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Zieren RC, Zondervan PJ, Pienta KJ, Bex A, de Reijke TM, Bins AD. Diagnostic liquid biopsy biomarkers in renal cell cancer. Nat Rev Urol 2024; 21:133-157. [PMID: 37758847 DOI: 10.1038/s41585-023-00818-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 09/29/2023]
Abstract
The clinical presentation of renal cell cancer (RCC) is shifting towards incidental and early detection, creating new challenges in RCC diagnosis. Overtreatment might be reduced with the development of new diagnostic biomarkers to distinguish benign from malignant small renal masses (SRMs). Differently from tissue biopsies, liquid biopsies are obtained from a patient's blood or urine and, therefore, are minimally invasive and suitable for longitudinal monitoring. The most promising types of liquid biopsy biomarkers for RCC diagnosis are circulating tumour cells, extracellular vesicles (EVs) and cell-free DNA. Circulating tumour cell assays have the highest specificity, with low processing time and costs. However, the biological characteristics and low sensitivity limit the use of these markers in SRM diagnostics. Cell-free DNA might complement the diagnosis of high-volume RCC, but the potential for clinical application in SRMs is limited. EVs have the highest biological abundance and the highest sensitivity in identifying low-volume disease; moreover, the molecular characteristics of these markers make EVs suitable for multiple analytical applications. Thus, currently, EV assays have the greatest potential for diagnostic application in RCC (including identification of SRMs). All these liquid biomarkers have potential in clinical practice, pending validation studies. Biomarker implementation will be needed to also improve characterization of RCC subtypes. Last, diagnostic biomarkers might be extended to prognostic or predictive applications.
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Affiliation(s)
- Richard C Zieren
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands.
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
| | - Patricia J Zondervan
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Kenneth J Pienta
- The Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Axel Bex
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, United Kingdom
- Division of Surgery and Interventional Science, University College London, London, United Kingdom
- The Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Theo M de Reijke
- Department of Urology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Adriaan D Bins
- Department of Medical Oncology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
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2
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Cui JZ, Chew ZH, Lim LHK. New insights into nucleic acid sensor AIM2: The potential benefit in targeted therapy for cancer. Pharmacol Res 2024; 200:107079. [PMID: 38272334 DOI: 10.1016/j.phrs.2024.107079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024]
Abstract
The AIM2 inflammasome represents a multifaceted oligomeric protein complex within the innate immune system, with the capacity to perceive double-stranded DNA (dsDNA) and engage in diverse physiological reactions and disease contexts, including cancer. While originally conceived as a discerning DNA sensor, AIM2 has demonstrated its capability to discern various nucleic acid variations, encompassing RNA and DNA-RNA hybrids. Through its interaction with nucleic acids, AIM2 orchestrates the assembly of a complex involving multiple proteins, aptly named the AIM2 inflammasome, which facilitates the enzymatic cleavage of proinflammatory cytokines, namely pro-IL-1β and pro-IL-18. This process, in turn, underpins its pivotal biological role. In this review, we provide a systematic summary and discussion of the latest advancements in AIM2 sensing various types of nucleic acids. Additionally, we discuss the modulation of AIM2 activation, which can cause cell death, including pyroptosis, apoptosis, and autophagic cell death. Finally, we fully illustrate the evidence for the dual role of AIM2 in different cancer types, including both anti-tumorigenic and pro-tumorigenic functions. Considering the above information, we uncover the therapeutic promise of modulating the AIM2 inflammasome in cancer treatment.
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Affiliation(s)
- Jian-Zhou Cui
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS-Cambridge Immunophenotyping Centre, Life Science Institute, National University of Singapore, Singapore.
| | - Zhi Huan Chew
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lina H K Lim
- Translational Immunology Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; NUS Immunology Program, Life Sciences Institute, National University of Singapore, Singapore; NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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3
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Haller N, Reichel T, Zimmer P, Behringer M, Wahl P, Stöggl T, Krüger K, Simon P. Blood-Based Biomarkers for Managing Workload in Athletes: Perspectives for Research on Emerging Biomarkers. Sports Med 2023; 53:2039-2053. [PMID: 37341908 PMCID: PMC10587296 DOI: 10.1007/s40279-023-01866-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2023] [Indexed: 06/22/2023]
Abstract
At present, various blood-based biomarkers have found their applications in the field of sports medicine. This current opinion addresses biomarkers that warrant consideration in future research for monitoring the athlete training load. In this regard, we identified a variety of emerging load-sensitive biomarkers, e.g., cytokines (such as IL-6), chaperones (such as heat shock proteins) or enzymes (such as myeloperoxidase) that could improve future athlete load monitoring as they have shown meaningful increases in acute and chronic exercise settings. In some cases, they have even been linked to training status or performance characteristics. However, many of these markers have not been extensively studied and the cost and effort of measuring these parameters are still high, making them inconvenient for practitioners so far. We therefore outline strategies to improve knowledge of acute and chronic biomarker responses, including ideas for standardized study settings. In addition, we emphasize the need for methodological advances such as the development of minimally invasive point-of-care devices as well as statistical aspects related to the evaluation of these monitoring tools to make biomarkers suitable for regular load monitoring.
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Affiliation(s)
- Nils Haller
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University of Mainz, Mainz, Germany
- Department of Sport and Exercise Science, University of Salzburg, Salzburg, Austria
| | - Thomas Reichel
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus-Liebig-University Gießen, Giessen, Germany
| | - Philipp Zimmer
- Division of Performance and Health (Sports Medicine), Institute for Sport and Sport Science, TU Dortmund University, Dortmund, Germany
| | - Michael Behringer
- Department of Sports Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Patrick Wahl
- Department of Exercise Physiology, German Sport University Cologne, Cologne, Germany
| | - Thomas Stöggl
- Department of Sport and Exercise Science, University of Salzburg, Salzburg, Austria
- Red Bull Athlete Performance Center, Salzburg, Austria
| | - Karsten Krüger
- Department of Exercise Physiology and Sports Therapy, Institute of Sports Science, Justus-Liebig-University Gießen, Giessen, Germany
| | - Perikles Simon
- Department of Sports Medicine, Rehabilitation and Disease Prevention, Johannes Gutenberg University of Mainz, Mainz, Germany.
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Mattox AK, Douville C, Wang Y, Popoli M, Ptak J, Silliman N, Dobbyn L, Schaefer J, Lu S, Pearlman AH, Cohen JD, Tie J, Gibbs P, Lahouel K, Bettegowda C, Hruban RH, Tomasetti C, Jiang P, Chan KA, Lo YMD, Papadopoulos N, Kinzler KW, Vogelstein B. The Origin of Highly Elevated Cell-Free DNA in Healthy Individuals and Patients with Pancreatic, Colorectal, Lung, or Ovarian Cancer. Cancer Discov 2023; 13:2166-2179. [PMID: 37565753 PMCID: PMC10592331 DOI: 10.1158/2159-8290.cd-21-1252] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/16/2022] [Accepted: 08/09/2023] [Indexed: 08/12/2023]
Abstract
Cell-free DNA (cfDNA) concentrations from patients with cancer are often elevated compared with those of healthy controls, but the sources of this extra cfDNA have never been determined. To address this issue, we assessed cfDNA methylation patterns in 178 patients with cancers of the colon, pancreas, lung, or ovary and 64 patients without cancer. Eighty-three of these individuals had cfDNA concentrations much greater than those generally observed in healthy subjects. The major contributor of cfDNA in all samples was leukocytes, accounting for ∼76% of cfDNA, with neutrophils predominating. This was true regardless of whether the samples were derived from patients with cancer or the total plasma cfDNA concentration. High levels of cfDNA observed in patients with cancer did not come from either neoplastic cells or surrounding normal epithelial cells from the tumor's tissue of origin. These data suggest that cancers may have a systemic effect on cell turnover or DNA clearance. SIGNIFICANCE The origin of excess cfDNA in patients with cancer is unknown. Using cfDNA methylation patterns, we determined that neither the tumor nor the surrounding normal tissue contributes this excess cfDNA-rather it comes from leukocytes. This finding suggests that cancers have a systemic impact on cell turnover or DNA clearance. See related commentary by Thierry and Pisareva, p. 2122. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Austin K. Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joy Schaefer
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Steve Lu
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Alexander H. Pearlman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Jeanne Tie
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter Gibbs
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kamel Lahouel
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Cristian Tomasetti
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Peiyong Jiang
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - K.C. Allen Chan
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Yuk Ming Dennis Lo
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
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5
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Leick KM, Tomanek-Chalkley A, Coleman KL, Chan CHF. Peritoneal Cell-Free Tumor DNA is a Biomarker of Locoregional and Peritoneal Recurrence in Resected Pancreatic Ductal Adenocarcinomas. Ann Surg Oncol 2023; 30:6652-6660. [PMID: 37303025 DOI: 10.1245/s10434-023-13701-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
BACKGROUND Recurrence after curative-intent pancreatectomy for pancreatic ductal adenocarcinomas (PDAC) is quite frequent with locoregional and peritoneal recurrence in about one-third of cases. We hypothesize that peritoneal cell-free tumor DNA (ptDNA) present in the intraoperative peritoneal lavage (PL) fluid may be used as a predictive biomarker of locoregional and peritoneal recurrence. PATIENTS AND METHODS Under institutional review board (IRB)-approved protocol, pre- and postresection PL fluids were collected from PDAC patients undergoing curative-intent pancreatectomy. PL fluids from PDAC patients with pathologically proven peritoneal metastasis were also collected as positive controls. Cell-free DNA was extracted from PL fluids. Droplet digital PCR (ddPCR) was performed using ddPCR KRAS G12/G13 screening kit. Recurrence-free survival (RFS) based on KRAS-mutant ptDNA level was determined using Kaplan-Meier methods. RESULTS KRAS-mutant ptDNA was detected in PL fluids from all PDAC patients. KRAS-mutant ptDNA was detected in 11/21 (52%) preresection and 15/18 (83%) postresection PL fluid samples. With a median follow-up of 23.6 months, 12 patients developed recurrence (8 locoregional/peritoneal recurrence, 9 pulmonary/hepatic recurrence); 5/8 (63%) and 6/6 (100%) patients with mutant allele frequency (MAF) of > 0.10% in pre- and postresection PL fluids, respectively, developed recurrence. Using a cutoff value of 0.10% MAF, the presence of KRAS-mutant ptDNA in postresection PL fluid predicted a significantly shortened time to locoregional and peritoneal recurrence (median RFS of 8.9 months versus not reached, P = 0.003). CONCLUSIONS This study suggests that ptDNA in postresection PL fluids may be a useful biomarker to predict locoregional and peritoneal recurrence in resected PDAC patients.
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Affiliation(s)
- Katie M Leick
- Department of Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Ann Tomanek-Chalkley
- Department of Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Kristen L Coleman
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, USA
| | - Carlos H F Chan
- Department of Surgery, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
- Holden Comprehensive Cancer Center, University of Iowa Hospitals and Clinics, Iowa City, IA, USA.
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Medina JE, Dracopoli NC, Bach PB, Lau A, Scharpf RB, Meijer GA, Andersen CL, Velculescu VE. Cell-free DNA approaches for cancer early detection and interception. J Immunother Cancer 2023; 11:e006013. [PMID: 37696619 PMCID: PMC10496721 DOI: 10.1136/jitc-2022-006013] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/03/2023] [Indexed: 09/13/2023] Open
Abstract
Rapid advancements in the area of early cancer detection have brought us closer to achieving the goals of finding cancer early enough to treat or cure it, while avoiding harms of overdiagnosis. We evaluate progress in the development of early cancer detection tests in the context of the current principles for cancer screening. We review cell-free DNA (cfDNA)-based approaches using mutations, methylation, or fragmentomes for early cancer detection. Lastly, we discuss the challenges in demonstrating clinical utility of these tests before integration into routine clinical care.
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Affiliation(s)
- Jamie E Medina
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Anna Lau
- Delfi Diagnostics Inc, Baltimore, Maryland, USA
| | - Robert B Scharpf
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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Sharma P, Gupta RK, Anthwal D, Dass M, Yadav R, Behera A, Sethi S, Singhal R, Dhooria S, Aggarwal AN, Haldar S. Evaluation of Mycobacterium tuberculosis derived cell-free DNA using pleural fluid and paired plasma samples for the diagnosis of pleural tuberculosis. Tuberculosis (Edinb) 2023; 142:102369. [PMID: 37536090 DOI: 10.1016/j.tube.2023.102369] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/13/2023] [Accepted: 06/25/2023] [Indexed: 08/05/2023]
Abstract
Pleural tuberculosis (pTB) is a grave clinical challenge. A novel cell-free M. tuberculosis DNA (cfM.tb-DNA) probe-based-qPCR assay was developed for the diagnosis of pTB. Total cell-free DNA was extracted from pleural fluid (PF) and paired plasma samples and cfM.tb-DNA was quantified by probe-based qPCR targeting devR (109-bp) gene of M. tuberculosis in patients with pleural effusion. Patient categorization was done using 'Composite-Reference-Standard' formulated for the study. Assay cut-offs were determined from samples in the 'Development set' (n = 17; 'Definite & Probable' pTB; n = 9 and 'Non-TB'; n = 8) by ROC-curve analysis and applied to 'Validation set' (n = 112; 'Definite' pTB; n = 8, 'Probable' pTB; n = 34, 'Possible' pTB; n = 28 and 'Non-TB'; n = 42). cfM.tb-DNA qPCR had a sensitivity of 62.5% (95%CI; 24.4,91.4) in 'Definite' pTB category and 59.5% (95%CI; 43.2,74.3) in 'Definite & Probable' pTB category with 95.2% (95%CI; 83.8,99.4) specificity using PF. In plasma (n = 85), the assay had a sub-optimal sensitivity of 7.6% (95%CI; 0.95,25.1) with 88.2% (95%CI; 72.5,96.7) specificity in 'Definite & Probable' pTB group. Xpert MTB/RIF assay detected only six-samples in the 'Validation set'. Logistic regression analysis indicated that PF-cfM.tb-DNA qPCR provided incremental advantage over existing pTB diagnostic algorithms. To the best of our knowledge, this is the first report describing the utility of cfM.tb-DNA for pTB diagnosis in India.
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Affiliation(s)
- Pratibha Sharma
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Kumar Gupta
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Divya Anthwal
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Manisha Dass
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Yadav
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashish Behera
- Department of Internal Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sunil Sethi
- Department of Medical Microbiology, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ritu Singhal
- Department of Microbiology, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Sahajal Dhooria
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Ashutosh Nath Aggarwal
- Department of Pulmonary Medicine, Post Graduate Institute of Medical Education and Research, Chandigarh, India
| | - Sagarika Haldar
- Department of Experimental Medicine and Biotechnology, Post Graduate Institute of Medical Education and Research, Chandigarh, India.
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8
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Meriranta L, Pitkänen E, Leppä S. Blood has never been thicker: Cell-free DNA fragmentomics in the liquid biopsy toolbox of B-cell lymphomas. Semin Hematol 2023; 60:132-141. [PMID: 37455222 DOI: 10.1053/j.seminhematol.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/30/2023] [Accepted: 06/24/2023] [Indexed: 07/18/2023]
Abstract
Liquid biopsies utilizing plasma circulating tumor DNA (ctDNA) are anticipated to revolutionize decision-making in cancer care. In the field of lymphomas, ctDNA-based blood tests represent the forefront of clinically applicable tools to harness decades of genomic research for disease profiling, quantification, and detection. More recently, the discovery of nonrandom fragmentation patterns in cell-free DNA (cfDNA) has opened another avenue of liquid biopsy research beyond mutational interrogation of ctDNA. Through examination of structural features, nucleotide content, and genomic distribution of massive numbers of plasma cfDNA molecules, the study of fragmentomics aims at identifying new tools that augment existing ctDNA-based analyses and discover new ways to profile cancer from blood tests. Indeed, the characterization of aberrant lymphoma ctDNA fragment patterns and harnessing them with powerful machine-learning techniques are expected to unleash the potential of nonmutant molecules for liquid biopsy purposes. In this article, we review cfDNA fragmentomics as an emerging approach in the ctDNA research of B-cell lymphomas. We summarize the biology behind the formation of cfDNA fragment patterns and discuss the preanalytical and technical limitations faced with current methodologies. Then we go through the advances in the field of lymphomas and envision what other noninvasive tools based on fragment characteristics could be explored. Last, we place fragmentomics as one of the facets of ctDNA analyses in emerging multiview and multiomics liquid biopsies. We pay attention to the unknowns in the field of cfDNA fragmentation biology that warrant further mechanistic investigation to provide rational background for the development of these precision oncology tools and understanding of their limitations.
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Affiliation(s)
- Leo Meriranta
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
| | - Esa Pitkänen
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Institute for Molecular Medicine Finland (FIMM), HILIFE, Helsinki, Finland
| | - Sirpa Leppä
- Applied Tumor Genomics, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Department of Oncology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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Fleischhacker M, Arslan E, Reinicke D, Eisenmann S, Theil G, Kollmeier J, Schäper C, Grah C, Klawonn F, Holdenrieder S, Schmidt B. Cell-Free Methylated PTGER4 and SHOX2 Plasma DNA as a Biomarker for Therapy Monitoring and Prognosis in Advanced Stage NSCLC Patients. Diagnostics (Basel) 2023; 13:2131. [PMID: 37443525 DOI: 10.3390/diagnostics13132131] [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: 05/03/2023] [Revised: 06/13/2023] [Accepted: 06/15/2023] [Indexed: 07/15/2023] Open
Abstract
Notwithstanding some improvement in the earlier detection of patients with lung cancer, most of them still present with a late-stage disease at the time of diagnosis. Next to the most frequently utilized factors affecting the prognosis of lung cancer patients (stage, performance, and age), the recent application of biomarkers obtained by liquid profiling has gained more acceptance. In our study, we aimed to answer these questions: (i) Is the quantification of free-circulating methylated PTGER4 and SHOX2 plasma DNA a useful method for therapy monitoring, and is this also possible for patients treated with different therapy regimens? (ii) Is this approach possible when blood-drawing tubes, which allow for a delayed processing of blood samples, are utilized? Baseline values for mPTGER4 and mSHOX2 do not allow for clear discrimination between different response groups. In contrast, the combination of the methylation values for both genes shows a clear difference between responders vs. non-responders at the time of re-staging. Furthermore, blood drawing into tubes stabilizing the sample allows researchers more flexibility.
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Affiliation(s)
- Michael Fleischhacker
- Klinik für Innere Medizin-Schwerpunkt Pneumologie und Schlafmedizin, DRK Kliniken Berlin/Mitte, 13359 Berlin, Germany
| | - Erkan Arslan
- Lungenarztpraxis Berlin-Reinickendorf, 13403 Berlin, Germany
| | - Dana Reinicke
- Department für Innere Medizin, Universitätsklinikum Halle/Saale, 06120 Halle (Saale), Germany
| | - Stefan Eisenmann
- Department für Innere Medizin, Universitätsklinikum Halle/Saale, 06120 Halle (Saale), Germany
| | - Gerit Theil
- Department für Innere Medizin, Universitätsklinikum Halle/Saale, 06120 Halle (Saale), Germany
| | - Jens Kollmeier
- Lungenklinik Heckeshorn, Helios Klinikum Emil von Behring, 14165 Berlin, Germany
| | - Christoph Schäper
- Klinik und Poliklinik für Innere Medizin B, Universitätsmedizin Greifswald, 17475 Greifswald, Germany
| | - Christian Grah
- Gemeinschaftskrankenhaus Havelhöhe, Pneumologie und Lungenkrebszentrum, 14089 Berlin, Germany
| | - Frank Klawonn
- Department of Computer Science, Ostfalia University, 38302 Wolfenbüttel, Germany
- Biostatistics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Stefan Holdenrieder
- Munich Biomarker Research Center, Institute of Laboratory Medicine, German Heart Centre, Technical University Munich, Lazarettstraße 36, 80636 Munich, Germany
| | - Bernd Schmidt
- Klinik für Innere Medizin-Schwerpunkt Pneumologie und Schlafmedizin, DRK Kliniken Berlin/Mitte, 13359 Berlin, Germany
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10
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Brockley LJ, Souza VGP, Forder A, Pewarchuk ME, Erkan M, Telkar N, Benard K, Trejo J, Stewart MD, Stewart GL, Reis PP, Lam WL, Martinez VD. Sequence-Based Platforms for Discovering Biomarkers in Liquid Biopsy of Non-Small-Cell Lung Cancer. Cancers (Basel) 2023; 15:cancers15082275. [PMID: 37190212 DOI: 10.3390/cancers15082275] [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: 03/07/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
Lung cancer detection and monitoring are hampered by a lack of sensitive biomarkers, which results in diagnosis at late stages and difficulty in tracking response to treatment. Recent developments have established liquid biopsies as promising non-invasive methods for detecting biomarkers in lung cancer patients. With concurrent advances in high-throughput sequencing technologies and bioinformatics tools, new approaches for biomarker discovery have emerged. In this article, we survey established and emerging biomarker discovery methods using nucleic acid materials derived from bodily fluids in the context of lung cancer. We introduce nucleic acid biomarkers extracted from liquid biopsies and outline biological sources and methods of isolation. We discuss next-generation sequencing (NGS) platforms commonly used to identify novel biomarkers and describe how these have been applied to liquid biopsy. We highlight emerging biomarker discovery methods, including applications of long-read sequencing, fragmentomics, whole-genome amplification methods for single-cell analysis, and whole-genome methylation assays. Finally, we discuss advanced bioinformatics tools, describing methods for processing NGS data, as well as recently developed software tailored for liquid biopsy biomarker detection, which holds promise for early diagnosis of lung cancer.
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Affiliation(s)
- Liam J Brockley
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Vanessa G P Souza
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Aisling Forder
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | | | - Melis Erkan
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
| | - Nikita Telkar
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
- British Columbia Children's Hospital Research Institute, Vancouver, BC V5Z 4H4, Canada
| | - Katya Benard
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Jessica Trejo
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Matt D Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Greg L Stewart
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Patricia P Reis
- Molecular Oncology Laboratory, Experimental Research Unit, School of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, SP, Brazil
| | - Wan L Lam
- British Columbia Cancer Research Institute, Vancouver, BC V5Z 1L3, Canada
| | - Victor D Martinez
- Department of Pathology and Laboratory Medicine, IWK Health Centre, Halifax, NS B3K 6R8, Canada
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS B3K 6R8, Canada
- Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
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11
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Stebbing J, Takis PG, Sands CJ, Maslen L, Lewis MR, Gleason K, Page K, Guttery D, Fernandez-Garcia D, Primrose L, Shaw JA. Comparison of phenomics and cfDNA in a large breast screening population: the Breast Screening and Monitoring Study (BSMS). Oncogene 2023; 42:825-832. [PMID: 36693953 PMCID: PMC10005936 DOI: 10.1038/s41388-023-02591-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
To assess their roles in breast cancer diagnostics, we aimed to compare plasma cell-free DNA (cfDNA) levels with the circulating metabolome in a large breast screening cohort of women recalled for mammography, including healthy women and women with mammographically detected breast diseases, ductal carcinoma in situ and invasive breast cancer: the Breast Screening and Monitoring Study (BSMS). In 999 women, plasma was analyzed by nuclear magnetic resonance (NMR) and Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-MS) and then processed to isolate and quantify total cfDNA. NMR and UPLC-MS results were compared with data for 186 healthy women derived from the AIRWAVE cohort. Results showed no significant differences between groups for all metabolites, whereas invasive cancers had significantly higher plasma cfDNA levels than all other groups. When stratified the supervised OPLS-DA analysis and total cfDNA concentration showed high discrimination accuracy between invasive cancers and the disease/medication-free subjects. Furthermore, comparison of OPLS-DA data for invasive breast cancers with the AIRWAVE cohort showed similar discrimination between breast cancers and healthy controls. This is the first report of agreement between metabolomics and plasma cfDNA levels for discriminating breast cancer from healthy subjects in a true screening population. It also emphasizes the importance of sample standardization. Follow on studies will involve analysis of candidate features in a larger validation series as well as comparing results with serial plasma samples taken at the next routine screening mammography appointment. The findings here help establish the role of plasma analysis in the diagnosis of breast cancer in a large real-world cohort.
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Affiliation(s)
- Justin Stebbing
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, Hammersmith, London, W12 0NN, UK
- School of Life Sciences, Faculty of Science and Engineering, ARU, East Road, Cambridge, CB1 1PT, UK
| | - Panteleimon G Takis
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK.
| | - Caroline J Sands
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
| | - Lynn Maslen
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
| | - Matthew R Lewis
- National Phenome Centre and Imperial Clinical Phenotyping Centre & Section of Bioanalytical Chemistry, Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, UK
| | - Kelly Gleason
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, Hammersmith, London, W12 0NN, UK
| | - Karen Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - David Guttery
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Daniel Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Lindsay Primrose
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
| | - Jacqueline A Shaw
- Department of Surgery and Cancer, Imperial College London, Du Cane Road, Hammersmith, London, W12 0NN, UK
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, LE2 7LX, UK
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12
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Qi T, Pan M, Shi H, Wang L, Bai Y, Ge Q. Cell-Free DNA Fragmentomics: The Novel Promising Biomarker. Int J Mol Sci 2023; 24:ijms24021503. [PMID: 36675018 PMCID: PMC9866579 DOI: 10.3390/ijms24021503] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/04/2023] [Accepted: 01/04/2023] [Indexed: 01/15/2023] Open
Abstract
Cell-free DNA molecules are released into the plasma via apoptotic or necrotic events and active release mechanisms, which carry the genetic and epigenetic information of its origin tissues. However, cfDNA is the mixture of various cell fragments, and the efficient enrichment of cfDNA fragments with diagnostic value remains a great challenge for application in the clinical setting. Evidence from recent years shows that cfDNA fragmentomics' characteristics differ in normal and diseased individuals without the need to distinguish the source of the cfDNA fragments, which makes it a promising novel biomarker. Moreover, cfDNA fragmentomics can identify tissue origins by inferring epigenetic information. Thus, further insights into the fragmentomics of plasma cfDNA shed light on the origin and fragmentation mechanisms of cfDNA during physiological and pathological processes in diseases and enhance our ability to take the advantage of plasma cfDNA as a molecular diagnostic tool. In this review, we focus on the cfDNA fragment characteristics and its potential application, such as fragment length, end motifs, jagged ends, preferred end coordinates, as well as nucleosome footprints, open chromatin region, and gene expression inferred by the cfDNA fragmentation pattern across the genome. Furthermore, we summarize the methods for deducing the tissue of origin by cfDNA fragmentomics.
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Affiliation(s)
- Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Min Pan
- School of Medicine, Southeast University, Nanjing 210097, China
| | - Huajuan Shi
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liangying Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yunfei Bai
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
- Correspondence: ; Tel./Fax: +86-025-83792396
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13
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Abstract
The high fragmentation of nuclear circulating DNA (cirDNA) relies on chromatin organization and protection or packaging within mononucleosomes, the smallest and the most stabilized structure in the bloodstream. The detection of differing size patterns, termed fragmentomics, exploits information about the nucleosomal packing of DNA. Fragmentomics not only implies size pattern characterization but also considers the positioning and occupancy of nucleosomes, which result in cirDNA fragments being protected and persisting in the circulation. Fragmentomics can determine tissue of origin and distinguish cancer-derived cirDNA. The screening power of fragmentomics has been considerably strengthened in the omics era, as shown in the ongoing development of sophisticated technologies assisted by machine learning. Fragmentomics can thus be regarded as a strategy for characterizing cancer within individuals and offers an alternative or a synergistic supplement to mutation searches, methylation, or nucleosome positioning. As such, it offers potential for improving diagnostics and cancer screening.
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Affiliation(s)
- A.R. Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, and ICM, Institut régional du Cancer de Montpellier, Montpellier 34298, France,Corresponding author
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14
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Cell-Free DNA as a New Biomarker of IVF Success, Independent of Any Infertility Factor, Including Endometriosis. Diagnostics (Basel) 2023; 13:diagnostics13020208. [PMID: 36673018 PMCID: PMC9858053 DOI: 10.3390/diagnostics13020208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/31/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
Cell-free DNA fragments detected in blood and in other biological fluids are released from apoptotic/necrotic cells. In this study, we analyzed cfDNA levels in follicular fluid (FF) samples from patients with infertility. Samples were collected from 178 infertile women and cfDNA was extracted and quantified by qPCR, using ALU115 and ALU247 primers, and statistical correlations were performed. We found that cfDNA concentration was significantly higher in FF pools from women aged 35 and over than in women under 35 years of age (p = 0.017). We also found that q247 cfDNA levels were significantly higher in women with an associated female factor, such as endometriosis, PCOS and POF, compared with women with no specific cause of infertility (p = 0.033). The concentration of cfDNA did not vary significantly in each group of women with an associated female factor. The concentration of cfDNA was significantly higher in the FF of women that obtained embryos with a high fragmentation rate, compared to embryos with a low fragmentation rate (p = 0.007). Finally, we found that women who did not become pregnant during IVF treatments had higher q247 cfDNA levels (p = 0.043). The quantification of cfDNA could be an important biomarker of follicular micro-environment quality to predict embryo quality and the success of IVF, making them more specific and effective.
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15
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Chen H, Xu C, Fang Z, Mao S. Cell-Free DNA, MicroRNAs, Proteins, and Peptides as Liquid Biopsy Biomarkers in Prostate Cancer and Bladder Cancer. Methods Mol Biol 2023; 2695:165-179. [PMID: 37450118 DOI: 10.1007/978-1-0716-3346-5_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Liquid biopsy, as a novel noninvasive tool for biomarker discovery, has gained a lot of attention and represents a significant innovation in precision medicine. Due to its minimally invasive nature, liquid biopsy has fewer complications and can be scheduled more frequently to provide individualized snapshots of the disease at successive time points. This is particularly valuable in providing simultaneous measurements of tumor burden during treatment and early detection of tumor recurrence or drug resistance. Blood-based liquid biopsy is an attractive, minimally invasive alternative, which has shown promise in diagnosis, risk stratification, disease monitoring, and more. Urine has gained popularity due to its less invasive sampling, the ability to easily repeat samples, and the ability to track tumor evolution in real time, making it a powerful tool for diagnosis and treatment monitoring, especially in urologic cancers. In this review, we provide a detailed discussion on the potential clinical applications of prostate cancer (PCa) and bladder cancer (BCa), with cell-free DNA (cfDNA), microRNAs (miRNAs), proteins, and peptides as liquid biopsy biomarkers.
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Affiliation(s)
- Haoran Chen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Chenyang Xu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zujun Fang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Shanhua Mao
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
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16
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Takousis P, Devonshire AS, Redshaw N, von Baumgarten L, Whale AS, Jones GM, Fernandez-Gonzalez A, Martin J, Foy CA, Alexopoulos P, Huggett JF, Perneczky R. A standardised methodology for the extraction and quantification of cell-free DNA in cerebrospinal fluid and application to evaluation of Alzheimer's disease and brain cancers. N Biotechnol 2022; 72:97-106. [PMID: 36202346 DOI: 10.1016/j.nbt.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 09/23/2022] [Accepted: 10/01/2022] [Indexed: 11/27/2022]
Abstract
Cerebrospinal fluid (CSF) is a source of diagnostic biomarkers for a range of neurological conditions. Cell-free DNA (cfDNA) is detected in CSF and differences in the concentration of cell-free mitochondrial DNA have been reported in studies of neurodegenerative disorders including Alzheimer's disease (AD). However, the influence of pre-analytical steps has not been investigated for cfDNA in CSF and there is no standardised approach for quantification of total cfDNA (copies of nuclear genome or mitochondria-derived gene targets). In this study, the suitability of four extraction methods was evaluated: QIAamp Circulating Nucleic Acid (Qiagen), Quick-cfDNA Serum & Plasma (Zymo), NucleoSnap® DNA Plasma (Macherey-Nagel) and Plasma/Serum Circulating DNA Purification Mini (Norgen) kits, for cfDNA extraction from CSF of controls and AD dementia patients, utilising a spike-in control for extraction efficiency and fragment size. One of the optimal extraction methods was applied to a comparison of cfDNA concentrations in CSF from control subjects, AD dementia and primary and secondary brain tumour patients. Extraction efficiency based on spike-in recovery was similar in all three groups whilst both endogenous mitochondrial and nucleus-derived cfDNA was significantly higher in CSF from cancer patients compared to control and AD groups, which typically contained < 100 genome copies/mL. This study shows that it is feasible to measure low concentration nuclear and mitochondrial gene targets in CSF and that normalisation of extraction yield can help control pre-analytical variability influencing biomarker measurements.
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Affiliation(s)
- Petros Takousis
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK
| | - Alison S Devonshire
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK.
| | - Nicholas Redshaw
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Louisa von Baumgarten
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany; Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany
| | - Alexandra S Whale
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Gerwyn M Jones
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Ana Fernandez-Gonzalez
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Jan Martin
- Department of Anaesthesiology and Intensive Care Medicine, Technical University Munich, Munich, Germany
| | - Carole A Foy
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Panagiotis Alexopoulos
- Department of Psychiatry, University of Patras, Rion Patras, Greece; Department of Psychiatry and Psychotherapy, Technical University Munich, Munich, Germany
| | - Jim F Huggett
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Robert Perneczky
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK; Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
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17
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Lagarde A, Le Collen L, Boulagnon C, Brixi H, Durlach A, Mougel G, Cuny T, Delemer B, Barlier A, Romanet P. Early Detection of Relapse by ctDNA Sequencing in a Patient with Metastatic Thymic Tumor and MEN1 Mosaicism. J Clin Endocrinol Metab 2022; 107:e4154-e4158. [PMID: 35904487 DOI: 10.1210/clinem/dgac454] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Indexed: 11/19/2022]
Abstract
CONTEXT Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disease caused by inactivating mutations in the MEN1 gene. In the literature, few cases of MEN1 have been reported because of mosaic MEN1 mutations. OBJECTIVE We performed an extensive molecular characterization in several lesions and blood samples, including plasmatic circulating cell-free DNA (ccfDNA) in an exceptional case of a patient with MEN1 mosaicism causing primary hyperparathyroidism, multiple pancreatic neuroendocrine tumors (NETs), and a metastatic thymic NET. METHODS Blood, ccfDNA and multiple tissue analysis were performed by next-generation sequencing. RESULTS MEN1 mosaicism was confirmed by multiple tissue analysis. Somatic analysis of the largest pancreatic NET revealed the same MEN1 second-hit mutation as found in the thymic lesion, demonstrating its metastatic origin from the thymic lesion. Moreover, in ccfDNA we found the mosaic MEN1 mutation but also the somatic second-hit mutation found in the thymic primary tumor, revealing the presence of circulating tumor DNA (ctDNA). After surgical removal of the pancreatic metastasis, the mutated fraction of both mutations decreased, before increasing again several weeks before a new clinical relapse, suggesting that thymic ctDNA may be used as an early tumor biomarker. CONCLUSION This exceptional MEN1 case highlighted (1) the importance of looking for MEN1 mosaicism, (2) that MEN1 mosaicism can cause very aggressive disease, and (3) the interest in analyzing ccfDNA for confirming MEN1 mosaicism but also as a potential tumor biomarker for NET.
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Affiliation(s)
- Arnaud Lagarde
- Aix Marseille Univ, APHM, INSERM, MMG, Hospital La Conception Laboratory of Molecular Biology, Marseille, France
| | - Lauriane Le Collen
- Department of Endocrinology Diabetology, University of Reims , Reims, France
- Inserm/CNRS UMR 1283/8199, Institut Pasteur de Lille , EGID, Lille, France
- Department of Clinical Genetics, University of Reims , Reims, France
| | - Camille Boulagnon
- Biopathology Laboratory, Pôle de Biologie Territorial, CHU de Reims, 51092 Reims, France
- Université de Reims Champagne Ardenne (URCA), CNRS, UMR 7369 MEDyC, Reims, France
| | - Hedia Brixi
- Department of Gastroenterology and Digestive Oncology, Reims University Hospital, Reims, France
| | - Anne Durlach
- Biopathology Laboratory, Pôle de Biologie Territorial, CHU de Reims, 51092 Reims, France
- Inserm UMR-S 1250, 51092 Reims, France
| | - Grégory Mougel
- Aix Marseille Univ, APHM, INSERM, MMG, Hospital La Conception Laboratory of Molecular Biology, Marseille, France
| | - Thomas Cuny
- Aix Marseille Univ, APHM, INSERM, MMG, Hospital La Conception Department of endocrinology, Marseille, France
| | - Brigitte Delemer
- Department of Endocrinology Diabetology, University of Reims , Reims, France
| | - Anne Barlier
- Aix Marseille Univ, APHM, INSERM, MMG, Hospital La Conception Laboratory of Molecular Biology, Marseille, France
| | - Pauline Romanet
- Aix Marseille Univ, APHM, INSERM, MMG, Hospital La Conception Laboratory of Molecular Biology, Marseille, France
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18
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Paulson V, Konnick EQ, Lockwood CH. When Tissue Is the Issue. Clin Lab Med 2022; 42:485-496. [DOI: 10.1016/j.cll.2022.05.005] [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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19
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Liquid biopsy and non-small cell lung cancer: are we looking at the tip of the iceberg? Br J Cancer 2022; 127:383-393. [PMID: 35264788 PMCID: PMC9345955 DOI: 10.1038/s41416-022-01777-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 02/16/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
The possibility to analyse the tumour genetic material shed in the blood is undoubtedly one of the main achievements of translational research in the latest years. In the modern clinical management of advanced non-small cell lung cancer, molecular characterisation plays an essential role. In parallel, immunotherapy is widely employed, but reliable predictive markers are not available yet. Liquid biopsy has the potential to face the two issues and to increase its role in advanced NSCLC in the next future. The aim of this review is to summarise the main clinical applications of liquid biopsy in advanced non-small cell lung cancer, underlining both its potential and limitations from a clinically driven perspective.
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20
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Yan X, Liu C. Clinical application and prospect of MRD evaluation in lung cancer based on ctDNA level: A review. TUMORI JOURNAL 2022:3008916221101927. [PMID: 35815471 DOI: 10.1177/03008916221101927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Lung cancer is one of the most malignant cancers in China with a rising incidence rate. Despite the fact that surgical treatment is the only possible cure for lung cancer, its long-term efficacy is compromised by the high level of postoperative local recurrence rate. Minimal residual disease is the leading cause of tumor recurrence, yet the suggested combination of clinical, radiological and serological (carcinoembryonic antigen) tests fails to reveal the underlying residual tissue in all stage I-III lung cancer cases, which makes tumor recurrence surveillance timely. Through monitoring circulating tumor DNA, the minimal residual disease level can be accessed and provide guidance for more precise postoperative personalized treatment, and its scientific feasibility can revolutionize lung cancer therapy. In the present review we summarized the progress of circulating tumor DNA in lung cancer minimal residual disease detection and discussed its application value in guiding precise treatment of lung cancer.
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Affiliation(s)
- Xing Yan
- The Second Affiliated Hospital of Dalian Medical University Thoracic surgery, DaLian, China
| | - Changhong Liu
- The Second Affiliated Hospital of Dalian Medical University Thoracic surgery, DaLian, China
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21
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Feasibility of Cell-Free DNA Measurement from the Earlobe during Physiological Exercise Testing. Diagnostics (Basel) 2022; 12:diagnostics12061379. [PMID: 35741187 PMCID: PMC9222055 DOI: 10.3390/diagnostics12061379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/27/2022] [Accepted: 05/30/2022] [Indexed: 11/30/2022] Open
Abstract
Circulating, cell-free DNA (cfDNA) has been discussed as an upcoming blood-based biomarker in exercise physiology, reflecting important aspects of exercise load. cfDNA blood sampling has evolved from elaborate venous to efficient capillary sampling from the fingertips. In this study, we aimed to evaluate the principal feasibility of cfDNA blood sampling from the earlobe. Therefore, we obtained cfDNA concentrations from the fingertips, earlobe, and the antecubital vein during physiological exercise testing. Significantly higher concentrations were obtained from the earlobe compared to fingertip samples. All of the measurement methods showed good to excellent repeatability (ICCs of 0.85 to 0.93). In addition, the control experiments revealed that repeated sampling from the earlobe but not from the fingertips increased cfDNA at rest. In summary, cfDNA sampling is feasible for all sampling sources. However, at rest, cfDNA collected from the earlobe tend to increase over time in the absence of physical load, potentially limiting this sampling method.
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22
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Mamtimin M, Pinarci A, Han C, Braun A, Anders HJ, Gudermann T, Mammadova-Bach E. Extracellular DNA Traps: Origin, Function and Implications for Anti-Cancer Therapies. Front Oncol 2022; 12:869706. [PMID: 35574410 PMCID: PMC9092261 DOI: 10.3389/fonc.2022.869706] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 12/16/2022] Open
Abstract
Extracellular DNA may serve as marker in liquid biopsies to determine individual diagnosis and prognosis in cancer patients. Cell death or active release from various cell types, including immune cells can result in the release of DNA into the extracellular milieu. Neutrophils are important components of the innate immune system, controlling pathogens through phagocytosis and/or the release of neutrophil extracellular traps (NETs). NETs also promote tumor progression and metastasis, by modulating angiogenesis, anti-tumor immunity, blood clotting and inflammation and providing a supportive niche for metastasizing cancer cells. Besides neutrophils, other immune cells such as eosinophils, dendritic cells, monocytes/macrophages, mast cells, basophils and lymphocytes can also form extracellular traps (ETs) during cancer progression, indicating possible multiple origins of extracellular DNA in cancer. In this review, we summarize the pathomechanisms of ET formation generated by different cell types, and analyze these processes in the context of cancer. We also critically discuss potential ET-inhibiting agents, which may open new therapeutic strategies for cancer prevention and treatment.
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Affiliation(s)
- Medina Mamtimin
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Akif Pinarci
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany
| | - Chao Han
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Attila Braun
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany
| | - Hans-Joachim Anders
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
| | - Thomas Gudermann
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,German Center for Lung Research, Munich, Germany
| | - Elmina Mammadova-Bach
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilians-University, Munich, Germany.,Division of Nephrology, Department of Medicine IV, Ludwig-Maximilians-University Hospital, Munich, Germany
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23
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Zhu JW, Charkhchi P, Akbari MR. Potential clinical utility of liquid biopsies in ovarian cancer. Mol Cancer 2022; 21:114. [PMID: 35545786 PMCID: PMC9092780 DOI: 10.1186/s12943-022-01588-8] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/27/2022] [Indexed: 12/11/2022] Open
Abstract
Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. One of the main challenges in the management of OC is the late clinical presentation of disease that results in poor survival. Conventional tissue biopsy methods and serological biomarkers such as CA-125 have limited clinical applications. Liquid biopsy is a novel sampling method that analyzes distinctive tumour components released into the peripheral circulation, including circulating tumour DNA (ctDNA), circulating tumour cells (CTCs), cell-free RNA (cfRNA), tumour-educated platelets (TEPs) and exosomes. Increasing evidence suggests that liquid biopsy could enhance the clinical management of OC by improving early diagnosis, predicting prognosis, detecting recurrence, and monitoring response to treatment. Capturing the unique tumour genetic landscape can also guide treatment decisions and the selection of appropriate targeted therapies. Key advantages of liquid biopsy include its non-invasive nature and feasibility, which allow for serial sampling and longitudinal monitoring of dynamic tumour changes over time. In this review, we outline the evidence for the clinical utility of each liquid biopsy component and review the advantages and current limitations of applying liquid biopsy in managing ovarian cancer. We also highlight future directions considering the current challenges and explore areas where more studies are warranted to elucidate its emerging clinical potential.
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Affiliation(s)
- Jie Wei Zhu
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada.,Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Parsa Charkhchi
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada
| | - Mohammad R Akbari
- Women's College Research Institute, Women's College Hospital, University of Toronto, 76 Grenville St, Toronto, ON, M5S 1B2, Canada. .,Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, ON, Canada. .,Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada.
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24
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The History and Future of Basic and Translational Cell-Free DNA Research at a Glance. Diagnostics (Basel) 2022; 12:diagnostics12051192. [PMID: 35626347 PMCID: PMC9139999 DOI: 10.3390/diagnostics12051192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/29/2022] [Accepted: 05/03/2022] [Indexed: 11/30/2022] Open
Abstract
We discuss the early history of the structure of DNA and its involvement in gene structure as well as its mobility in and between cells and between tissues in the form of circulating cell-free DNA (cfDNA). This is followed by a view of the present status of the studies on cfDNA and clinical applications of circulating cell-free tumor DNA (ctDNA). The future developments and roles of ctDNA are also considered.
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25
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Merk C, Martling A, Lindberg J, Benhaim L, Taieb J, Lind P. Circulating tumor DNA (ctDNA) in adjuvant therapy of early stage colon cancer: current status and future perspectives. Acta Oncol 2022; 61:523-530. [PMID: 35139729 DOI: 10.1080/0284186x.2022.2033831] [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] [Indexed: 12/24/2022]
Abstract
BACKGROUND This article reviews the current knowledge on circulating tumor DNA (ctDNA) in early stage colon cancer and ongoing trials on ctDNA-guided treatment in the adjuvant setting. METHODS A literature search of Pubmed was performed to identify studies on ctDNA in early stage colon cancer and neoadjuvant or adjuvant treatment. For ongoing trials, we searched clinicaltrials.gov and the Australian New Zealand Clinical Trials Registry (ANZCTR). RESULTS Several studies show that ctDNA is a strong predictor for recurrence and survival after surgery and adjuvant chemotherapy. The specificity of this marker is extremely high, and the sensitivity is increasing with the development of technology. Recurrences can be detected very early and the analysis can potentially be used to guide neoadjuvant and adjuvant treatment. Ongoing and planned studies are now looking into escalation and de-escalation of therapy according to ctDNA-status after surgery. CONCLUSION Serial measurement of ctDNA shows great promise as a marker for both prognosis and response to treatment in early colon cancer. Future studies will show whether we can use this analysis for tailoring treatment for patients in the adjuvant and neoadjuvant setting. With improved technology, ctDNA has the potential of becoming a 'game-changer' in the treatment of early stage colon cancers.
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Affiliation(s)
- Cecilia Merk
- Department of Upper Abdominal Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Martling
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Léonor Benhaim
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université de Paris, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
- Department of Visceral and Surgical Oncology, Villejuif, France
| | - Julien Taieb
- Department of Gastroenterology and Gastrointestinal Oncology, Hôpital Européen Georges-Pompidou, AP-HP, Université de Paris, Paris, France
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, Université de Paris, USPC, Equipe labellisée Ligue Nationale Contre le Cancer, SIRIC CARPEM, Paris, France
| | - Pehr Lind
- Department of Clinical Science and Education, Karolinska Institutet, Södersjukhuset, Sweden
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26
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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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27
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Lote H, Chau I. Emerging HER2-directed therapeutic agents for gastric cancer in early phase clinical trials. Expert Opin Investig Drugs 2022; 31:59-78. [PMID: 35034511 DOI: 10.1080/13543784.2022.2030311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
INTRODUCTION HER2 positive gastric cancer is a distinct subgroup overexpressing the HER2 receptor. For a decade, first-line Trastuzumab was the only licensed HER2-directed therapy for HER2 positive advanced gastric cancer following results from the ToGA trial in 2010 demonstrating a survival benefit when added to chemotherapy. Within the last year, significant advances have taken place in the field of HER2-directed gastric cancer therapy. AREAS COVERED This review discusses pivotal clinical trial results and summarises current clinical trials of HER2-directed therapy in gastric cancer. Evidence for HER2-directed antibodies, immunotherapy, immune stimulating antibody conjugates, antibody-drug conjugates (including DESTINY trial results) and tyrosine kinase inhibitors are placed into clinical context. Key challenges including resistance mechanisms and drug toxicities are outlined. Search terms 'HER2' and 'gastric cancer' were entered into ClinicalTrials.gov, Pubmed and Google. Only English-language studies were included. EXPERT OPINION Clinical management of HER2 positive gastric cancer patients is likely to change significantly over the next 5 years. Checkpoint inhibition is likely to be used alongside HER2-directed therapy and chemotherapy first-line in advanced disease. Trastuzumab deruxtecan is likely to be offered second-line and beyond. The sheer number of clinical trials of HER2-directed therapy in gastric cancer are testament to progress and potential.
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Affiliation(s)
- Hazel Lote
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom.,Department Molecular Pathology, The Institute of Cancer Research, London and Surrey, United Kingdom
| | - Ian Chau
- Department of Medicine, Royal Marsden Hospital, London and Surrey, United Kingdom
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28
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Sassu CM, Palaia I, Boccia SM, Caruso G, Perniola G, Tomao F, Di Donato V, Musella A, Muzii L. Role of Circulating Biomarkers in Platinum-Resistant Ovarian Cancer. Int J Mol Sci 2021; 22:ijms222413650. [PMID: 34948446 PMCID: PMC8707281 DOI: 10.3390/ijms222413650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 02/07/2023] Open
Abstract
Ovarian cancer (OC) is the second most common cause of death in women with gynecological cancer. Considering the poor prognosis, particularly in the case of platinum-resistant (PtR) disease, a huge effort was made to define new biomarkers able to help physicians in approaching and treating these challenging patients. Currently, most data can be obtained from tumor biopsy samples, but this is not always available and implies a surgical procedure. On the other hand, circulating biomarkers are detected with non-invasive methods, although this might require expensive techniques. Given the fervent hope in their value, here we focused on the most studied circulating biomarkers that could play a role in PtR OC.
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29
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At the dawn: cell-free DNA fragmentomics and gene regulation. Br J Cancer 2021; 126:379-390. [PMID: 34815523 PMCID: PMC8810841 DOI: 10.1038/s41416-021-01635-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 11/03/2021] [Accepted: 11/09/2021] [Indexed: 12/14/2022] Open
Abstract
Epigenetic mechanisms play instrumental roles in gene regulation during embryonic development and disease progression. However, it is challenging to non-invasively monitor the dynamics of epigenomes and related gene regulation at inaccessible human tissues, such as tumours, fetuses and transplanted organs. Circulating cell-free DNA (cfDNA) in peripheral blood provides a promising opportunity to non-invasively monitor the genomes from these inaccessible tissues. The fragmentation patterns of plasma cfDNA are unevenly distributed in the genome and reflect the in vivo gene-regulation status across multiple molecular layers, such as nucleosome positioning and gene expression. In this review, we revisited the computational and experimental approaches that have been recently developed to measure the cfDNA fragmentomics across different resolutions comprehensively. Moreover, cfDNA in peripheral blood is released following cell death, after apoptosis or necrosis, mainly from haematopoietic cells in healthy people and diseased tissues in patients. Several cfDNA-fragmentomics approaches showed the potential to identify the tissues-of-origin in cfDNA from cancer patients and healthy individuals. Overall, these studies paved the road for cfDNA fragmentomics to non-invasively monitor the in vivo gene-regulatory dynamics in both peripheral immune cells and diseased tissues.
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30
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Deveson IW, Gong B, Lai K, LoCoco JS, Richmond TA, Schageman J, Zhang Z, Novoradovskaya N, Willey JC, Jones W, Kusko R, Chen G, Madala BS, Blackburn J, Stevanovski I, Bhandari A, Close D, Conroy J, Hubank M, Marella N, Mieczkowski PA, Qiu F, Sebra R, Stetson D, Sun L, Szankasi P, Tan H, Tang LY, Arib H, Best H, Burgher B, Bushel PR, Casey F, Cawley S, Chang CJ, Choi J, Dinis J, Duncan D, Eterovic AK, Feng L, Ghosal A, Giorda K, Glenn S, Happe S, Haseley N, Horvath K, Hung LY, Jarosz M, Kushwaha G, Li D, Li QZ, Li Z, Liu LC, Liu Z, Ma C, Mason CE, Megherbi DB, Morrison T, Pabón-Peña C, Pirooznia M, Proszek PZ, Raymond A, Rindler P, Ringler R, Scherer A, Shaknovich R, Shi T, Smith M, Song P, Strahl M, Thodima VJ, Tom N, Verma S, Wang J, Wu L, Xiao W, Xu C, Yang M, Zhang G, Zhang S, Zhang Y, Shi L, Tong W, Johann DJ, Mercer TR, Xu J. Evaluating the analytical validity of circulating tumor DNA sequencing assays for precision oncology. Nat Biotechnol 2021; 39:1115-1128. [PMID: 33846644 PMCID: PMC8434938 DOI: 10.1038/s41587-021-00857-z] [Citation(s) in RCA: 103] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/15/2021] [Indexed: 02/08/2023]
Abstract
Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.
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Affiliation(s)
- Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Binsheng Gong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Kevin Lai
- Bioinformatics, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Todd A Richmond
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Zhihong Zhang
- Research and Development, Burning Rock Biotech, Shanghai, China
| | | | - James C Willey
- Departments of Medicine, Pathology, and Cancer Biology, College of Medicine and Life Sciences, University of Toledo Health Sciences Campus, Toledo, OH, USA
| | | | | | - Guangchun Chen
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Bindu Swapna Madala
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - James Blackburn
- Cancer Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St. Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Igor Stevanovski
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Devin Close
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Michael Hubank
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | | | - Fujun Qiu
- Research and Development, Burning Rock Biotech, Shanghai, China
| | - Robert Sebra
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Lihyun Sun
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Philippe Szankasi
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | - Haowen Tan
- Primbio Genes Biotechnology, East Lake High-tech Development Zone, Wuhan, Hubei, China
| | - Lin-Ya Tang
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Hanane Arib
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Hunter Best
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
- Departments of Pathology and Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Pierre R Bushel
- National Institute of Environmental Health Sciences, Research Triangle Park, Morrisville, NC, USA
| | - Fergal Casey
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Simon Cawley
- Clinical Sequencing Division, Thermo Fisher Scientific, South San Francisco, CA, USA
| | - Chia-Jung Chang
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Jonathan Choi
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | - Jorge Dinis
- Roche Sequencing Solutions, Inc., Pleasanton, CA, USA
| | | | - Agda Karina Eterovic
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Liang Feng
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | | | - Kristina Giorda
- Marketing, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | | | | | - Li-Yuan Hung
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Mirna Jarosz
- NGS Products and Services, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Garima Kushwaha
- Market & Application Development Bioinformatics, Roche Sequencing Solutions Inc., Pleasanton, CA, USA
| | - Dan Li
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Quan-Zhen Li
- Department of Immunology, Genomics and Microarray Core Facility, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Zhiguang Li
- Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Liang-Chun Liu
- Clinical Diagnostic Division, Thermo Fisher Scientific, Fremont, CA, USA
| | - Zhichao Liu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Charles Ma
- Cancer Genetics, Inc., Rutherford, NJ, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dalila B Megherbi
- CMINDS Research Center, Department of Electrical and Computer Engineering, College of Engineering, University of Massachusetts Lowell, Lowell, MA, USA
| | | | | | - Mehdi Pirooznia
- Bioinformatics and Computational Biology Laboratory, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paula Z Proszek
- NIHR Biomedical Research Centre, Royal Marsden Hospital, Sutton, Surrey, UK
| | | | - Paul Rindler
- R&D Genomics MPS, Institute for Clinical and Experimental Pathology ARUP Laboratories, Salt Lake City, UT, USA
| | | | - Andreas Scherer
- Institute for Molecular Medicine Finland (FIMM), Nordic EMBL Partnership for Molecular Medicine, HiLIFE Unit, Biomedicum Helsinki 2U (D302b), University of Helsinki, Helsinki, Finland
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
| | | | - Tieliu Shi
- Center for Bioinformatics and Computational Biology and the Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Melissa Smith
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ping Song
- Institute for Personalized Cancer Therapy, MD Anderson Cancer Center, Houston, TX, USA
| | - Maya Strahl
- Icahn Institute and Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Nikola Tom
- EATRIS ERIC- European Infrastructure for Translational Medicine, Amsterdam, The Netherlands
- Center of Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | | | - Jiashi Wang
- Research and Development, Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Leihong Wu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Wenzhong Xiao
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Chang Xu
- Research and Development, QIAGEN Sciences, Inc., Frederick, MD, USA
| | - Mary Yang
- Department of Information Science, University of Arkansas at Little Rock, Little Rock, AR, USA
| | | | - Sa Zhang
- Clinical Laboratory, Burning Rock Biotech, Guangzhou, China
| | - Yilin Zhang
- Elim Biopharmaceuticals, Inc., Hayward, CA, USA
| | - Leming Shi
- State Key Laboratory of Genetic Engineering, School of Life Sciences and Shanghai Cancer Hospital/Cancer Institute, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Fudan-Gospel Joint Research Center for Precision Medicine, Fudan University, Shanghai, China
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA
| | - Donald J Johann
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Timothy R Mercer
- St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- Genomics and Epigenetics Theme, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Queensland, QLD, Australia.
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, AR, USA.
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31
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Udomruk S, Orrapin S, Pruksakorn D, Chaiyawat P. Size distribution of cell-free DNA in oncology. Crit Rev Oncol Hematol 2021; 166:103455. [PMID: 34464717 DOI: 10.1016/j.critrevonc.2021.103455] [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: 07/06/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022] Open
Abstract
Tumor-specific, circulating cell-free DNA (cfDNA) in liquid biopsy test is a novel promising biomarker in the advancement of cancer management, including early diagnosis, screening, prognosis, identification of actionable targets, and serial tumor monitoring. The specific size pattern of DNA fragments derived from cancer cells is observed to differ from that of cfDNA fragments shed by non-cancer cells. Research into the physiological and biological properties of cfDNA reveals the molecular signature carried by each cfDNA fragments, which can reflect their tissue origins, as well as the mutational profiles with significant genetic alterations. Understanding the fragmentation and size distribution of cfDNA might be a valuable hotspot in liquid biopsy research, with the potential to drive innovation in oncology.
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Affiliation(s)
- Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Santhasiri Orrapin
- Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand; Department of Orthopedics, Faculty of Medicine, Chiang Mai University, 110 Intawaroros, Sriphoom, Muang, Chiang Mai 50200, Thailand.
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; Musculoskeletal Science and Translational Research Center (MSTR), Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand.
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The relevance of liquid biopsy in surgical oncology: The application of perioperative circulating nucleic acid dynamics in improving patient outcomes. Surgeon 2021; 20:e163-e173. [PMID: 34362650 DOI: 10.1016/j.surge.2021.06.006] [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: 01/06/2021] [Revised: 06/13/2021] [Accepted: 06/23/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Liquid biopsy is gaining increasing clinical utility in the management of cancer patients. The main components of a liquid biopsy are circulating nucleic acids, circulating tumour cells and extracellular vesicles such as exosomes. Circulating nucleic acids including cell free DNA (cfDNA) and circulating tumour DNA (ctDNA) in particular have been the focus of recent attention as they have demonstrated excellent potential in cancer screening, provision of prognostic information and in genomic profiling of a tumour without the need for repeated tissue biopsies. The aim of this review was to explore the current evidence in relation to the use of liquid biopsy in the perioperative setting and identify ways in which liquid biopsy may be applied in the future. METHODS This narrative review is based on a comprehensive literature search up to the 1st of June 2020 for papers relevant to the application of liquid biopsy in surgical oncology, focusing particularly on the perioperative period. RESULTS Recent evidence has demonstrated that perioperative liquid biopsy can accurately stratify patients' risk of recurrence compared to conventional biomarkers. Attention to the perioperative dynamics of liquid biopsy components can potentially provide new understanding of the complex relationship between surgery and cancer outcome. In addition, careful evaluation of liquid biopsy components in the perioperative window may provide important diagnostic and therapeutic information for cancer patients. CONCLUSION The rapidly evolving concept of the liquid biopsy has the potential to become the cornerstone for decision making around surveillance and adjuvant therapies the era of personalised medicine.
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Lou J, Yu S, Feng L, Guo X, Wang M, Branco AT, Li T, Lemos B. Environmentally induced ribosomal DNA (rDNA) instability in human cells and populations exposed to hexavalent chromium [Cr (VI)]. ENVIRONMENT INTERNATIONAL 2021; 153:106525. [PMID: 33774497 PMCID: PMC8477438 DOI: 10.1016/j.envint.2021.106525] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 05/12/2023]
Abstract
Hexavalent Chromium [Cr (VI)] is an established toxicant, carcinogen, and a significant source of public health concern. The multicopy ribosomal DNA (rDNA) array is mechanistically linked to aging and cancer, is the most evolutionarily conserved segment of the human genome, and gives origin to nucleolus, a nuclear organelle where ribosomes are assembled. Here we show that exposure to Cr (VI) induces instability in the rDNA, triggering cycles of rapid, specific, and transient amplification and contraction of the array in human cells. The dynamic of environmentally responsive rDNA copy number (CN) amplification and contraction occurs at doses to which millions of individuals are regularly exposed. Finally, analyses of human populations occupationally exposed to Cr (VI) indicate that environmental exposure history and drinking habits but not age shape extensive naturally occurring rDNA copy number variation. Our observations identify a novel pathway of response to hexavalent chromium exposure and raise the prospect that a suite of environmental determinants of rDNA copy number remain to be discovered.
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Affiliation(s)
- Jianlin Lou
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA; School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Shoukai Yu
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Xinnian Guo
- School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Meng Wang
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alan T Branco
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tao Li
- School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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Lakatos G, Köhne CH, Bodoky G. Current therapy of advanced colorectal cancer according to RAS/RAF mutational status. Cancer Metastasis Rev 2021; 39:1143-1157. [PMID: 32648137 DOI: 10.1007/s10555-020-09913-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal cancer is a clinically and molecularly heterogeneous disease. Currently, extended RAS and BRAF mutation testing is obligatory in routine clinical practice before starting any treatment in the metastatic setting. Treatment decision making also includes assessment of the clinical condition of the patient, definition of the treatment goal, and consideration of the primary tumor site. Biological treatment is part of the first-line drug combination unless contraindicated. Mutational status is significantly associated with the outcome of patients and is strongly predictive for anti-EGFR-targeted therapy. The prognosis of RAS mutant CRC is clearly inferior to wild-type cases. RAS remains an elusive target, and specific treatment options are not yet available. Recently, promising results of a direct KRAS G12C inhibitor have been reported; however, further confirmation is needed. The biomarker landscape in mCRC is evolving; new promising markers are awaited with the chance of more precise targeted treatment.
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Affiliation(s)
- Gábor Lakatos
- Department of Oncology, South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary.
| | - Claus-Henning Köhne
- Klinikum Oldenburg, University Clinic of Oncology and Haematology, Oldenburg, Germany
| | - György Bodoky
- Department of Oncology, South-Pest Hospital Centre - National Institute for Infectology and Haematology, Budapest, Hungary
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Yu G, Shen Y, Ye B, Shi Y. Diagnostic accuracy of Mycobacterium tuberculosis cell-free DNA for tuberculosis: A systematic review and meta-analysis. PLoS One 2021; 16:e0253658. [PMID: 34161399 PMCID: PMC8221493 DOI: 10.1371/journal.pone.0253658] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/10/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Diagnosis of tuberculosis (TB) is still difficult. The purpose of our study was to evaluate the diagnostic accuracy of Mycobacterium tuberculosis cell-free DNA (cfDNA) for diagnosing of TB. METHODS We searched relevant databases for studies that used cfDNA to diagnose TB. We evaluated the accuracy of cfDNA compared with the composite reference standard (CRS) and culture. True positive, false positive, false negative, and true negative values for cfDNA were obtained first, then the estimated pooled sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and the area under the summary receiver operating characteristic (SROC) curve (AUC) of cfDNA for diagnosing TB were calculated with 95% confidence intervals (CIs). Heterogeneity was determined using the I2 statistic. When the heterogeneity was obvious, the source of heterogeneity was further discussed. RESULTS We included 14 independent studies comparing cfDNA with the CRS, and 4 studies compared with culture. The pooled sensitivity, specificity, PPV, NPV, DOR, and AUC of the SROC were 68%, 98%,99%, 62%, 83, and 0.97 as compared with the CRS, respectively. The pooled sensitivity, specificity, PPV, NPV, DOR, and AUC of the SROC were 48%, 91%, 92%, 60%, 5, and 0.88 as compared with culture, respectively. The heterogeneity between studies was significant. CONCLUSIONS The accuracy of cfDNA testing for TB diagnosis was good compared with CRS and culture. cfDNA can be used for rapid early diagnosis of TB.
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Affiliation(s)
- Guocan Yu
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yanqin Shen
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bo Ye
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yan Shi
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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Lee IS, Ahn J, Kim K, Okugawa Y, Toiyama Y, Hur H, Goel A. A blood-based transcriptomic signature for noninvasive diagnosis of gastric cancer. Br J Cancer 2021; 125:846-853. [PMID: 34163003 DOI: 10.1038/s41416-021-01461-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/01/2021] [Accepted: 06/02/2021] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Delayed detection of tumours contributes to poor prognosis in patients with gastric cancer (GC). The invasive nature of endoscopy and the absence of an effective serum markers highlight the need to develop novel, noninvasive biomarkers. METHODS We performed biomarker discovery and validation to identify candidate genes in three gene expression data sets. After validating the gene panel in clinical tissues, we translated the gene panel into serum samples by performing training and validation in 89 samples from GC patients and 54 from healthy donors in two independent cohorts. RESULTS We identified a nine-gene panel in the discovery phase, with subsequent validation in tissue specimens. Using a serum training cohort, we developed a 5-gene risk prediction formulae for the diagnosis of GC; bootstrapped analysis exhibited an AUC of 0.896. We validated this 5-gene biomarker panel using an independent serum cohort, yielding an AUC of 0.947. This biomarker panel successfully identified GC, regardless of tumour histology. Notably, biomarker performance for detection of stage 1 and 2 GC displayed an AUC of 0.928 and 0.980 in both serum cohorts. CONCLUSIONS We identified a novel 5-gene biomarker panel for noninvasive diagnosis of GC, which might serve as a potential diagnostic tool for early detection.
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Affiliation(s)
- In-Seob Lee
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA.,Department of Surgery, Asan Medical Centre, University of Ulsan College of Medicine, Seoul, Korea
| | - Jiyoung Ahn
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, Korea
| | - Yoshinaga Okugawa
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Yuji Toiyama
- Department of Gastrointestinal and Pediatric Surgery, Division of Reparative Medicine, Institute of Life Sciences, Mie University Graduate School of Medicine, Mie, Japan
| | - Hoon Hur
- Department of Surgery, Ajou University of School of Medicine, Suwon, Korea.,Cancer Biology Graduate Program, Ajou University Graduate School of Medicine, Suwon, Korea
| | - Ajay Goel
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA, USA. .,City of Hope Comprehensive Cancer Centre, Duarte, CA, USA.
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Corbetta M, Chiereghin C, De Simone I, Soldà G, Zuradelli M, Giunta M, Lughezzani G, Buffi NM, Hurle R, Saita A, Casale P, Asselta R, Lazzeri M, Guazzoni G, Duga S. Post-Biopsy Cell-Free DNA From Blood: An Open Window on Primary Prostate Cancer Genetics and Biology. Front Oncol 2021; 11:654140. [PMID: 34109115 PMCID: PMC8181420 DOI: 10.3389/fonc.2021.654140] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 04/23/2021] [Indexed: 01/09/2023] Open
Abstract
Circulating cell-free DNA (ccfDNA), released from normal and cancerous cells, is a promising biomarker for cancer detection as in neoplastic patients it is enriched in tumor-derived DNA (ctDNA). ctDNA contains cancer-specific mutations and epigenetic modifications, which can have diagnostic/prognostic value. However, in primary tumors, and in particular in localized prostate cancer (PCa), the fraction of ctDNA is very low and conventional strategies to study ccfDNA are unsuccessful. Here we demonstrate that prostate biopsy, by causing multiple injuries to the organ, leads to a significant increase in plasma concentration of ccfDNA (P<0.0024) in primary PCa patients. By calculating the minor allele fraction at patient-specific somatic mutations pre- and post-biopsy, we show that ctDNA is significantly enriched (from 3.9 to 164 fold) after biopsy, representing a transient “molecular window” to access and analyze ctDNA. Moreover, we show that newly released ccfDNA contains a larger fraction of di-, tri- and multi-nucleosome associated DNA fragments. This feature could be exploited to further enrich prostate-derived ccfDNA and to analyze epigenetic markers. Our data represent a proof-of-concept that liquid tumor profiling from peripheral blood performed just after the biopsy procedure can open a “valuable molecular metastatic window” giving access to the tumor genetic asset, thus providing an opportunity for early cancer detection and individual genomic profiling in the view of PCa precision medicine.
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Affiliation(s)
| | | | - Ilaria De Simone
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Milan, Italy
| | - Monica Zuradelli
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Humanitas Cancer Center, Milan, Italy
| | - Michele Giunta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Giovanni Lughezzani
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Milan, Italy
| | - Nicolò Maria Buffi
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Milan, Italy
| | | | | | | | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Milan, Italy
| | - Massimo Lazzeri
- Department of Biomedical Sciences, Humanitas University, Milan, Italy
| | - Giorgio Guazzoni
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Milan, Italy
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Milan, Italy.,IRCCS Humanitas Research Hospital, Milan, Italy
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Weber ZT, Collier KA, Tallman D, Forman J, Shukla S, Asad S, Rhoades J, Freeman S, Parsons HA, Williams NO, Barroso-Sousa R, Stover EH, Mahdi H, Cibulskis C, Lennon NJ, Ha G, Adalsteinsson VA, Tolaney SM, Stover DG. Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer. Genome Med 2021; 13:89. [PMID: 34016182 PMCID: PMC8136103 DOI: 10.1186/s13073-021-00895-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 04/23/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) offers minimally invasive means to repeatedly interrogate tumor genomes, providing opportunities to monitor clonal dynamics induced by metastasis and therapeutic selective pressures. In metastatic cancers, ctDNA profiling allows for simultaneous analysis of both local and distant sites of recurrence. Despite the promise of ctDNA sampling, its utility in real-time genetic monitoring remains largely unexplored. METHODS In this exploratory analysis, we characterize high-frequency ctDNA sample series collected over narrow time frames from seven patients with metastatic triple-negative breast cancer, each undergoing treatment with Cabozantinib, a multi-tyrosine kinase inhibitor (NCT01738438, https://clinicaltrials.gov/ct2/show/NCT01738438 ). Applying orthogonal whole exome sequencing, ultra-low pass whole genome sequencing, and 396-gene targeted panel sequencing, we analyzed 42 plasma-derived ctDNA libraries, representing 4-8 samples per patient with 6-42 days between samples. Integrating tumor fraction, copy number, and somatic variant information, we model tumor clonal dynamics, predict neoantigens, and evaluate consistency of genomic information from orthogonal assays. RESULTS We measured considerable variation in ctDNA tumor faction in each patient, often conflicting with RECIST imaging response metrics. In orthogonal sequencing, we found high concordance between targeted panel and whole exome sequencing in both variant detection and variant allele frequency estimation (specificity = 95.5%, VAF correlation, r = 0.949), Copy number remained generally stable, despite resolution limitations posed by low tumor fraction. Through modeling, we inferred and tracked distinct clonal populations specific to each patient and built phylogenetic trees revealing alterations in hallmark breast cancer drivers, including TP53, PIK3CA, CDK4, and PTEN. Our modeling revealed varied responses to therapy, with some individuals displaying stable clonal profiles, while others showed signs of substantial expansion or reduction in prevalence, with characteristic alterations of varied literature annotation in relation to the study drug. Finally, we predicted and tracked neoantigen-producing alterations across time, exposing translationally relevant detection patterns. CONCLUSIONS Despite technical challenges arising from low tumor content, metastatic ctDNA monitoring can aid our understanding of response and progression, while minimizing patient risk and discomfort. In this study, we demonstrate the potential for high-frequency monitoring of evolving genomic features, providing an important step toward scalable, translational genomics for clinical decision making.
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Affiliation(s)
- Zachary T Weber
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Katharine A Collier
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA
| | - David Tallman
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Juliet Forman
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sachet Shukla
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
- Translational Immunogenomics Lab, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Sarah Asad
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Justin Rhoades
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Samuel Freeman
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Heather A Parsons
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Nicole O Williams
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA
| | | | - Elizabeth H Stover
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Haider Mahdi
- Department of Obstetrics and Gynecology, Cleveland Clinic, Cleveland, OH, 44195, USA
- Department of Surgery, Case Comprehensive Cancer Center, Cleveland, OH, 44106, USA
| | - Carrie Cibulskis
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Niall J Lennon
- Broad Institute of Harvard & MIT, 415 Main St., Cambridge, MA, 02412, USA
| | - Gavin Ha
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | | | - Sara M Tolaney
- Department of Medical Oncology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA, 02215, USA
| | - Daniel G Stover
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 W. 12th Avenue, Columbus, OH, 43210, USA.
- Division of Medical Oncology, Department of Medicine, College of Medicine, The Ohio State University, 320 W. 10th Avenue, Columbus, OH, 43210, USA.
- Biomedical Research Tower, Room 984, Ohio State University Comprehensive Cancer Center, Stefanie Spielman Comprehensive Breast Center, Columbus, OH, 43210, USA.
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Stance of MRD in Non-Hodgkin's Lymphoma and its upsurge in the novel era of cell-free DNA. Clin Transl Oncol 2021; 23:2206-2219. [PMID: 33991328 DOI: 10.1007/s12094-021-02635-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 05/02/2021] [Indexed: 10/21/2022]
Abstract
Cancer genomics has evolved over the years from understanding the pathogenesis of cancer to screening the future possibilities of cancer occurrence. Understanding the genetic profile of tumors holds a prognostic as well as a predictive value in this era of therapeutic surveillance, molecular remission, and precision medicine. Identifying molecular markers in tumors is the current standard of approach, and requires an efficient combination of an accessible sample type and a profoundly sensitive technique. Liquid biopsy or cell-free DNA has evolved as a novel sample type with promising results in recent years. Although cell-free DNA has significant role in various cancer types, this review focuses on its application in Non-Hodgkin's Lymphoma. Beginning with the current concept and clinical relevance of minimal residual disease in Non-Hodgkin's lymphoma, we discuss the literature on circulating DNA and its evolving application in the realm of cutting-edge technology.
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Nakatsuka T, Nakagawa H, Hayata Y, Wake T, Yamada T, Nishibatake Kinoshita M, Nakagomi R, Sato M, Minami T, Uchino K, Enooku K, Kudo Y, Tanaka Y, Kishikawa T, Otsuka M, Tateishi R, Koike K. Post-treatment cell-free DNA as a predictive biomarker in molecular-targeted therapy of hepatocellular carcinoma. J Gastroenterol 2021; 56:456-469. [PMID: 33712873 DOI: 10.1007/s00535-021-01773-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 02/27/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Liquid biopsies, particularly those involving circulating tumor DNA (ctDNA), are rapidly emerging as a non-invasive alternative to tumor biopsies. However, clinical applications of ctDNA analysis in hepatocellular carcinoma (HCC) have not been fully elucidated. METHODS We measured the amount of plasma-derived cell-free DNA (cfDNA) in HCC patients before (n = 100) and a few days after treatment (n = 87), including radiofrequency ablation, transarterial chemoembolization, and molecular-targeted agents (MTAs), and prospectively analyzed their associations with clinical parameters and prognosis. TERT promoter mutations in cfDNA were analyzed using droplet digital PCR. Furthermore, we performed a comprehensive mutational analysis of post-treatment cfDNA via targeted ultra-deep sequencing (22,000× coverage) in a panel of 275 cancer-related genes in selected patients. RESULTS Plasma cfDNA levels increased significantly according to HCC clinical stage, and a high cfDNA level was independently associated with a poor prognosis. TERT promoter mutations were detected in 45% of all cases but were not associated with any clinical characteristics. cfDNA levels increased significantly a few days after treatment, and a greater increase in post-treatment cfDNA levels was associated with a greater therapeutic response to MTAs. The detection rate of TERT mutations increased to 57% using post-treatment cfDNA, suggesting that the ctDNA was enriched. Targeted ultra-deep sequencing using post-treatment cfDNA after administering lenvatinib successfully detected various gene mutations and obtained promising results in lenvatinib-responsive cases. CONCLUSIONS Post-treatment cfDNA analysis may facilitate the construction of biomarkers for predicting MTA treatment effects.
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Affiliation(s)
- Takuma Nakatsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hayato Nakagawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Yuki Hayata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Taijiro Wake
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tomoharu Yamada
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Mizuki Nishibatake Kinoshita
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Ryo Nakagomi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Masaya Sato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Department of Clinical Laboratory Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tatsuya Minami
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Koji Uchino
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kenichiro Enooku
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yotaro Kudo
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Yasuo Tanaka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Takahiro Kishikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Ryosuke Tateishi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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Can Circulating Cell-Free DNA or Circulating Tumor DNA Be a Promising Marker in Ovarian Cancer? JOURNAL OF ONCOLOGY 2021; 2021:6627241. [PMID: 33936202 PMCID: PMC8062166 DOI: 10.1155/2021/6627241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 03/24/2021] [Accepted: 03/31/2021] [Indexed: 12/29/2022]
Abstract
In recent years, the studies on ovarian cancer have made great progress, but the morbidity and mortality of patients with ovarian cancer are still very high. Due to the lack of effective early screening and detecting tools, 70% of ovarian cancer patients are diagnosed at an advanced stage. The overall survival rate of ovarian cancer patients treated with surgical combined with chemotherapy has not been significantly improved, and they usually relapse or resist chemotherapy. Therefore, a novel tumor marker is beneficial for the diagnosis and prognosis of patients with ovarian cancer. As the index of "liquid biopsy," circulating cell-free DNA/circulating tumor DNA (cfDNA/ctDNA) has attracted a lot of attention. It has more remarkable advantages than traditional methods and gives a wide range of clinical applications in kinds of solid tumors. This review attempts to illuminate the important value of cfDNA/ctDNA in ovarian cancer, including diagnosis, monitoring, and prognosis. Meanwhile, we will present future directions and challenges for detection of cfDNA/ctDNA.
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Extracellular DNA in blood products and its potential effects on transfusion. Biosci Rep 2021; 40:222322. [PMID: 32150264 PMCID: PMC7098128 DOI: 10.1042/bsr20192770] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 01/18/2020] [Accepted: 03/03/2020] [Indexed: 02/05/2023] Open
Abstract
Blood transfusions are sometimes necessary after a high loss of blood due to injury or surgery. Some people need regular transfusions due to medical conditions such as haemophilia or cancer. Studies have suggested that extracellular DNA including mitochondrial DNA present in the extracellular milieu of transfused blood products has biological actions that are capable of activating the innate immune systems and potentially contribute to some adverse reactions in transfusion. From the present work, it becomes increasingly clear that extracellular DNA encompassed mitochondrial DNA is far from being biologically inert in blood products. It has been demonstrated to be present in eligible blood products and thus can be transfused to blood recipients. Although the presence of extracellular DNA in human plasma was initially detected in 1948, some aspects have not been fully elucidated. In this review, we summarize the potential origins, clearance mechanisms, relevant structures, and potential role of extracellular DNA in the innate immune responses and its relationship with individual adverse reactions in transfusion.
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Tran L, Xiao JF, Agarwal N, Duex JE, Theodorescu D. Advances in bladder cancer biology and therapy. Nat Rev Cancer 2021; 21:104-121. [PMID: 33268841 PMCID: PMC10112195 DOI: 10.1038/s41568-020-00313-1] [Citation(s) in RCA: 301] [Impact Index Per Article: 100.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/26/2022]
Abstract
The field of research in bladder cancer has seen significant advances in recent years. Next-generation sequencing has identified the genes most mutated in bladder cancer. This wealth of information allowed the definition of driver mutations, and identification of actionable therapeutic targets, as well as a clearer picture of patient prognosis and therapeutic direction. In a similar vein, our understanding of the cellular aspects of bladder cancer has grown. The identification of the cellular geography and the populations of different cell types and quantifications of normal and abnormal cell types in tumours provide a better prediction of therapeutic response. Non-invasive methods of diagnosis, including liquid biopsies, have seen major advances as well. These methods will likely find considerable utility in assessing minimal residual disease following treatment and for early-stage diagnosis. A significant therapeutic impact on patients with bladder cancer is found in the use of immune checkpoint inhibitor therapeutics. These therapeutics have been shown to cure some patients with bladder cancer and significantly decrease adverse events. These developments provide patients with better monitoring opportunities, unique therapeutic options and greater hope for prolonged survival.
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Affiliation(s)
- Linda Tran
- Department of Surgery (Urology), Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - Jin-Fen Xiao
- Department of Surgery (Urology), Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - Neeraj Agarwal
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
- Department of Medicine (Hematology/Oncology), Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Jason E Duex
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA
| | - Dan Theodorescu
- Department of Surgery (Urology), Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cedars-Sinai Samuel Oschin Comprehensive Cancer Institute, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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Zhang Y, Yao Y, Xu Y, Li L, Gong Y, Zhang K, Zhang M, Guan Y, Chang L, Xia X, Li L, Jia S, Zeng Q. Pan-cancer circulating tumor DNA detection in over 10,000 Chinese patients. Nat Commun 2021; 12:11. [PMID: 33397889 PMCID: PMC7782482 DOI: 10.1038/s41467-020-20162-8] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 11/10/2020] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor DNA (ctDNA) provides a noninvasive approach to elucidate a patient's genomic landscape and actionable information. Here, we design a ctDNA-based study of over 10,000 pan-cancer Chinese patients. Using parallel sequencing between plasma and white blood cells, 14% of plasma cell-free DNA samples contain clonal hematopoiesis (CH) variants, for which detectability increases with age. After eliminating CH variants, ctDNA is detected in 73.5% of plasma samples, with small cell lung cancer (91.1%) and prostate cancer (87.9%) showing the highest detectability. The landscape of putative driver genes revealed by ctDNA profiling is similar to that in a tissue-based database (R2 = 0.87, p < 0.001) but also shows some discrepancies, such as higher EGFR (44.8% versus 25.2%) and lower KRAS (6.8% versus 27.2%) frequencies in non-small cell lung cancer, and a higher TP53 frequency in hepatocellular carcinoma (53.1% versus 28.6%). Up to 41.2% of plasma samples harbor drug-sensitive alterations. These findings may be helpful for identifying therapeutic targets and combined treatment strategies.
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Affiliation(s)
- Yongliang Zhang
- Health Management Institute, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100089, P. R. China
| | - Yu Yao
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shanxi, P. R. China
| | - Yaping Xu
- Geneplus-Beijing Institute, Beijing, 102206, P. R. China
| | - Lifeng Li
- Geneplus-Beijing Institute, Beijing, 102206, P. R. China
| | - Yan Gong
- Health Management Institute, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100089, P. R. China
| | - Kai Zhang
- Department of Cancer Prevention, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100010, P. R. China
| | - Meng Zhang
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, P. R. China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing, 102206, P. R. China
| | - Lianpeng Chang
- Geneplus-Beijing Institute, Beijing, 102206, P. R. China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing, 102206, P. R. China
| | - Lin Li
- Department of Medical Oncology, Beijing Hospital, National Center of Gerontology, Beijing, 100010, P. R. China.,Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, 100010, P. R. China
| | - Shuqin Jia
- Department of Molecular Diagnostics, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute, Beijing, 100142, P. R. China.
| | - Qiang Zeng
- Health Management Institute, The Second Medical Center & National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing, 100089, P. R. China.
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Koçana CÇ, Toprak SF, Sözer S. Extracellular genetic materials and their application in clinical practice. Cancer Genet 2020; 252-253:48-63. [PMID: 33387935 DOI: 10.1016/j.cancergen.2020.12.006] [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: 06/11/2020] [Revised: 11/12/2020] [Accepted: 12/20/2020] [Indexed: 11/20/2022]
Abstract
This study reviews the possible origins, functional roles, and diagnostic applications of 'extracellular genetic material' (EGM), a novel term introduced to cover DNA, RNA, and DNA/RNA-related molecules released from all types of cells into the extracellular region. The literature on EGMs shows them to play a dual role in diverse, fine-tuning mechanisms involved in both homeostasis and pathological events, including cancerogenesis and genometastasis. Recent developments in the next-generation technology have provided successful applications of low quantities of genomic materials into the diagnostic field, yielding high sensitivity and specificity in test results. Also, the successful application of EGMs into diagnostics has afforded promising outcomes for researchers and clinicians. This study of EGM provides a deeper understanding of the subject as an area of interest, especially cell-free DNA, aiming toward the eventual development of new therapeutic applications and diagnostic strategies.
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Affiliation(s)
- Cemal Çağıl Koçana
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selin Fulya Toprak
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Selçuk Sözer
- Department of Genetic, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey.
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Alves G, Chantre M, Delmonico L. The contribution of the 20th century discoveries on the circulating DNA as biomarkers for cancer screening. AN ACAD BRAS CIENC 2020; 92:e20200919. [PMID: 33206793 DOI: 10.1590/0001-3765202020200919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/13/2020] [Indexed: 01/22/2023] Open
Abstract
Circulating DNA can be released in the biological fluids by a physiological process and by different pathological conditions. The first reports detecting circulating DNA in human plasma date from the late 40s. Even when specific pathological conditions were analyzed, the clinical importance of circulating DNA remained unclear. After PCR introduction, genetic and epigenetic alterations in circulating DNA gained more prominence for understanding the mechanisms of cancer development and progression. Nowadays, the circulating DNA assays are highlighted for their clinical relevance for cancer screening in liquid biopsy. In this review, we described the landscape of studies on circulating DNA isolated from human plasma or serum and the molecular tools used to obtain these findings throughout the 20th century and the current application in cancer.
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Affiliation(s)
- Gilda Alves
- Universidade do Estado do Rio de Janeiro/UERJ, Faculdade de Ciências Médicas, Departamento de Patologia e Laboratórios, Laboratório de Marcadores Circulantes, Avenida Prof. Manuel de Abreu, 444, 4° andar, Vila Isabel, 20550-170 Rio de Janeiro, RJ, Brazil
| | - Mariana Chantre
- Universidade do Estado do Rio de Janeiro/UERJ, Faculdade de Ciências Médicas, Departamento de Patologia e Laboratórios, Laboratório de Marcadores Circulantes, Avenida Prof. Manuel de Abreu, 444, 4° andar, Vila Isabel, 20550-170 Rio de Janeiro, RJ, Brazil
| | - Lucas Delmonico
- Universidade Federal do Rio de Janeiro/UFRJ, Instituto de Biofísica Carlos Chagas Filho/IBCCF, Laboratório de Radiações em Biologia, Avenida Carlos Chagas Filho, 373, Bloco G, Sala G0-036, Cidade Universitária, 21941-902 Rio de Janeiro, RJ, Brazil
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Wang GA, Xie X, Mansour H, Chen F, Matamoros G, Sanchez AL, Fan C, Li F. Expanding detection windows for discriminating single nucleotide variants using rationally designed DNA equalizer probes. Nat Commun 2020; 11:5473. [PMID: 33122648 PMCID: PMC7596233 DOI: 10.1038/s41467-020-19269-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications. Herein, we introduce a DNA equalizer gate (DEG) approach, a class of simulation-guided nucleic acid hybridization probes that drastically expand detection windows for discriminating single nucleotide variants in double-stranded DNA (dsDNA) via the user-definable transformation of the quantitative relationship between the detection signal and target concentrations. A thermodynamic-driven theoretical model was also developed, which quantitatively simulates and predicts the performance of DEG. The effectiveness of DEG for expanding detection windows and improving sequence selectivity was demonstrated both in silico and experimentally. As DEG acts directly on dsDNA, it is readily adaptable to nucleic acid amplification techniques, such as polymerase chain reaction (PCR). The practical usefulness of DEG was demonstrated through the simultaneous detection of infections and the screening of drug-resistance in clinical parasitic worm samples collected from rural areas of Honduras.
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Affiliation(s)
- Guan A Wang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Xiaoyu Xie
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Hayam Mansour
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Department of Cell Biology, National Research Centre, Cairo, 12622, Egypt
| | - Fangfang Chen
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Gabriela Matamoros
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Microbiology Research Institute, National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - Ana L Sanchez
- Department of Health Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
- Microbiology Research Institute, National Autonomous University of Honduras (UNAH), Tegucigalpa, Honduras
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, 201240, Shanghai, China
| | - Feng Li
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry, Sichuan University, 610064, Chengdu, Sichuan, China.
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, ON, L2S 3A1, Canada.
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48
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Putative Origins of Cell-Free DNA in Humans: A Review of Active and Passive Nucleic Acid Release Mechanisms. Int J Mol Sci 2020; 21:ijms21218062. [PMID: 33137955 PMCID: PMC7662960 DOI: 10.3390/ijms21218062] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 10/27/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Through various pathways of cell death, degradation, and regulated extrusion, partial or complete genomes of various origins (e.g., host cells, fetal cells, and infiltrating viruses and microbes) are continuously shed into human body fluids in the form of segmented cell-free DNA (cfDNA) molecules. While the genetic complexity of total cfDNA is vast, the development of progressively efficient extraction, high-throughput sequencing, characterization via bioinformatics procedures, and detection have resulted in increasingly accurate partitioning and profiling of cfDNA subtypes. Not surprisingly, cfDNA analysis is emerging as a powerful clinical tool in many branches of medicine. In addition, the low invasiveness of longitudinal cfDNA sampling provides unprecedented access to study temporal genomic changes in a variety of contexts. However, the genetic diversity of cfDNA is also a great source of ambiguity and poses significant experimental and analytical challenges. For example, the cfDNA population in the bloodstream is heterogeneous and also fluctuates dynamically, differs between individuals, and exhibits numerous overlapping features despite often originating from different sources and processes. Therefore, a deeper understanding of the determining variables that impact the properties of cfDNA is crucial, however, thus far, is largely lacking. In this work we review recent and historical research on active vs. passive release mechanisms and estimate the significance and extent of their contribution to the composition of cfDNA.
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Pellini B, Szymanski J, Chin RI, Jones PA, Chaudhuri AA. Liquid Biopsies Using Circulating Tumor DNA in Non-Small Cell Lung Cancer. Thorac Surg Clin 2020; 30:165-177. [PMID: 32327175 DOI: 10.1016/j.thorsurg.2020.01.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Liquid biopsies for the diagnosis and treatment of lung cancer have developed rapidly, driven primarily by technical advances in sensitivity to detect circulating tumor DNA (ctDNA). Still, technical limitations such as the challenge of detecting low-level ctDNA variants and distinguishing tumor-related variants from clonal hematopoiesis remain. With further technical advancements, new applications for ctDNA analysis are emerging including detection of post-treatment molecular residual disease (MRD), clinical trial selection, and early cancer detection. This chapter reviews the current state of ctDNA testing in NSCLC, the underlying technological advances enabling ctDNA detection, and the potential to expand ctDNA analysis to new applications.
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Affiliation(s)
- Bruna Pellini
- Department of Medicine, Division of Oncology, Washington University School of Medicine, Division of Oncology Campus Box 8056, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Jeffrey Szymanski
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Re-I Chin
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Paul A Jones
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA
| | - Aadel A Chaudhuri
- Department of Radiation Oncology, Division of Cancer Biology, Washington University School of Medicine, Radiation Oncology Campus Box 8224, 660 South Euclid Avenue, St Louis, MO 63110, USA.
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50
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Forman A, Sotelo J. Tumor-Based Genetic Testing and Familial Cancer Risk. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036590. [PMID: 31570381 DOI: 10.1101/cshperspect.a036590] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
As genetic testing on somatic tumor tissue becomes a more routine part of personalized cancer treatment, a growing opportunity arises to identify hereditary germline variants within those results. These germline results can affect future cancer screening for both patients and their family members. Finding this germline information can be complicated as a result of differences between somatic and germline testing processes, nomenclature, and outcome goals (e.g., treatment impact). The goal of this review is to highlight differences between somatic and germline testing and outline a potential guide to allow for appropriate clinical interpretation of somatic testing results in order to better facilitate genetic counseling referrals and confirmatory germline testing.
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Affiliation(s)
- Andrea Forman
- Department of Clinical Genetics, Risk Assessment Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Jilliane Sotelo
- Center for Cancer Genetics and Prevention, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA
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