNA release in response to ionizing radiation, and, surprisingly, apoptosis plays a comparatively minor role in some tumors. Based on our results, we propose a model to explain cfDNA release from cells over time, with important implications for future studies.
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Affiliation(s)
- Ariana Rostami
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Meghan Lambie
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Caberry W Yu
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Vuk Stambolic
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - John N Waldron
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Radiation Oncology, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada
| | - Scott V Bratman
- Princess Margaret Cancer Center, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada; Department of Radiation Oncology, University of Toronto, 149 College Street, Toronto, ON M5T 1P5, Canada.
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Kamp EJCA, Dinjens WNM, Doukas M, Bruno MJ, de Jonge PJF, Peppelenbosch MP, de Vries AC. Optimal tissue sampling during ERCP and emerging molecular techniques for the differentiation of benign and malignant biliary strictures. Therap Adv Gastroenterol 2021; 14:17562848211002023. [PMID: 33948111 PMCID: PMC8053835 DOI: 10.1177/17562848211002023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 02/04/2023] Open
Abstract
Patients with cholangiocarcinoma have poor survival since the majority of patients are diagnosed at a stage precluding surgical resection, due to locally irresectable tumors and/or metastases. Optimization of diagnostic strategies, with a principal role for tissue diagnosis, is essential to detect cancers at an earlier stage amenable to curative treatment. Current barriers for a tissue diagnosis include both insufficient tissue sampling and a difficult cyto- or histopathological assessment. During endoscopic retrograde cholangiopancreatography, optimal brush sampling includes obtaining more than one brush within an individual patient to increase its diagnostic value. Currently, no significant increase of the diagnostic accuracy for the new cytology brush devices aiming to enhance the cellularity of brushings versus standard biliary brush devices has been demonstrated. Peroral cholangioscopy with bile duct biopsies appears to be a valuable tool in the diagnostic work-up of indeterminate biliary strictures, and may overcome current technical difficulties of fluoroscopic-guided biopsies. Over the past years, molecular techniques to detect chromosomal instability, mutations and methylation profiling of tumors have revolutionized, and implementation of these techniques on biliary tissue during diagnostic work-up of biliary strictures may be awaited in the near future. Fluorescence in situ hybridization has already been implemented in routine diagnostic evaluation of biliary strictures in several centers. Next-generation sequencing is promising for standard diagnostic care in biliary strictures, and recent studies have shown adequate detection of prevalent genomic alterations in KRAS, TP53, CDKN2A, SMAD4, PIK3CA, and GNAS on biliary brush material. Detection of DNA methylation of tumor suppressor genes and microRNAs may evolve over the coming years to a valuable diagnostic tool for cholangiocarcinoma. This review summarizes optimal strategies for biliary tissue sampling during endoscopic retrograde cholangiopancreatography and focuses on the evolving molecular techniques on biliary tissue to improve the differentiation of benign and malignant biliary strictures.
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Affiliation(s)
- Eline J. C. A. Kamp
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Winand N. M. Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Michail Doukas
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, The Netherlands
| | - Marco J. Bruno
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Pieter Jan F. de Jonge
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Maikel P. Peppelenbosch
- Department of Gastroenterology and Hepatology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Annemarie C. de Vries
- Department of Gastroenterology & Hepatology, Erasmus MC, University Medical Center Rotterdam, Doctor Molewaterplein 40, Room Na-609, Rotterdam, 3015 GD, The Netherlands
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Ferreira D, Miranda J, Martins-Lopes P, Adega F, Chaves R. Future Perspectives in Detecting EGFR and ALK Gene Alterations in Liquid Biopsies of Patients with NSCLC. Int J Mol Sci 2021; 22:ijms22083815. [PMID: 33916986 PMCID: PMC8067613 DOI: 10.3390/ijms22083815] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/28/2021] [Accepted: 04/03/2021] [Indexed: 02/07/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) is a major cause of death worldwide. Alterations in such genes as EGFR and ALK are considered important biomarkers in NSCLC due to the existence of targeted therapies with specific tyrosine kinase inhibitors (TKIs). However, specific resistance-related mutations can occur during TKI treatment, which often result in therapy inefficacy. Liquid biopsies arise as a reliable tool for the early detection of these types of alterations, allowing a non-invasive follow-up of the patients. Furthermore, they can be essential for cancer screening, initial diagnosis and to check surgery success. Despite the great advantages of liquid biopsies in NSCLC and the high input that next-generation sequencing (NGS) approaches can provide in this field, its use in oncology is still limited. With improvement of assay sensitivity and the establishment of clinical guidelines for liquid biopsy analysis, it is expected that they will be used in routine procedures. This review focuses on the usefulness of liquid biopsies of NSCLC patients as a means to detect alterations in EGFR and ALK genes and in disease management, highlighting the impact of NGS methods.
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Affiliation(s)
- Daniela Ferreira
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Juliana Miranda
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Paula Martins-Lopes
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Department of Genetics and Biotechnology (DGB), University of Trás-os-Montes e Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Filomena Adega
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
| | - Raquel Chaves
- Biosystems and Integrative Sciences Institute (BioISI), Faculty of Sciences, University of Lisboa, 1749-016 Lisbon, Portugal; (D.F.); (J.M.); (P.M.-L.); (F.A.)
- Correspondence: ; Tel.: +351-259-350936
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Leers MPG. Circulating tumor DNA and their added value in molecular oncology. Clin Chem Lab Med 2021; 58:152-161. [PMID: 31490771 DOI: 10.1515/cclm-2019-0436] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022]
Abstract
New methods for molecular diagnosis are now available in oncology thanks to the discovery of circulating tumor DNA molecules in the plasma of cancer patients. By utilizing blood samples, rather than traditional tissue sampling, clinical practice is on the verge of new discoveries from the analysis of cell-free DNA (cfDNA). The method, known as a "liquid biopsy", consists of analyzing therapeutic targets and drug-resistant conferring gene mutations in circulating tumor cells (CTC) and cell-free circulating tumor DNA (ctDNA). These are subsequently released from primary tumors and metastatic deposits into the peripheral blood. The advantages of the method can be observed in the diagnosis, but also in the choice of treatment for solid tumors (e.g. non-small cell lung carcinomas [NSCLC]). In order to interpret the results, an understanding of the biological characteristics of circulating tumor DNA is required. Currently there is no consensus as to how a liquid biopsy should be conducted. In this review, we will assess the pros of ctDNA as analytes in peripheral blood samples and its impact on clinical applications in solid tumors and hematological malignancies. We will also address practical issues facing clinical implementation, such as pre-analytical factors. Moreover, we will emphasize the open questions that remain when considering the current state of personalized medicine and targeted therapy.
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Affiliation(s)
- Math P G Leers
- Department of Clinical Chemistry and Hematology, Zuyderland Medical Center Sittard-Geleen, Dr. H. Van der Hoffplein 1, P.O. Box 5500, 6130 MB Sittard, The Netherlands
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