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El-Ahmad P, Mendes-Silva AP, Diniz BS. Liquid Biopsy in Neuropsychiatric Disorders: A Step Closer to Precision Medicine. Mol Neurobiol 2024:10.1007/s12035-024-04492-y. [PMID: 39298102 DOI: 10.1007/s12035-024-04492-y] [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: 02/08/2024] [Accepted: 09/11/2024] [Indexed: 09/21/2024]
Abstract
Psychiatric disorders are among the leading causes of disease burden worldwide. Despite their significant impact, their diagnosis remains challenging due to symptom heterogeneity, psychiatric comorbidity, and the lack of objective diagnostic tests and well-defined biomarkers. Leveraging genomic, epigenomic, and fragmentomic technologies, circulating cell-free DNA (ccfDNA)-based liquid biopsies have emerged as a potential non-invasive diagnosis and disease-monitoring tool. ccfDNA is a DNA species released into circulation from all types of cells through passive and active mechanisms and can serve as a biomarker for various diseases, namely, cancer. Despite their potential, the application of ccfDNA in neuropsychiatry remains underdeveloped. In this review, we provide an overview of liquid biopsies and their components, with a particular focus on ccfDNA. With a summary of pre-analytical practices and current ccfDNA technologies, we highlight the current state of research regarding the use of ccfDNA as a biomarker for neuropsychiatric disorders. Finally, we discuss future steps to unlock ccfDNA's potential in clinical practice.
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Affiliation(s)
- Perla El-Ahmad
- UConn Center on Aging, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA.
| | - Ana Paula Mendes-Silva
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada
- Department of Psychiatry, University of Saskatchewan, Saskatoon, Canada
| | - Breno S Diniz
- UConn Center on Aging, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA.
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2
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Hou Y, Meng X, Zhou X. Systematically Evaluating Cell-Free DNA Fragmentation Patterns for Cancer Diagnosis and Enhanced Cancer Detection via Integrating Multiple Fragmentation Patterns. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2308243. [PMID: 38881520 PMCID: PMC11321639 DOI: 10.1002/advs.202308243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 04/12/2024] [Indexed: 06/18/2024]
Abstract
Cell-free DNA (cfDNA) fragmentation patterns have immense potential for early cancer detection. However, the definition of fragmentation varies, ranging from the entire genome to specific genomic regions. These patterns have not been systematically compared, impeding broader research and practical implementation. Here, 1382 plasma cfDNA sequencing samples from 8 cancer types are collected. Considering that cfDNA within open chromatin regions is more susceptible to fragmentation, 10 fragmentation patterns within open chromatin regions as features and employed machine learning techniques to evaluate their performance are examined. All fragmentation patterns demonstrated discernible classification capabilities, with the end motif showing the highest diagnostic value for cross-validation. Combining cross and independent validation results revealed that fragmentation patterns that incorporated both fragment length and coverage information exhibited robust predictive capacities. Despite their diagnostic potential, the predictive power of these fragmentation patterns is unstable. To address this limitation, an ensemble classifier via integrating all fragmentation patterns is developed, which demonstrated notable improvements in cancer detection and tissue-of-origin determination. Further functional bioinformatics investigations on significant feature intervals in the model revealed its impressive ability to identify critical regulatory regions involved in cancer pathogenesis.
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Affiliation(s)
- Yuying Hou
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhan430070China
| | - Xiang‐Yu Meng
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhan430070China
- Health Science CenterHubei Minzu UniversityEnshi445000China
- Hubei Provincial Clinical Medical Research Center for NephropathyHubei Minzu UniversityEnshi445000China
| | - Xionghui Zhou
- Hubei Key Laboratory of Agricultural BioinformaticsCollege of InformaticsHuazhong Agricultural UniversityWuhan430070China
- Key Laboratory of Smart Farming for Agricultural AnimalsMinistry of Agriculture and Rural AffairsWuhan430070China
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3
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Lindskrog SV, Dyrskjøt L. Towards circulating tumor DNA-guided treatment of muscle-invasive bladder cancer. Transl Androl Urol 2024; 13:1056-1060. [PMID: 38983478 PMCID: PMC11228676 DOI: 10.21037/tau-24-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/10/2024] [Indexed: 07/11/2024] Open
Affiliation(s)
- Sia Viborg Lindskrog
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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4
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Kurabayashi A, Fukuhara H, Furihata K, Iwashita W, Furihata M, Inoue K. Photodynamic Diagnosis and Therapy in Non-Muscle-Invasive Bladder Cancer. Cancers (Basel) 2024; 16:2299. [PMID: 39001362 PMCID: PMC11240600 DOI: 10.3390/cancers16132299] [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: 04/19/2024] [Revised: 06/17/2024] [Accepted: 06/19/2024] [Indexed: 07/16/2024] Open
Abstract
Bladder cancer (BC) possesses distinct molecular profiles that influence progression depending on its biological nature and delivered treatment intensity. Muscle-invasive BC (MIBC) and non-MIBC (NMIBC) demonstrate great intrinsic heterogeneity regarding different prognoses, survival, progression, and treatment outcomes. Transurethral resection of bladder tumor (TURBT) is the standard of care in treating NMIBC and serves both diagnostic and therapeutic purposes despite the prevalent recurrence and progression among many patients. In particular, flat urothelial carcinoma in situ and urothelial carcinoma with lamina propria invasion are the major precursors of MIBC. A new-generation photosensitizer, 5-Aminolevulinic acid (5-ALA), demonstrates high tumor specificity by illuminating the tumor lesion with a specific wavelength of light to produce fluorescence and has been studied for photodynamic diagnosis to detect precise tumor areas by TURBT. Additionally, it has been applied for treatment by producing its cytotoxic reactive oxygen species, as well as screening for urological carcinomas by excreting porphyrin in the blood and urine. Moreover, 5-ALA may contribute to screening before and after TURBT in NMIBC. Here, we summarize the updated evidence and ongoing research on photodynamic technology for NMIBC, providing insight into the potential for improving patient outcomes.
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Affiliation(s)
- Atsushi Kurabayashi
- Department of Pathology, Kochi Medical School, Nankoku 783-8505, Kochi, Japan
| | - Hideo Fukuhara
- Department of Urology, Kochi Medical School, Nankoku 783-8505, Kochi, Japan
| | - Kaoru Furihata
- Department of Pathology, Kochi Medical School, Nankoku 783-8505, Kochi, Japan
| | - Waka Iwashita
- Department of Pathology, Kochi Medical School, Nankoku 783-8505, Kochi, Japan
| | - Mutsuo Furihata
- Department of Pathology, Kochi Medical School, Nankoku 783-8505, Kochi, Japan
| | - Keiji Inoue
- Department of Urology, Kochi Medical School, Nankoku 783-8505, Kochi, Japan
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5
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Jiang S, Zhao D, Wang C, Liu X, Yang Q, Bao X, Dong T, Li G, Gu Y, Ye Y, Sun B, Xu S, Zhou X, Fan L, Tang L. Clinical evaluation of droplet digital PCR in the early identification of suspected sepsis patients in the emergency department: a prospective observational study. Front Cell Infect Microbiol 2024; 14:1358801. [PMID: 38895732 PMCID: PMC11183271 DOI: 10.3389/fcimb.2024.1358801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/07/2024] [Indexed: 06/21/2024] Open
Abstract
Background Rapid and accurate diagnosis of the causative agents is essential for clinical management of bloodstream infections (BSIs) that might induce sepsis/septic shock. A considerable number of suspected sepsis patients initially enter the health-care system through an emergency department (ED), hence it is vital to establish an early strategy to recognize sepsis and initiate prompt care in ED. This study aimed to evaluate the diagnostic performance and clinical value of droplet digital PCR (ddPCR) assay in suspected sepsis patients in the ED. Methods This was a prospective single-centered observational study including patients admitted to the ED from 25 October 2022 to 3 June 2023 with suspected BSIs screened by Modified Shapiro Score (MSS) score. The comparison between ddPCR and blood culture (BC) was performed to evaluate the diagnostic performance of ddPCR for BSIs. Meanwhile, correlative analysis between ddPCR and the inflammatory and prognostic-related biomarkers were conducted to explore the relevance. Further, the health economic evaluation of the ddPCR was analyzed. Results 258 samples from 228 patients, with BC and ddPCR performed simultaneously, were included in this study. We found that ddPCR results were positive in 48.13% (103 of 214) of episodes, with identification of 132 pathogens. In contrast, BC only detected 18 positives, 88.89% of which were identified by ddPCR. When considering culture-proven BSIs, ddPCR shows an overall sensitivity of 88.89% and specificity of 55.61%, the optimal diagnostic power for quantifying BSI through ddPCR is achieved with a copy cutoff of 155.5. We further found that ddPCR exhibited a high accuracy especially in liver abscess patients. Among all the identified virus by ddPCR, EBV has a substantially higher positive rate with a link to immunosuppression. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity as well as prognosis. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs. Conclusions The multiplexed ddPCR delivers precise and quantitative load data on the causal pathogen, offers the ability to monitor the patient's condition and may serve as early warning of sepsis in time-urgent clinical situations as ED. Importance Early detection and effective administration of antibiotics are essential to improve clinical outcomes for those with life-threatening infection in the emergency department. ddPCR, an emerging tool for rapid and sensitive pathogen identification used as a precise bedside test, has developed to address the current challenges of BSI diagnosis and precise treatment. It characterizes sensitivity, specificity, reproducibility, and absolute quantifications without a standard curve. ddPCR can detect causative pathogens and related resistance genes in patients with suspected BSIs within a span of three hours. In addition, it can identify polymicrobial BSIs and dynamically monitor changes in pathogenic microorganisms in the blood and can be used to evaluate antibiotic efficacy and survival prognosis. Moreover, the copies of pathogens in ddPCR were positively correlated with various markers of inflammation, coagulation, immunity. With high sensitivity and specificity, ddPCR facilitates precision antimicrobial stewardship and reduces health care costs.
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Affiliation(s)
- Sen Jiang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Dongyang Zhao
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Chunxue Wang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiandong Liu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Qian Yang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaowei Bao
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Tiancao Dong
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Gen Li
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yi Gu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Yangqin Ye
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Bingke Sun
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Shumin Xu
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
| | - Xiaohui Zhou
- School of Medicine, Tongji University, Shanghai, China
- Research Center for Translational Medicine, Shanghai Heart Failure Research Center, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Lieying Fan
- School of Medicine, Tongji University, Shanghai, China
- Department of Clinical Laboratory, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lunxian Tang
- Department of Internal Emergency Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- School of Medicine, Tongji University, Shanghai, China
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Cardelli M, Marchegiani F, Stripoli P, Piacenza F, Recchioni R, Di Rosa M, Giacconi R, Malavolta M, Galeazzi R, Arosio B, Cafarelli F, Spannella F, Cherubini A, Lattanzio F, Olivieri F. Plasma cfDNA abundance as a prognostic biomarker for higher risk of death in geriatric cardiovascular patients. Mech Ageing Dev 2024; 219:111934. [PMID: 38604436 DOI: 10.1016/j.mad.2024.111934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/07/2024] [Accepted: 04/08/2024] [Indexed: 04/13/2024]
Abstract
The management of geriatric cardiovascular disease (CVD) patients with multimorbidity remains challenging and could potentially be improved by integrating clinical data with innovative prognostic biomarkers. In this context, the analysis of circulating analytes, including cell-free DNA (cfDNA), appears particularly promising. Here, we investigated circulating cfDNA (measured through the quantification of 247 bp and 115 bp Alu genomic fragments) in a cohort of 244 geriatric CVD patients with multimorbidity hospitalised for acute CVD or non-CVD events. Survival analysis showed a direct association between Alu 247 cfDNA abundance and risk of death, particularly evident in the first six months after admission for acute CVD events. Higher plasma cfDNA concentration was associated with mortality in the same period of time. The cfDNA integrity (Alu 247/115), although not associated with outcome, appeared to be useful in discriminating patients in whom Alu 247 cfDNA abundance is most effective as a prognostic biomarker. The cfDNA parameters were associated with several biochemical markers of inflammation and myocardial damage. In conclusion, an increase in plasma cfDNA abundance at hospital admission is indicative of a higher risk of death in geriatric CVD patients, especially after acute CVD events, and its analysis may be potentially useful for risk stratification.
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Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | | | - Pierpaolo Stripoli
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona 60121, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | - Rina Recchioni
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona 60121, Italy
| | - Mirko Di Rosa
- Centre for Biostatistics and Applied Geriatric Clinical Epidemiology, IRCCS INRCA, Ancona 60124, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy
| | - Roberta Galeazzi
- Clinic of Laboratory and Precision Medicine, IRCCS INRCA, Ancona 60121, Italy
| | - Beatrice Arosio
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy; Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | | | - Francesco Spannella
- Internal Medicine and Geriatrics, IRCCS INRCA, Via della Montagnola 81, Ancona 60127, Italy; Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60126, Italy
| | - Antonio Cherubini
- Geriatria, Accettazione Geriatrica e Centro di Ricerca per L'invecchiamento, IRCCS INRCA, Ancona 60127, Italy
| | | | - Fabiola Olivieri
- Advanced Technology Center for Aging Research, IRCCS INRCA, Ancona 60121, Italy; Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona 60126, Italy; Scientific Direction, IRCCS INRCA, Ancona, Italy
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7
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Li L, Henkle E, Youngquist BM, Seo S, Hamed K, Melnick D, Lyon CJ, Jiang L, Zelazny AM, Hu TY, Winthrop KL, Ning B. Serum Cell-Free DNA-based Detection of Mycobacterium avium Complex Infection. Am J Respir Crit Care Med 2024; 209:1246-1254. [PMID: 38190702 PMCID: PMC11146540 DOI: 10.1164/rccm.202303-0401oc] [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: 03/08/2023] [Accepted: 01/04/2024] [Indexed: 01/10/2024] Open
Abstract
Rationale: Mycobacterium avium complex (MAC) is the most common cause of nontuberculous mycobacterial (NTM) pulmonary disease (PD), which exhibits increasing global incidence. Current microbiologic methods routinely used in clinical practice lack sensitivity and have long latencies, leading to delays in diagnosis and treatment initiation and evaluation. A clustered regularly interspaced short palindromic repeats (CRISPR)-based assay that measures MAC cell-free DNA (cfDNA) concentrations in serum could provide a rapid means to detect MAC infection and monitor response to antimicrobial treatment. Objectives: To develop and optimize a CRISPR MAC assay for MAC infection detection and to evaluate its diagnostic and prognostic performance in two MAC disease cohorts. Methods: MAC cfDNA serum concentrations were measured in individuals with diagnoses of MAC disease or who had bronchiectasis or chronic obstructive pulmonary disease diagnoses without histories of NTM PD or NTM-positive sputum cultures. Diagnostic performance was analyzed using pretreatment serum from two cohorts. Serum MAC cfDNA changes during MAC PD treatment were evaluated in a subset of patients with MAC PD who received macrolide-based multidrug regimens. Measurements and Main Results: The CRISPR MAC assay detected MAC cfDNA in MAC PD with 97.6% (91.6-99.7%) sensitivity and 97.6% (91.5-99.7%) specificity overall. Serum MAC cfDNA concentrations markedly decreased after MAC-directed treatment initiation in patients with MAC PD who demonstrated MAC culture conversion. Conclusions: This study provides preliminary evidence for the utility of a serum-based CRISPR MAC assay to rapidly detect MAC infection and monitor the response to treatment.
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Affiliation(s)
- Lin Li
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, and
| | | | - Brady M. Youngquist
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, and
| | - Seungyeon Seo
- Department of Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, MD; and
| | | | | | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, and
| | - Li Jiang
- Department of Laboratory Medicine and Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital, Chengdu, China
| | - Adrian M. Zelazny
- Department of Laboratory Medicine, NIH Clinical Center, NIH, Bethesda, MD; and
| | - Tony Y. Hu
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, and
- Department of Biomedical Engineering, School of Science and Engineering, Tulane University, New Orleans, LA
| | - Kevin L. Winthrop
- Division of Infectious Diseases, Schools of Medicine and Public Health, Oregon Health & Science University, Portland, OR
| | - Bo Ning
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, and
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Slootbeek PHJ, Tolmeijer SH, Mehra N, Schalken JA. Therapeutic biomarkers in metastatic castration-resistant prostate cancer: does the state matter? Crit Rev Clin Lab Sci 2024; 61:178-204. [PMID: 37882463 DOI: 10.1080/10408363.2023.2266482] [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: 06/07/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
The treatment of metastatic castration-resistant prostate cancer (mCRPC) has been fundamentally transformed by our greater understanding of its complex biological mechanisms and its entrance into the era of precision oncology. A broad aim is to use the extreme heterogeneity of mCRPC by matching already approved or new targeted therapies to the correct tumor genotype. To achieve this, tumor DNA must be obtained, sequenced, and correctly interpreted, with individual aberrations explored for their druggability, taking into account the hierarchy of driving molecular pathways. Although tumor tissue sequencing is the gold standard, tumor tissue can be challenging to obtain, and a biopsy from one metastatic site or primary tumor may not provide an accurate representation of the current genetic underpinning. Sequencing of circulating tumor DNA (ctDNA) might catalyze precision oncology in mCRPC, as it enables real-time observation of genomic changes in tumors and allows for monitoring of treatment response and identification of resistance mechanisms. Moreover, ctDNA can be used to identify mutations that may not be detected in solitary metastatic lesions and can provide a more in-depth understanding of inter- and intra-tumor heterogeneity. Finally, ctDNA abundance can serve as a prognostic biomarker in patients with mCRPC.The androgen receptor (AR)-axis is a well-established therapeutical target for prostate cancer, and through ctDNA sequencing, insights have been obtained in (temporal) resistance mechanisms that develop through castration resistance. New third-generation AR-axis inhibitors are being developed to overcome some of these resistance mechanisms. The druggability of defects in the DNA damage repair machinery has impacted the treatment landscape of mCRPC in recent years. For patients with deleterious gene aberrations in genes linked to homologous recombination, particularly BRCA1 or BRCA2, PARP inhibitors have shown efficacy compared to the standard of care armamentarium, but platinum-based chemotherapy may be equally effective. A hierarchy exists in genes associated with homologous recombination, where, besides the canonical genes in this pathway, not every other gene aberration predicts the same likelihood of response. Moreover, evidence is emerging on cross-resistance between therapies such as PARP inhibitors, platinum-based chemotherapy and even radioligand therapy that target this genotype. Mismatch repair-deficient patients can experience a beneficial response to immune checkpoint inhibitors. Activation of other cellular signaling pathways such as PI3K, cell cycle, and MAPK have shown limited success with monotherapy, but there is potential in co-targeting these pathways with combination therapy, either already witnessed or anticipated. This review outlines precision medicine in mCRPC, zooming in on the role of ctDNA, to identify genomic biomarkers that may be used to tailor molecularly targeted therapies. The most common druggable pathways and outcomes of therapies matched to these pathways are discussed.
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Affiliation(s)
- Peter H J Slootbeek
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Sofie H Tolmeijer
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Niven Mehra
- Department of Medical Oncology, Radboud university medical center, Nijmegen, The Netherland
| | - Jack A Schalken
- Department of Experimental Urology, Research Institute of Medical Innovation, Radboud university medical center, Nijmegen, The Netherlands
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9
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Poulet G, Hulot JS, Blanchard A, Bergerot D, Xiao W, Ginot F, Boutonnet-Rodat A, Justine A, Beinse G, Geromel V, Pellegrina L, Azizi M, Laurent-Puig P, Benhaim L, Taly V. Circadian rhythm and circulating cell-free DNA release on healthy subjects. Sci Rep 2023; 13:21675. [PMID: 38065990 PMCID: PMC10709451 DOI: 10.1038/s41598-023-47851-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
In the last decade, clinical studies have investigated the clinical relevance of circulating cell-free-DNA (ccfDNA) as a diagnostic and prognosis tool in various diseases including cancers. However, limited knowledge on ccfDNA biology restrains its full development in the clinical practice. To improve our understanding, we evaluated the impact of the circadian rhythm on ccfDNA release in healthy subjects over a 24-h period. 10 healthy female subjects underwent blood sampling at 8am and 20 healthy male subjects underwent serial blood sampling (8:00 AM, 9:00 AM, 12:00 PM, 4:00 PM, 8:00 PM, 12:00 AM, 4 AM (+ 1 Day) and 8 AM (+ 1 Day)). We performed digital droplet-based PCR (ddPCR) assays to target 2 DNA fragments (69 & 243 bp) located in the KRAS gene to determine the ccfDNA concentration and fragmentation profile. As control, half of the samples were re-analyzed by capillary miniaturized electrophoresis (BIAbooster system). Overall, we did not detect any influence of the circadian rhythm on ccfDNA release. Instead, we observed a decrease in the ccfDNA concentration after meal ingestion, suggesting either a post-prandial effect or a technical detection bias due to a higher plasma load in lipids and triglycerides. We also noticed a potential effect of gender, weight and creatinine levels on ccfDNA concentration.
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Affiliation(s)
- Geoffroy Poulet
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Eurofins-Biomnis, Gerland, Lyon, France
| | - Jean-Sébastien Hulot
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Anne Blanchard
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Damien Bergerot
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Wenjin Xiao
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | | | | | - Abdelli Justine
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Guillaume Beinse
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | | | | | - Michel Azizi
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Pierre Laurent-Puig
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Biochemistry Department - Unit of Pharmacogenetic and Molecular Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Leonor Benhaim
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.
- Department of Visceral and Surgical Oncology, Gustave Roussy, Villejuif, France.
| | - Valerie Taly
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.
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10
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Dyrskjøt L, Hansel DE, Efstathiou JA, Knowles MA, Galsky MD, Teoh J, Theodorescu D. Bladder cancer. Nat Rev Dis Primers 2023; 9:58. [PMID: 37884563 PMCID: PMC11218610 DOI: 10.1038/s41572-023-00468-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Bladder cancer is a global health issue with sex differences in incidence and prognosis. Bladder cancer has distinct molecular subtypes with multiple pathogenic pathways depending on whether the disease is non-muscle invasive or muscle invasive. The mutational burden is higher in muscle-invasive than in non-muscle-invasive disease. Commonly mutated genes include TERT, FGFR3, TP53, PIK3CA, STAG2 and genes involved in chromatin modification. Subtyping of both forms of bladder cancer is likely to change considerably with the advent of single-cell analysis methods. Early detection signifies a better disease prognosis; thus, minimally invasive diagnostic options are needed to improve patient outcomes. Urine-based tests are available for disease diagnosis and surveillance, and analysis of blood-based cell-free DNA is a promising tool for the detection of minimal residual disease and metastatic relapse. Transurethral resection is the cornerstone treatment for non-muscle-invasive bladder cancer and intravesical therapy can further improve oncological outcomes. For muscle-invasive bladder cancer, radical cystectomy with neoadjuvant chemotherapy is the standard of care with evidence supporting trimodality therapy. Immune-checkpoint inhibitors have demonstrated benefit in non-muscle-invasive, muscle-invasive and metastatic bladder cancer. Effective management requires a multidisciplinary approach that considers patient characteristics and molecular disease characteristics.
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Affiliation(s)
- Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Donna E Hansel
- Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Matthew D Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremy Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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11
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Kim V, Guberina M, Bechrakis NE, Lohmann DR, Zeschnigk M, Le Guin CHD. Release of Cell-Free Tumor DNA in the Plasma of Uveal Melanoma Patients Under Radiotherapy. Invest Ophthalmol Vis Sci 2023; 64:35. [PMID: 37862025 PMCID: PMC10599159 DOI: 10.1167/iovs.64.13.35] [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: 03/31/2023] [Accepted: 10/01/2023] [Indexed: 10/21/2023] Open
Abstract
Purpose Uveal melanoma (UM) is a tumor of the eye that metastasizes in approximately half of cases. Prognostic testing requires accessibility to tumor tissue, which is usually not available with eye-preserving therapies. Noninvasive approaches to prognostic testing that provide valuable information for patient care are therefore needed. The aim of this study was to evaluate the use of circulating cell-free plasma DNA analysis in UM patients undergoing brachytherapy. Methods The study recruited 26 uveal melanoma patients referred to the department between February and October 2020. Blood samples were collected at various time points before, during, and after treatment, and deep amplicon sequencing was used to identify oncogenic variant alleles of the GNAQ and GNA11 genes, which serve as indicators for the presence of circulating tumor DNA (ctDNA). Results The results showed that all patients were ctDNA negative before brachytherapy. In 31% of patients, ctDNA was detected during therapy. The variant allele fraction of GNAQ or GNA11 alleles in ctDNA positive samples ranged from 0.24% to 2% and correlates with the largest basal diameter and thickness of the tumor. Conclusions The findings suggest that brachytherapy increases the presence of tumor DNA in the plasma of UM patients. Thus ctDNA analysis may offer a noninvasive approach for prognostic testing. However, efforts are still required to lower the limit of detection for tumor-specific genetic alterations.
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Affiliation(s)
- Viktoria Kim
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Maja Guberina
- Department of Radiotherapy, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nikolaos E Bechrakis
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Claudia H D Le Guin
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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12
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Wuerdemann N, Joosse S, Klasen C, Prinz J, Demers I, George J, Speel EJM, Wagner S, Klußmann JP. [ctHPV-DNA based precision oncology for patients with oropharyngeal cancer - Where are we?]. Laryngorhinootologie 2023; 102:728-734. [PMID: 37364603 DOI: 10.1055/a-2092-3837] [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] [Indexed: 06/28/2023]
Abstract
Human papillomavirus (HPV) is an established etiologic factor for cancers in the head and neck region, specifically for Oropharyngeal Squamous Cell Carcinoma (OPSCC). The comparatively good overall survival justifies the current discussion regarding therapy de-escalation for patients with a low-risk profile. In addition to the immunohistochemistry-based biomarker p16INK4a, there is still a need for diagnostic and prognostic biomarkers that allow risk stratification and monitoring during therapy and follow-up of these patients. In recent years, liquid biopsy, especially in the form of plasma samples, has gained importance and is already used to monitor viral DNA in patients with Epstein-Barr virus-associated nasopharyngeal carcinoma. Circulating DNA (ctDNA) released by the tumor into the bloodstream is particularly suitable for a high specificity in detecting virus-associated tumors. Detection of viral E6 and E7 oncogenes in HPV-positive OPSCC is predominantly performed by droplet digital/quantitative PCR as well as next generation sequencing. Detection of circulating HPV-DNA derived from tumor cells (ctHPV-DNA) at diagnosis is associated with advanced tumor stage, locoregional and distant metastases. Longitudinal studies have further demonstrated that detectable and/or increasing ctHPV-DNA levels are associated with treatment failure and disease relapse. However, a standardization of the diagnostic procedure is necessary before introducing liquid biopsy into the clinical routine. In the future, this might allow a valid reflection of disease progression in HPV-positive OPSCC.
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Affiliation(s)
- Nora Wuerdemann
- Klinik für Hals-, Nasen-, Ohrenheilkunde, Kopf- und Halschirurgie, Uniklinik Köln, Köln, Deutschland
- Klinik für Innere Medizin I, Uniklinik Köln, Köln, Deutschland
| | - Simon Joosse
- Abteilung für Tumorbiologie, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Deutschland
| | - Charlotte Klasen
- Klinik für Hals-, Nasen-, Ohrenheilkunde, Kopf- und Halschirurgie, Uniklinik Köln, Köln, Deutschland
| | - Johanna Prinz
- Klinik für Innere Medizin I, Uniklinik Köln, Köln, Deutschland
| | - Imke Demers
- Institut für Pathologie, Maastricht Universität, GROW-School für Onkologie und Entwicklungsbiologie, Maastricht, Niederlande
| | - Julie George
- Klinik für Hals-, Nasen-, Ohrenheilkunde, Kopf- und Halschirurgie, Uniklinik Köln, Köln, Deutschland
| | - Ernst-Jan Maria Speel
- Institut für Pathologie, Maastricht Universität, GROW-School für Onkologie und Entwicklungsbiologie, Maastricht, Niederlande
- GROW-School für Onkologie und Entwicklungsbiologie, Institut für Pathologie, Maastricht Universität, Maastricht, Niederlande
| | - Steffen Wagner
- Klinik für Hals-, Nasen-, Ohrenheilkunde, Kopf- und Halschirurgie, Justus-Liebig-Universität Gießen, Gießen, Deutschland
| | - Jens Peter Klußmann
- Klinik für Hals-, Nasen-, Ohrenheilkunde, Kopf- und Halschirurgie, Uniklinik Köln, Köln, Deutschland
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13
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Liu W, Wang C, Pan F, Shao J, Cui Y, Han D, Zhang H. Clinical Application of a Multiplex Droplet Digital PCR in the Rapid Diagnosis of Children with Suspected Bloodstream Infections. Pathogens 2023; 12:pathogens12050719. [PMID: 37242389 DOI: 10.3390/pathogens12050719] [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: 03/15/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Droplet digital PCR (ddPCR) recently has been shown to be a potential diagnostic tool for adults with bloodstream infections (BSIs); however, its application in children remains obscure. In this study, 76 blood samples of children with suspected BSIs were synchronously detected by traditional blood cultures (BCs) and ddPCRs. Our team validated the diagnostic performance of ddPCR including sensitivity, specificity, and positive and negative predictive values. The 76 pediatric patients from the hematology department (67.1%), the pediatric intensive care unit (PICU, 27.6%), and other departments (5.2%) were enrolled. The positive rate of ddPCR results was 47.9%, whereas that for BC was 6.6%. In addition, the time consumption of ddPCR was shorter, only for 4.7 ± 0.9 h, in comparison with the detection timing of BC (76.7 ± 10.4 h, p < 0.01). The levels of agreement and disagreement between BC and ddPCR were 96.1% and 4.2%, and the negative agreement reached 95.6%. The sensitivity of ddPCR was 100%, with corresponding specificities ranging from 95.3 to 100.0%. In addition, a total of nine viruses were identified by ddPCR. In China, the multiplexed ddPCR first could be a tool for the rapid and accurate diagnosis of children with suspected BSIs and can be an early indicator of the possibility of viraemia in children with immunosuppression.
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Affiliation(s)
- Wenxin Liu
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Chun Wang
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Jingbo Shao
- Department of Hematology/Oncology, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Yun Cui
- Department of Critical Care Medicine, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai 200062, China
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14
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Bou Zerdan M, Kassab J, Saba L, Haroun E, Bou Zerdan M, Allam S, Nasr L, Macaron W, Mammadli M, Abou Moussa S, Chaulagain CP. Liquid biopsies and minimal residual disease in lymphoid malignancies. Front Oncol 2023; 13:1173701. [PMID: 37228488 PMCID: PMC10203459 DOI: 10.3389/fonc.2023.1173701] [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: 02/25/2023] [Accepted: 04/21/2023] [Indexed: 05/27/2023] Open
Abstract
Minimal residual disease (MRD) assessment using peripheral blood instead of bone marrow aspirate/biopsy specimen or the biopsy of the cancerous infiltrated by lymphoid malignancies is an emerging technique with enormous interest of research and technological innovation at the current time. In some lymphoid malignancies (particularly ALL), Studies have shown that MRD monitoring of the peripheral blood may be an adequate alternative to frequent BM aspirations. However, additional studies investigating the biology of liquid biopsies in ALL and its potential as an MRD marker in larger patient cohorts in treatment protocols are warranted. Despite the promising data, there are still limitations in liquid biopsies in lymphoid malignancies, such as standardization of the sample collection and processing, determination of timing and duration for liquid biopsy analysis, and definition of the biological characteristics and specificity of the techniques evaluated such as flow cytometry, molecular techniques, and next generation sequencies. The use of liquid biopsy for detection of minimal residual disease in T-cell lymphoma is still experimental but it has made significant progress in multiple myeloma for example. Recent attempt to use artificial intelligence may help simplify the algorithm for testing and may help avoid inter-observer variation and operator dependency in these highly technically demanding testing process.
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Affiliation(s)
- Maroun Bou Zerdan
- Department of Internal Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | - Joseph Kassab
- Cleveland Clinic, Research Institute, Cleveland, OH, United States
| | - Ludovic Saba
- Department of Hematology-Oncology, Myeloma and Amyloidosis Program, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
| | - Elio Haroun
- Department of Medicine, State University of New York (SUNY) Upstate Medical University, New York, NY, United States
| | | | - Sabine Allam
- Department of Medicine and Medical Sciences, University of Balamand, Balamand, Lebanon
| | - Lewis Nasr
- University of Texas MD Anderson Cancer Center, Texas, TX, United States
| | - Walid Macaron
- University of Texas MD Anderson Cancer Center, Texas, TX, United States
| | - Mahinbanu Mammadli
- Department of Internal Medicine, State University of New York (SUNY) Upstate Medical University, Syracuse, NY, United States
| | | | - Chakra P. Chaulagain
- Department of Hematology-Oncology, Myeloma and Amyloidosis Program, Maroone Cancer Center, Cleveland Clinic Florida, Weston, FL, United States
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15
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Bello S, Lasierra AB, López-Vergara L, de Diego C, Torralba L, de Gopegui PR, Lahoz R, Abadía C, Godino J, Cebollada A, Jimeno B, Bello C, Tejada A, Torres A. IL-6 and cfDNA monitoring throughout COVID-19 hospitalization are accurate markers of its outcomes. Respir Res 2023; 24:125. [PMID: 37147677 PMCID: PMC10161166 DOI: 10.1186/s12931-023-02426-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 04/18/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Severe COVID-19 entails a dysregulated immune response, most likely inflammation related to a lack of virus control. A better understanding of immune toxicity, immunosuppression balance, and COVID-19 assessments could help determine whether different clinical presentations are driven by specific types of immune responses. The progression of the immune response and tissular damage could predict outcomes and may help in the management of patients. METHODS We collected 201 serum samples from 93 hospitalised patients classified as moderately, severely, and critically ill. We differentiated the viral, early inflammatory, and late inflammatory phases and included 72 patients with 180 samples in separate stages for longitudinal study and 55 controls. We studied selected cytokines, P-selectin, and the tissue damage markers lactate dehydrogenase (LDH) and cell-free DNA (cfDNA). RESULTS TNF-α, IL-6, IL-8, and G-CSF were associated with severity and mortality, but only IL-6 increased since admission in the critical patients and non-survivors, correlating with damage markers. The lack of a significant decrease in IL-6 levels in the critical patients and non-survivors in the early inflammatory phase (a decreased presence in the other patients) suggests that these patients did not achieve viral control on days 10-16. For all patients, lactate dehydrogenase and cfDNA levels increased with severity, and cfDNA levels increased in the non-survivors from the first sample (p = 0.002) to the late inflammatory phase (p = 0.031). In the multivariate study, cfDNA was an independent risk factor for mortality and ICU admission. CONCLUSIONS The distinct progression of IL-6 levels in the course of the disease, especially on days 10-16, was a good marker of progression to critical status and mortality and could guide the start of IL-6 blockade. cfDNA was an accurate marker of severity and mortality from admission and throughout COVID-19 progression.
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Affiliation(s)
- Salvador Bello
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Avenida Isabel La Católica 1-9, 50009, Zaragoza, Spain.
| | | | - Lucía López-Vergara
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Avenida Isabel La Católica 1-9, 50009, Zaragoza, Spain
| | - Cristina de Diego
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Avenida Isabel La Católica 1-9, 50009, Zaragoza, Spain
| | - Laura Torralba
- Department of Pulmonary Medicine, Miguel Servet University Hospital, CIBERES, Instituto de Investigación Sanitaria (ISS) Aragón, Avenida Isabel La Católica 1-9, 50009, Zaragoza, Spain
| | | | - Raquel Lahoz
- Department of Biochemistry, Miguel Servet University Hospital, Zaragoza, Spain
| | - Claudia Abadía
- Department of Biochemistry, Miguel Servet University Hospital, Zaragoza, Spain
| | - Javier Godino
- Department of Cytometry and Cell Separation, Aragon Institute of Health Sciences (IACS), Zaragoza, Spain
| | - Alberto Cebollada
- Biocomputing Technical Scientific Service, Aragon Institute of Health Sciences (IACS), Zaragoza, Spain
| | - Beatriz Jimeno
- Department of Cytometry and Cell Separation, Aragon Institute of Health Sciences (IACS), Zaragoza, Spain
| | - Carlota Bello
- Department of Radiology, Hospital Clínico Lozano Blesa, Zaragoza, Spain
| | - Antonio Tejada
- Intensive Care Unit, Miguel Servet University Hospital, Zaragoza, Spain
| | - Antoni Torres
- Servei de Pneumologia, Hospital Clinic, Universitat de Barcelona, IDIBAPS, ICREA, CIBERESUCICOVID, Barcelona, Spain
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16
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Gaitsch H, Franklin RJM, Reich DS. Cell-free DNA-based liquid biopsies in neurology. Brain 2023; 146:1758-1774. [PMID: 36408894 PMCID: PMC10151188 DOI: 10.1093/brain/awac438] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/26/2022] [Accepted: 11/10/2022] [Indexed: 11/22/2022] Open
Abstract
This article reviews recent developments in the application of cell-free DNA-based liquid biopsies to neurological diseases. Over the past few decades, an explosion of interest in the use of accessible biofluids to identify and track molecular disease has revolutionized the fields of oncology, prenatal medicine and others. More recently, technological advances in signal detection have allowed for informative analysis of biofluids that are typically sparse in cells and other circulating components, such as CSF. In parallel, advancements in epigenetic profiling have allowed for novel applications of liquid biopsies to diseases without characteristic mutational profiles, including many degenerative, autoimmune, inflammatory, ischaemic and infectious disorders. These events have paved the way for a wide array of neurological conditions to benefit from enhanced diagnostic, prognostic, and treatment abilities through the use of liquid biomarkers: a 'liquid biopsy' approach. This review includes an overview of types of liquid biopsy targets with a focus on circulating cell-free DNA, methods used to identify and probe potential liquid biomarkers, and recent applications of such biomarkers to a variety of complex neurological conditions including CNS tumours, stroke, traumatic brain injury, Alzheimer's disease, epilepsy, multiple sclerosis and neuroinfectious disease. Finally, the challenges of translating liquid biopsies to use in clinical neurology settings-and the opportunities for improvement in disease management that such translation may provide-are discussed.
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Affiliation(s)
- Hallie Gaitsch
- NIH-Oxford-Cambridge Scholars Program, Wellcome-MRC Cambridge Stem Cell Institute and Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 1TN, UK
| | | | - Daniel S Reich
- Translational Neuroradiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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17
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Takahashi H, Yasui T, Hirano M, Shinjo K, Miyazaki Y, Shinoda W, Hasegawa T, Natsume A, Kitano Y, Ida M, Zhang M, Shimada T, Paisrisarn P, Zhu Z, Ohka F, Aoki K, Rahong S, Nagashima K, Yanagida T, Baba Y. Mutation detection of urinary cell-free DNA via catch-and-release isolation on nanowires for liquid biopsy. Biosens Bioelectron 2023; 234:115318. [PMID: 37172361 DOI: 10.1016/j.bios.2023.115318] [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: 01/17/2023] [Revised: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 05/14/2023]
Abstract
Cell-free DNA (cfDNA) and extracellular vesicles (EVs) are molecular biomarkers in liquid biopsies that can be applied for cancer detection, which are known to carry information on the necessary conditions for oncogenesis and cancer cell-specific activities after oncogenesis, respectively. Analyses for both cfDNA and EVs from the same body fluid can provide insights into screening and identifying the molecular subtypes of cancer; however, a major bottleneck is the lack of efficient and standardized techniques for the isolation of cfDNA and EVs from clinical specimens. Here, we achieved catch-and-release isolation by hydrogen bond-mediated binding of cfDNA in urine to zinc oxide (ZnO) nanowires, which also capture EVs by surface charge, and subsequently we identified genetic mutations in urinary cfDNA. The binding strength of hydrogen bonds between single-crystal ZnO nanowires and DNA was found to be equal to or larger than that of conventional hydrophobic interactions, suggesting the possibility of isolating trace amounts of cfDNA. Our results demonstrated that nanowire-based cancer screening assay can screen cancer and can identify the molecular subtypes of cancer in urine from brain tumor patients through EV analysis and cfDNA mutation analysis. We anticipate our method to be a starting point for more sophisticated diagnostic models of cancer screening and identification.
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Affiliation(s)
- Hiromi Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Blk N3, Level 2, Room 86 (N3-02c-86), 639798, Singapore.
| | - Takao Yasui
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan; Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan.
| | - Masaki Hirano
- Division of Molecular Oncology, Aichi Cancer Center Research Institute, Kanokoden, Chikusa-ku, Nagoya, 464-0021, Japan
| | - Keiko Shinjo
- Division of Cancer Biology, Graduate School of Medicine, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yusuke Miyazaki
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Wataru Shinoda
- Research Institute for Interdisciplinary Science, Okayama University, Okayama, 700-8530, Japan
| | - Takeshi Hasegawa
- Institute for Chemical Research, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Atsushi Natsume
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Yotaro Kitano
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Tsurumai-cho 65, Showa-ku, Nagoya, 466-8550, Japan
| | - Mikiko Ida
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Min Zhang
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Taisuke Shimada
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Piyawan Paisrisarn
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Zetao Zhu
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Fumiharu Ohka
- Department of Neurosurgery, Graduate School of Medicine, Nagoya University, Tsurumai-cho 65, Showa-ku, Nagoya, 466-8550, Japan
| | - Kosuke Aoki
- Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan
| | - Sakon Rahong
- College of Materials Innovation and Technology, King Mongkut's Institute of Technology Ladkrabang, Chalongkrung Rd., Ladkrabang, Bangkok, 10520, Thailand
| | - Kazuki Nagashima
- Japan Science and Technology Agency (JST), PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan; Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takeshi Yanagida
- Department of Applied Chemistry, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan; The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka-cho, Ibaraki, Osaka, 567-0047, Japan; Institute for Materials Chemistry and Engineering, Kyushu University, 6-1 Kasuga-Koen, Kasuga, Fukuoka, 816-8580, Japan
| | - Yoshinobu Baba
- Department of Biomolecular Engineering, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Institute of Nano-Life-Systems, Institutes of Innovation for Future Society, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8603, Japan; Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Anagawa 4-9-1, Inage-ku, Chiba, 263-8555, Japan.
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18
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Jenkins S, Zhang W, Steinberg SM, Nousome D, Houston N, Wu X, Armstrong TS, Burton E, Smart DD, Shah R, Peer CJ, Mozarsky B, Arisa O, Figg WD, Mendoza TR, Vera E, Brastianos P, Carter S, Gilbert MR, Anders CK, Connolly RM, Tweed C, Smith KL, Khan I, Lipkowitz S, Steeg PS, Zimmer AS. Phase I Study and Cell-Free DNA Analysis of T-DM1 and Metronomic Temozolomide for Secondary Prevention of HER2-Positive Breast Cancer Brain Metastases. Clin Cancer Res 2023; 29:1450-1459. [PMID: 36705597 PMCID: PMC10153633 DOI: 10.1158/1078-0432.ccr-22-0855] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/22/2022] [Accepted: 01/17/2023] [Indexed: 01/28/2023]
Abstract
PURPOSE Preclinical data showed that prophylactic, low-dose temozolomide (TMZ) significantly prevented breast cancer brain metastasis. We present results of a phase I trial combining T-DM1 with TMZ for the prevention of additional brain metastases after previous occurrence and local treatment in patients with HER2+ breast cancer. PATIENTS AND METHODS Eligible patients had HER2+ breast cancer with brain metastases and were within 12 weeks of whole brain radiation therapy (WBRT), stereotactic radiosurgery, and/or surgery. Standard doses of T-DM1 were administered intravenously every 21 days (3.6 mg/kg) and TMZ was given orally daily in a 3+3 phase I dose escalation design at 30, 40, or 50 mg/m2, continuously. DLT period was one 21-day cycle. Primary endpoint was safety and recommended phase II dose. Symptom questionnaires, brain MRI, and systemic CT scans were performed every 6 weeks. Cell-free DNA sequencing was performed on patients' plasma and CSF. RESULTS Twelve women enrolled, nine (75%) with prior SRS therapy and three (25%) with prior WBRT. Grade 3 or 4 AEs included thrombocytopenia (1/12), neutropenia (1/12), lymphopenia (6/12), and decreased CD4 (6/12), requiring pentamidine for Pneumocystis jirovecii pneumonia prophylaxis. No DLT was observed. Four patients on the highest TMZ dose underwent dose reductions. At trial entry, 6 of 12 patients had tumor mutations in CSF, indicating ongoing metastatic colonization despite a clear MRI. Median follow-up on study was 9.6 m (2.8-33.9); only 2 patients developed new parenchymal brain metastases. Tumor mutations varied with patient outcome. CONCLUSIONS Metronomic TMZ in combination with standard dose T-DM1 shows low-grade toxicity and potential activity in secondary prevention of HER2+ brain metastases.
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Affiliation(s)
- Sarah Jenkins
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
| | - Wei Zhang
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
| | - Seth M. Steinberg
- Biostatistics and Data Management Section; Center for Cancer Research, NCI, NIH
| | - Darryl Nousome
- Center for Cancer Research Collaborative Bioinformatics Resource, NCI, NIH
| | - Nicole Houston
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Dee Dee Smart
- Radiation Oncology Branch, Center for Cancer Research, NCI NIH
| | - Ritu Shah
- Neuro-Radiology, Clinical Center Cancer Research, NIH
| | - Cody J. Peer
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | - Brett Mozarsky
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | - Oluwatobi Arisa
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | - William D. Figg
- Clinical Pharmacology Program, Center for Cancer Research, NCI NIH
| | | | | | - Priscilla Brastianos
- Massachusetts General Hospital, Harvard Cancer Center, Harvard University, Boston, MA
| | - Scott Carter
- Division of Medical Sciences, Harvard University, Boston, MA
| | | | | | | | - Carol Tweed
- University of Maryland Oncology, Baltimore MD
| | - Karen L. Smith
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - Imran Khan
- Women’s Malignancies Branch; Center for Cancer Research, NCI, NIH
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19
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Moser T, Kühberger S, Lazzeri I, Vlachos G, Heitzer E. Bridging biological cfDNA features and machine learning approaches. Trends Genet 2023; 39:285-307. [PMID: 36792446 DOI: 10.1016/j.tig.2023.01.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 01/10/2023] [Accepted: 01/19/2023] [Indexed: 02/15/2023]
Abstract
Liquid biopsies (LBs), particularly using circulating tumor DNA (ctDNA), are expected to revolutionize precision oncology and blood-based cancer screening. Recent technological improvements, in combination with the ever-growing understanding of cell-free DNA (cfDNA) biology, are enabling the detection of tumor-specific changes with extremely high resolution and new analysis concepts beyond genetic alterations, including methylomics, fragmentomics, and nucleosomics. The interrogation of a large number of markers and the high complexity of data render traditional correlation methods insufficient. In this regard, machine learning (ML) algorithms are increasingly being used to decipher disease- and tissue-specific signals from cfDNA. Here, we review recent insights into biological ctDNA features and how these are incorporated into sophisticated ML applications.
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Affiliation(s)
- Tina Moser
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Stefan Kühberger
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Isaac Lazzeri
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Georgios Vlachos
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, Medical University of Graz, Graz, Austria.
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20
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Li S, Zhang E, Cai Z. Liquid biopsy by analysis of circulating myeloma cells and cell-free nucleic acids: a novel noninvasive approach of disease evaluation in multiple myeloma. Biomark Res 2023; 11:27. [PMID: 36890597 PMCID: PMC9997021 DOI: 10.1186/s40364-023-00469-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 02/26/2023] [Indexed: 03/10/2023] Open
Abstract
Multiple myeloma (MM) is an incurable hematological cancer with high spatial- and temporal-heterogeneity. Invasive single-point bone marrow sampling cannot capture the tumor heterogeneity and is difficult to repeat for serial assessments. Liquid biopsy is a technique for identifying and analyzing circulating MM cells and cell products produced by tumors and released into the circulation, allowing for the minimally invasive and comprehensive detection of disease burden and molecular alterations in MM and monitoring treatment response and disease progression. Furthermore, liquid biopsy can provide complementary information to conventional detection approaches and improve their prognostic values. This article reviewed the technologies and applications of liquid biopsy in MM.
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Affiliation(s)
- Shuchan Li
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, No. 79, Qingchun Road, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Enfan Zhang
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, No. 79, Qingchun Road, Hangzhou, Zhejiang, China.,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhen Cai
- Bone Marrow Transplantation Center, The First Affiliated Hospital, School of Medicine, Zhejiang University, No. 79, Qingchun Road, Hangzhou, Zhejiang, China. .,Institute of Hematology, Zhejiang University, Hangzhou, Zhejiang, China.
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21
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Škara L, Vodopić T, Pezelj I, Abramović I, Vrhovec B, Vrtarić A, Sinčić N, Tomas D, Bulimbašić S, Kuliš T, Ulamec M. Methylation pattern of caveolin-1 in prostate cancer as potential cfDNA biomarker. BIOMOLECULES AND BIOMEDICINE 2023; 23:176-186. [PMID: 36036057 PMCID: PMC9901895 DOI: 10.17305/bjbms.2022.7497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/01/2022] [Indexed: 02/03/2023]
Abstract
High prevalence and mortality of prostate cancer (PCa) are well known global health issues. Novel biomarkers for better identifying patients with PCa are the subject of extensive research. Prostate specific antigen (PSA) shows low specificity in screening and diagnostics, leading to unnecessary biopsies and health costs. Eighty patients with PCa and benign prostate hyperplasia (BPH) were included in the study. We analyzed CAV1 gene expression and methylation in tissue. CAV1 cfDNA methylation from blood and seminal plasma was accessed as a potential PCa biomarker. Although methylation in blood plasma did not differ between PCa and BPH patients, methylation in seminal plasma showed better PCa biomarker performances than tPSA (AUC 0.63 vs. AUC 0.52). Discrimination of BPH and Gleason grade group 1 PCa patients from patients with higher Gleason grade groups revealed very good performance as well (AUC 0.72). CAV1 methylation is useful biomarker with potential for further seminal plasma cfDNA research, but its diagnostic accuracy should be improved, as well as general knowledge about cfDNA in seminal plasma.
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Affiliation(s)
- Lucija Škara
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia,Correspondence to Lucija Škara:
| | - Tonći Vodopić
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Ivan Pezelj
- Department of Urology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Irena Abramović
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Borna Vrhovec
- Department of Urology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Alen Vrtarić
- Department of Clinical Chemistry, Sestre milosrdnice University Hospital Center, Zagreb, Croatia
| | - Nino Sinčić
- Department of Biology, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Davor Tomas
- Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia,Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Stela Bulimbašić
- Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia,Pathology and Cytology Department, University Hospital Center Zagreb, Zagreb, Croatia
| | - Tomislav Kuliš
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia,Department of Urology, University Hospital Center Zagreb, Zagreb, Croatia
| | - Monika Ulamec
- Scientific Group for Research on Epigenetic Biomarkers, University of Zagreb School of Medicine, Zagreb, Croatia,Scientific Centre of Excellence for Reproductive and Regenerative Medicine, University of Zagreb School of Medicine, Zagreb, Croatia,Ljudevit Jurak Clinical Department of Pathology and Cytology, Sestre milosrdnice University Hospital Center, Zagreb, Croatia,Department of Pathology, University of Zagreb School of Medicine, Zagreb, Croatia
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22
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Stejskal P, Goodarzi H, Srovnal J, Hajdúch M, van ’t Veer LJ, Magbanua MJM. Circulating tumor nucleic acids: biology, release mechanisms, and clinical relevance. Mol Cancer 2023; 22:15. [PMID: 36681803 PMCID: PMC9862574 DOI: 10.1186/s12943-022-01710-w] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/29/2022] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Despite advances in early detection and therapies, cancer is still one of the most common causes of death worldwide. Since each tumor is unique, there is a need to implement personalized care and develop robust tools for monitoring treatment response to assess drug efficacy and prevent disease relapse. MAIN BODY Recent developments in liquid biopsies have enabled real-time noninvasive monitoring of tumor burden through the detection of molecules shed by tumors in the blood. These molecules include circulating tumor nucleic acids (ctNAs), comprising cell-free DNA or RNA molecules passively and/or actively released from tumor cells. Often highlighted for their diagnostic, predictive, and prognostic potential, these biomarkers possess valuable information about tumor characteristics and evolution. While circulating tumor DNA (ctDNA) has been in the spotlight for the last decade, less is known about circulating tumor RNA (ctRNA). There are unanswered questions about why some tumors shed high amounts of ctNAs while others have undetectable levels. Also, there are gaps in our understanding of associations between tumor evolution and ctNA characteristics and shedding kinetics. In this review, we summarize current knowledge about ctNA biology and release mechanisms and put this information into the context of tumor evolution and clinical utility. CONCLUSIONS A deeper understanding of the biology of ctDNA and ctRNA may inform the use of liquid biopsies in personalized medicine to improve cancer patient outcomes.
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Affiliation(s)
- Pavel Stejskal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Josef Srovnal
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Olomouc, 779 00 Czech Republic
| | - Laura J. van ’t Veer
- Department of Laboratory Medicine, University of California San Francisco, 2340 Sutter Street, San Francisco, CA USA
| | - Mark Jesus M. Magbanua
- Department of Laboratory Medicine, University of California San Francisco, 2340 Sutter Street, San Francisco, CA USA
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23
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Cardelli M, Pierpaoli E, Marchegiani F, Marcheselli F, Piacenza F, Giacconi R, Recchioni R, Casoli T, Stripoli P, Provinciali M, Matacchione G, Giuliani A, Ramini D, Sabbatinelli J, Bonafè M, Di Rosa M, Cherubini A, Di Pentima C, Spannella F, Antonicelli R, Bonfigli AR, Olivieri F, Lattanzio F. Biomarkers of cell damage, neutrophil and macrophage activation associated with in-hospital mortality in geriatric COVID-19 patients. Immun Ageing 2022; 19:65. [PMID: 36522763 PMCID: PMC9751505 DOI: 10.1186/s12979-022-00315-7] [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: 04/26/2022] [Accepted: 10/10/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND The risk for symptomatic COVID-19 requiring hospitalization is higher in the older population. The course of the disease in hospitalised older patients may show significant variation, from mild to severe illness, ultimately leading to death in the most critical cases. The analysis of circulating biomolecules involved in mechanisms of inflammation, cell damage and innate immunity could lead to identify new biomarkers of COVID-19 severity, aimed to improve the clinical management of subjects at higher risk of severe outcomes. In a cohort of COVID-19 geriatric patients (n= 156) who required hospitalization we analysed, on-admission, a series of circulating biomarkers related to neutrophil activation (neutrophil elastase, LL-37), macrophage activation (sCD163) and cell damage (nuclear cfDNA, mithocondrial cfDNA and nuclear cfDNA integrity). The above reported biomarkers were tested for their association with in-hospital mortality and with clinical, inflammatory and routine hematological parameters. Aim of the study was to unravel prognostic parameters for risk stratification of COVID-19 patients. RESULTS Lower n-cfDNA integrity, higher neutrophil elastase and higher sCD163 levels were significantly associated with an increased risk of in-hospital decease. Median (IQR) values observed in discharged vs. deceased patients were: 0.50 (0.30-0.72) vs. 0.33 (0.22-0.62) for n-cfDNA integrity; 94.0 (47.7-154.0) ng/ml vs. 115.7 (84.2-212.7) ng/ml for neutrophil elastase; 614.0 (370.0-821.0) ng/ml vs. 787.0 (560.0-1304.0) ng/ml for sCD163. The analysis of survival curves in patients stratified for tertiles of each biomarker showed that patients with n-cfDNA integrity < 0.32 or sCD163 in the range 492-811 ng/ml had higher risk of in-hospital decease than, respectively, patients with higher n-cfDNA integrity or lower sCD163. These associations were further confirmed in multivariate models adjusted for age, sex and outcome-related clinical variables. In these models also high levels of neutrophil elastase (>150 ng/ml) appeared to be independent predictor of in-hospital death. An additional analysis of neutrophil elastase in patients stratified for n-cfDNA integrity levels was conducted to better describe the association of the studied parameters with the outcome. CONCLUSIONS On the whole, biomarkers of cell-free DNA integrity, neutrophil and macrophage activation might provide a valuable contribution to identify geriatric patients with high risk of COVID-19 in-hospital mortality.
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Affiliation(s)
- M. Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - E. Pierpaoli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - F. Marchegiani
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - F. Marcheselli
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - F. Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - R. Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - R. Recchioni
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - T. Casoli
- Center for Neurobiology of Aging, Scientific Technological Area, IRCCS INRCA, Via Birarelli 8, 60121 Ancona, Italy
| | - P. Stripoli
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - M. Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, Ancona, Italy
| | - G. Matacchione
- grid.7010.60000 0001 1017 3210Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - A. Giuliani
- grid.7010.60000 0001 1017 3210Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - D. Ramini
- Center of Clinical Pathology and Innovative Therapy, IRCCS INRCA, Ancona, Italy
| | - J. Sabbatinelli
- grid.411490.90000 0004 1759 6306SOD Medicina di Laboratorio, Azienda Ospedaliero Universitaria Ospedali Riuniti, Ancona, Italy
| | - M. Bonafè
- grid.6292.f0000 0004 1757 1758Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - M. Di Rosa
- Unit of Geriatric Pharmacoepidemiology and Biostatistics, IRCCS INRCA, Cosenza, Italy
| | - A. Cherubini
- Geriatria, Accettazione geriatrica e Centro di Ricerca per l’invecchiamento, IRCCS INRCA, Ancona, Italy
| | - C. Di Pentima
- Internal Medicine and Geriatrics, IRCCS INRCA, Via della Montagnola 81, 60127 Ancona, Italy
| | - F. Spannella
- Internal Medicine and Geriatrics, IRCCS INRCA, Via della Montagnola 81, 60127 Ancona, Italy
| | | | - A. R. Bonfigli
- Scientific Direction and Geriatric Unit, IRCCS INRCA, Ancona, Italy
| | - F. Olivieri
- grid.7010.60000 0001 1017 3210Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - F. Lattanzio
- Scientific Direction and Geriatric Unit, IRCCS INRCA, Ancona, Italy
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24
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Sampathi S, Chernyavskaya Y, Haney MG, Moore LH, Snyder IA, Cox AH, Fuller BL, Taylor TJ, Yan D, Badgett TC, Blackburn JS. Nanopore sequencing of clonal IGH rearrangements in cell-free DNA as a biomarker for acute lymphoblastic leukemia. Front Oncol 2022; 12:958673. [PMID: 36591474 PMCID: PMC9795051 DOI: 10.3389/fonc.2022.958673] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
Background Acute Lymphoblastic Leukemia (ALL) is the most common pediatric cancer, and patients with relapsed ALL have a poor prognosis. Detection of ALL blasts remaining at the end of treatment, or minimal residual disease (MRD), and spread of ALL into the central nervous system (CNS) have prognostic importance in ALL. Current methods to detect MRD and CNS disease in ALL rely on the presence of ALL blasts in patient samples. Cell-free DNA, or small fragments of DNA released by cancer cells into patient biofluids, has emerged as a robust and sensitive biomarker to assess cancer burden, although cfDNA analysis has not previously been applied to ALL. Methods We present a simple and rapid workflow based on NanoporeMinION sequencing of PCR amplified B cell-specific rearrangement of the (IGH) locus in cfDNA from B-ALL patient samples. A cohort of 5 pediatric B-ALL patient samples was chosen for the study based on the MRD and CNS disease status. Results Quantitation of IGH-variable sequences in cfDNA allowed us to detect clonal heterogeneity and track the response of individual B-ALL clones throughout treatment. cfDNA was detected in patient biofluids with clinical diagnoses of MRD and CNS disease, and leukemic clones could be detected even when diagnostic cell-count thresholds for MRD were not met. These data suggest that cfDNA assays may be useful in detecting the presence of ALL in the patient, even when blasts are not physically present in the biofluid sample. Conclusions The Nanopore IGH detection workflow to monitor cell-free DNA is a simple, rapid, and inexpensive assay that may ultimately serve as a valuable complement to traditional clinical diagnostic approaches for ALL.
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Affiliation(s)
- Shilpa Sampathi
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | - Yelena Chernyavskaya
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | - Meghan G. Haney
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States,Markey Cancer Center, University of Kentucky, Lexington, KY, United States,College of Medicine, University of Kentucky, Lexington, KY, United States
| | - L. Henry Moore
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States,College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Isabel A. Snyder
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States
| | - Anna H. Cox
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States,College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Brittany L. Fuller
- Department of Pediatric Oncology, University of Kentucky, Lexington, KY, United States
| | - Tamara J. Taylor
- Department of Pediatric Oncology, University of Kentucky, Lexington, KY, United States
| | - Donglin Yan
- Markey Cancer Center, University of Kentucky, Lexington, KY, United States,Department of Biostatistics, University of Kentucky, Lexington, KY, United States
| | - Tom C. Badgett
- Department of Pediatric Oncology, University of Kentucky, Lexington, KY, United States
| | - Jessica S. Blackburn
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, United States,Markey Cancer Center, University of Kentucky, Lexington, KY, United States,*Correspondence: Jessica S. Blackburn,
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25
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Bredno J, Venn O, Chen X, Freese P, Ofman JJ. Circulating Tumor DNA Allele Fraction: A Candidate Biological Signal for Multicancer Early Detection Tests to Assess the Clinical Significance of Cancers. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1368-1378. [PMID: 35948080 DOI: 10.1016/j.ajpath.2022.07.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/02/2022] [Accepted: 07/07/2022] [Indexed: 05/28/2023]
Abstract
Current imaging-based cancer screening approaches provide useful but limited prognostic information. Complementary to existing screening tests, cell-free DNA-based multicancer early detection (MCED) tests account for cancer biology [manifested through circulating tumor allele fraction (cTAF)], which could inform prognosis and help assess the cancer's clinical significance. This review discusses the factors affecting circulating tumor DNA (ctDNA) levels and cTAF, and their correlation with the cancer's clinical significance. Furthermore, it discusses the influence of cTAF on MCED test performance, which could help inform prognosis. Clinically significant cancers show higher ctDNA levels quantified by cTAF than indolent phenotype cancers within each stage. This is because more frequent mitosis and cell death combined with increased trafficking of cell-free DNA into circulation leads to greater vascularization and depth of tumor invasion. cTAF has been correlated with biomarkers for cancer aggressiveness and overall survival; cancers with lower cTAF had better survival when compared with cancers as determined by the higher cTAF and Surveillance, Epidemiology, and End Results-based survival for that cancer type at each stage. MCED-detected cancers in case-control studies had comparable survival to Surveillance, Epidemiology, and End Results-based survival at each stage. Because many MCED tests use ctDNA as an analyte, cTAF could provide a common metric to compare performance. The prognostic value of cTAF may allow MCED tests to preferentially detect clinically significant cancers at early stages when outcomes are favorable and this may avoid overdiagnosis.
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Affiliation(s)
- Joerg Bredno
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
| | - Oliver Venn
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California.
| | - Xiaoji Chen
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
| | - Peter Freese
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
| | - Joshua J Ofman
- GRAIL, LLC, a subsidiary of Illumina, Inc., Menlo Park, California
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Haseltine JM, Offin M, Flynn JR, Zhang Z, Lebow ES, Aziz K, Makhnin A, Eichholz J, Lim LP, Li M, Isbell JM, Gomez DR, Li BT, Rimner A. Tumor volume as a predictor of cell free DNA mutation detection in advanced non-small cell lung cancer. Transl Lung Cancer Res 2022; 11:1578-1590. [PMID: 36090640 PMCID: PMC9459617 DOI: 10.21037/tlcr-22-164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/14/2022] [Indexed: 01/13/2023]
Abstract
Background Cell free DNA (cfDNA) is an exciting biomarker with applications across the cancer care continuum. Determinants of cfDNA shedding dynamics remain an active research area. We performed a detailed analysis of tumor volume and factors associated with detection of cfDNA mutations. Methods Patients with advanced non-small cell lung cancers (NSCLCs) were prospectively enrolled on a plasma biomarker protocol. Next generation sequencing (NGS) was performed using a validated, bias-corrected, hybrid-capture panel assay of lung cancer-associated genes. Volume of tumor in different subsites and total tumor volume were determined through manual volume delineation using PET/CT and brain magnetic resonance imaging (MRI) imaging. The primary endpoint was detection of cfDNA mutation; secondary endpoints were overall survival (OS) and variant allele frequency (VAF). Results There were 110 patients included, 78 of whom had at least one mutation detected. Median total tumor volume for the entire cohort, patients with mutation detected, and patients with no mutation detected were 66 mL (range, 2-1,383 mL), 76 mL (range, 5-1,383 mL), and 45 mL (range, 2-460 mL), respectively (P=0.002; mutation detected vs. not). The optimal total tumor volume threshold to predict increased probability of mutation detection was 65 mL (P=0.006). Total tumor volume greater than 65 mL was a significant predictor of mutation detection on multivariate analysis (OR: 4.30, P=0.003). Significant predictors of OS were age (HR: 1.04, P=0.002), detection of cfDNA mutation (HR: 2.11, P=0.024), and presence of bone metastases (HR: 1.66, P=0.047). Conclusions Total tumor volume greater than 65 mL was associated with cfDNA mutation detection in patients with advanced NSCLC.
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Affiliation(s)
- Justin M. Haseltine
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Offin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jessica R. Flynn
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zhigang Zhang
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily S. Lebow
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Khaled Aziz
- Department of Radiation Oncology, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Alex Makhnin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jordan Eichholz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lee P. Lim
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - Mark Li
- Resolution Bioscience, Agilent Technologies, Kirkland, WA, USA
| | - James M. Isbell
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel R. Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andreas Rimner
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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Pesta M, Shetti D, Kulda V, Knizkova T, Houfkova K, Bagheri MS, Svaton M, Polivka J. Applications of Liquid Biopsies in Non-Small-Cell Lung Cancer. Diagnostics (Basel) 2022; 12:1799. [PMID: 35892510 PMCID: PMC9330570 DOI: 10.3390/diagnostics12081799] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/17/2022] Open
Abstract
The concept of liquid biopsy as an analysis tool for non-solid tissue carried out for the purpose of providing information about solid tumors was introduced approximately 20 years ago. Additional to the detection of circulating tumor cells (CTCs), the liquid biopsy approach quickly included the analysis of circulating tumor DNA (ctDNA) and other tumor-derived markers such as circulating cell-free RNA or extracellular vesicles. Liquid biopsy is a non-invasive technique for detecting multiple cancer-associated biomarkers that is easy to obtain and can reflect the characteristics of the entire tumor mass. Currently, ctDNA is the key component of the liquid biopsy approach from the point of view of the prognosis assessment, prediction, and monitoring of the treatment of non-small-cell lung cancer (NSCLC) patients. ctDNA in NSCLC patients carries variants or rearrangements that drive carcinogenesis, such as those in EGFR, KRAS, ALK, or ROS1. Due to advances in pharmacology, these variants are the subject of targeted therapy. Therefore, the detection of these variants has gained attention in clinical medicine. Recently, methods based on qPCR (ddPCR, BEAMing) and next-generation sequencing (NGS) are the most effective approaches for ctDNA analysis. This review addresses various aspects of the use of liquid biopsy with an emphasis on ctDNA as a biomarker in NSCLC patients.
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Affiliation(s)
- Martin Pesta
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Dattatrya Shetti
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Vlastimil Kulda
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic;
| | - Tereza Knizkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Katerina Houfkova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 323 00 Plzen, Czech Republic; (D.S.); (T.K.); (K.H.)
| | - Mahyar Sharif Bagheri
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
| | - Martin Svaton
- Department of Pneumology and Phthisiology, Faculty of Medicine in Pilsen, Charles University, University Hospital in Pilsen, E. Benese 13, 301 00 Plzen, Czech Republic;
| | - Jiri Polivka
- Department of Histology, Faculty of Medicine in Pilsen, Charles University, Karlovarska 48, 301 66 Plzen, Czech Republic; (M.S.B.); (J.P.)
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Doculara L, Trahair TN, Bayat N, Lock RB. Circulating Tumor DNA in Pediatric Cancer. Front Mol Biosci 2022; 9:885597. [PMID: 35647029 PMCID: PMC9133724 DOI: 10.3389/fmolb.2022.885597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
The measurement of circulating tumor DNA (ctDNA) has gained increasing prominence as a minimally invasive tool for the detection of cancer-specific markers in plasma. In adult cancers, ctDNA detection has shown value for disease-monitoring applications including tumor mutation profiling, risk stratification, relapse prediction, and treatment response evaluation. To date, there are ctDNA tests used as companion diagnostics for adult cancers and it is not understood why the same cannot be said about childhood cancer, despite the marked differences between adult and pediatric oncology. In this review, we discuss the current understanding of ctDNA as a disease monitoring biomarker in the context of pediatric malignancies, including the challenges associated with ctDNA detection in liquid biopsies. The data and conclusions from pediatric cancer studies of ctDNA are summarized, highlighting treatment response, disease monitoring and the detection of subclonal disease as applications of ctDNA. While the data from retrospective studies highlight the potential of ctDNA, large clinical trials are required for ctDNA analysis for routine clinical use in pediatric cancers. We outline the requirements for the standardization of ctDNA detection in pediatric cancers, including sample handling and reproducibility of results. With better understanding of the advantages and limitations of ctDNA and improved detection methods, ctDNA analysis may become the standard of care for patient monitoring in childhood cancers.
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Affiliation(s)
- Louise Doculara
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Toby N. Trahair
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children’s Hospital, Randwick, NSW, Australia
| | - Narges Bayat
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
| | - Richard B. Lock
- Children’s Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Sydney, NSW, Australia
- School of Women’s and Children’s Health, UNSW Sydney, Sydney, NSW, Australia
- University of New South Wales Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia
- *Correspondence: Richard B. Lock,
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Magnusson JM, Ricksten A, Dellgren G, Wasslavik C, Nordén R, Westin J, Boehmer J. Cell‐free DNA as a biomarker after lung transplantation: A proof‐of‐concept study. Immun Inflamm Dis 2022; 10:e620. [PMID: 35478446 PMCID: PMC9017613 DOI: 10.1002/iid3.620] [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: 10/23/2021] [Revised: 02/28/2022] [Accepted: 03/21/2022] [Indexed: 11/12/2022] Open
Abstract
Background Methods Results Conclusions
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Affiliation(s)
- Jesper M. Magnusson
- Transplant Institute Sahlgrenska University Hospital Gothenburg Sweden
- Department of Respiratory Medicine, Institute of Medicine, Sahlgrenska University Hospital University of Gothenburg Gothenburg Sweden
| | - Anne Ricksten
- Department of Clinical Chemistry Sahlgrenska University Hospital Gothenburg Sweden
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital University of Gothenburg Gothenburg Sweden
| | - Göran Dellgren
- Transplant Institute Sahlgrenska University Hospital Gothenburg Sweden
- Department of Cardiothoracic Surgery, Institute of Medicine, Sahlgrenska University Hospital University of Gothenburg Gothenburg Sweden
| | - Carina Wasslavik
- Department of Clinical Chemistry Sahlgrenska University Hospital Gothenburg Sweden
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska University Hospital University of Gothenburg Gothenburg Sweden
| | - Rickard Nordén
- Department of Clinical Microbiology Sahlgrenska University Hospital, Region Västra Götaland Gothenburg Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska University Hospital University of Gothenburg Gothenburg Sweden
| | - Johan Westin
- Department of Clinical Microbiology Sahlgrenska University Hospital, Region Västra Götaland Gothenburg Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska University Hospital University of Gothenburg Gothenburg Sweden
| | - Jens Boehmer
- Department of Pediatrics, Queen Silvias Children's Hospital Sahlgrenska University Hospital Gothenburg Sweden
- Department of Cardiology, Institute of Medicine, Sahlgrenska University Hospital University of Gothenburg Gothenburg Sweden
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Nagarajappa C, Rangappa SS, Balakrishna S. Oxidative nucleic acid damage as a biomarker for preeclampsia. J OBSTET GYNAECOL 2022; 42:1853-1856. [PMID: 35468029 DOI: 10.1080/01443615.2022.2048362] [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: 10/18/2022]
Abstract
Recent studies have reported that nucleic acid oxidation is elevated in preeclampsia. Furthermore, it is known that products of nucleic acid oxidation are eventually removed through the urine. The aim of this study was to check whether urine can be used as a non-invasive specimen to analyse nucleic acid oxidation in preeclampsia. We carried out a case-control study by enrolling preeclamptic pregnant (n = 31) and normotensive pregnant (n = 31) women. Urine samples from the study participants were collected and the levels of oxidised guanine species (a common product of nucleic acid oxidation) were determined by ELISA method. The urinary levels of oxidised guanine species were significantly higher in the preeclamptic pregnant group compared to the normotensive pregnant group (p = 0.001). The results were also analysed after stratifying the preeclamptic group in terms of severity and gestational age of onset. A significant difference was observed in both mild (p = 0.005) and severe preeclampsia (p = 0.01). However, a significant difference was observed only in the late onset (p = 0.001) and not in the early onset preeclampsia (p = 0.56). The results of this study show that oxidised guanine level is elevated in the urine of preeclamptic pregnant women. IMPACT STATEMENTWhat is already known on this subject? Nucleic acid oxidation is elevated in preeclampsia. However, the utility of urine (a non-invasive specimen) to analyse nucleic acid oxidation is not known.What do the results of this study add? This study shows that the levels of oxidised guanine (a marker of nucleic acid oxidation) are elevated in the urine of preeclamptic women.What are the implications of these findings for clinical practice and/or further research? Urinary levels of oxidised guanine may be developed as a non-invasive biomarker for preeclampsia.
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Affiliation(s)
- Chandrakala Nagarajappa
- Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
| | | | - Sharath Balakrishna
- Department of Cell Biology and Molecular Genetics, Sri Devaraj Urs Academy of Higher Education and Research, Kolar, Karnataka, India
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Kmeťová K, Čonka J, Janko J, Illés J, Uličná O, Celec P. Plasma DNA and deoxyribonuclease are associated with glucose metabolism in healthy mice. PLoS One 2022; 17:e0265099. [PMID: 35385497 PMCID: PMC8985945 DOI: 10.1371/journal.pone.0265099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/23/2022] [Indexed: 12/05/2022] Open
Abstract
It is currently unknown why obesity leads in some patients to prediabetes and metabolic syndrome. Microinflammation potentially caused by extracellular DNA is supposed to be involved. The aim of this cross-sectional study in healthy mice was to analyze the association between plasma extracellular DNA and glucose metabolism. Fasting glycemia and insulin were measured in healthy adult female mice that subsequently underwent an oral glucose tolerance test. Indices of glucose metabolism and insulin sensitivity were calculated. DNA was isolated from plasma and quantified fluorometrically. Deoxyribonuclease (DNase) activity of plasma was measured using the single radial enzyme diffusion method. Fasting glycemia correlated negatively with both, extracellular DNA and DNase (r = -0.44 and r = -0.32, respectively). DNase was associated positively with the incremental area under curve (r = 0.35), while extracellular DNA correlated negatively with total area under curve of glycemia during oral glucose tolerance test (r = -0.34). Measures of insulin sensitivity were found to be associated with neither extracellular DNA, nor DNase. The hypothesis of an association of low DNase with increased fasting glucose was partially proved. Surprisingly, low extracellular DNA is associated with higher fasting glucose and lower glucose tolerance in mice. As novel therapeutic targets for prediabetes and metabolic syndrome are highly needed, this study provides novel unexpected associations within the limitations of the focus on physiological variability as it was conducted on healthy mice. The causality of these associations should be proved in further interventional experiments.
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Affiliation(s)
- Katarína Kmeťová
- Faculty of Medicine, Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Jozef Čonka
- Faculty of Medicine, Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Jakub Janko
- Faculty of Medicine, Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Júlia Illés
- Faculty of Medicine, Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
| | - Oľga Uličná
- Faculty of Medicine, Pharmacobiochemical Laboratory of Third Department of Internal Medicine, Comenius University, Bratislava, Slovakia
| | - Peter Celec
- Faculty of Medicine, Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
- Faculty of Medicine, Institute of Pathophysiology, Comenius University, Bratislava, Slovakia
- Faculty of Natural Sciences, Department of Molecular Biology, Comenius University, Bratislava, Slovakia
- * E-mail:
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Colmenares R, Álvarez N, Barrio S, Martínez-López J, Ayala R. The Minimal Residual Disease Using Liquid Biopsies in Hematological Malignancies. Cancers (Basel) 2022; 14:1310. [PMID: 35267616 PMCID: PMC8909350 DOI: 10.3390/cancers14051310] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/23/2022] [Accepted: 02/27/2022] [Indexed: 12/02/2022] Open
Abstract
The study of cell-free DNA (cfDNA) and other peripheral blood components (known as "liquid biopsies") is promising, and has been investigated especially in solid tumors. Nevertheless, it is increasingly showing a greater utility in the diagnosis, prognosis, and response to treatment of hematological malignancies; in the future, it could prevent invasive techniques, such as bone marrow (BM) biopsies. Most of the studies about this topic have focused on B-cell lymphoid malignancies; some of them have shown that cfDNA can be used as a novel way for the diagnosis and minimal residual monitoring of B-cell lymphomas, using techniques such as next-generation sequencing (NGS). In myelodysplastic syndromes, multiple myeloma, or chronic lymphocytic leukemia, liquid biopsies may allow for an interesting genomic representation of the tumor clones affecting different lesions (spatial heterogeneity). In acute leukemias, it can be helpful in the monitoring of the early treatment response and the prediction of treatment failure. In chronic lymphocytic leukemia, the evaluation of cfDNA permits the definition of clonal evolution and drug resistance in real time. However, there are limitations, such as the difficulty in obtaining sufficient circulating tumor DNA for achieving a high sensitivity to assess the minimal residual disease, or the lack of standardization of the method, and clinical studies, to confirm its prognostic impact. This review focuses on the clinical applications of cfDNA on the minimal residual disease in hematological malignancies.
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Affiliation(s)
- Rafael Colmenares
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
| | - Noemí Álvarez
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Santiago Barrio
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
| | - Joaquín Martínez-López
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
| | - Rosa Ayala
- Hematology Department, Hospital Universitario 12 de Octubre, Instituto de Investigación Sanitaria Imas12, 28041 Madrid, Spain; (R.C.); (N.Á.); (S.B.); (J.M.-L.)
- Hematological Malignancies Clinical Research Unit, CNIO, 28029 Madrid, Spain
- Department of Medicine, Complutense University of Madrid, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Instituto Carlos III, 28029 Madrid, Spain
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Ozturk EA, Caner A. Liquid Biopsy for Promising Non-invasive Diagnostic Biomarkers in Parasitic Infections. Acta Parasitol 2022; 67:1-17. [PMID: 34176040 DOI: 10.1007/s11686-021-00444-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 06/16/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Liquid biopsy refers to the sampling and molecular analysis of body fluids such as blood, saliva, and urine in contrast to conventional tissue biopsies. Liquid biopsy approach can offer powerful non-invasive biomarkers (circulating markers) for diagnosis and monitoring treatment response of a variety of diseases, including parasitic infections. METHODS In this review, we concentrate on cell-free DNA (cfDNA), microRNA (miRNA), and exosomes in the published literature. RESULTS Considering the high prevalence and severity of parasitic infections worldwide, circulating biomarkers can provide a new insight into the diagnosis and prognosis of parasites in the near future. Moreover, identifying and characterizing parasite- or host-derived circulating markers are important for a better understanding of the pathogenesis of parasite infection and host-parasite relationship at the molecular level. Profiling of biomarkers for parasitic diseases is a promising potential field, though further studies and optimization strategies are required, both in vitro and in vivo. CONCLUSION In this review, we discuss three approaches in the liquid biopsy including circulating cfDNA, miRNAs, and exosomes for diagnosis and evaluation of parasites and summarize circulating biomarkers in non-invasive samples during parasitic infections.
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Affiliation(s)
- Eylem Akdur Ozturk
- Department of Parasitology, Çukurova University Faculty of Medicine, Adana, Turkey
| | - Ayse Caner
- Department of Parasitology, Ege University Faculty of Medicine, 35100, Izmir, Turkey.
- Cancer Research Center, Ege University, Izmir, Turkey.
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Jiang M, Zhou H, Jiang S, Yu H. A Review of Circulating Tumor DNA in the Diagnosis and Monitoring of Esophageal Cancer. Med Sci Monit 2022; 28:e934106. [PMID: 35210388 PMCID: PMC8886734 DOI: 10.12659/msm.934106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
Circulating tumor DNA (ctDNA) is a type of cell-free DNA released by tumor cells after necrosis and apoptosis, and it can be actively secreted by tumor cells. Since ctDNA is derived from various tumor sites, it can provide far more comprehensive genomic and epigenomic information than a single-site biopsy. Therefore, ctDNA can overcome tumor heterogeneity, which is the major limitation of a traditional tissue biopsy approach. Noninvasive ctDNA assays allow continuous real-time monitoring of the molecular status of cancers. Recently, ctDNA assays have been widely used in clinical practice, including cancer diagnosis, evaluation of therapeutic efficacy and prognosis, and monitoring of relapse and metastasis. Although ctDNA shows a high diagnostic performance in advanced esophageal cancer, it is far from satisfactory for early diagnosis of esophageal cancer. Monitoring the dynamic changes of ctDNA is beneficial for the evaluation of therapeutic efficacy and prediction of early recurrence in esophageal cancer. It is necessary to establish standards for individualized ctDNA detection in the evaluation of treatment response and surveillance of esophageal cancer and to develop clinical practice guideline for the systemic treatment of patients with "ctDNA recurrence." This review aims to provide an update on the role of ctDNA in the diagnosis and monitoring of esophageal cancer.
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Affiliation(s)
- Min Jiang
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Huilin Zhou
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Su Jiang
- Department of Rehabilitation, Taizhou People’s Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
| | - Hong Yu
- Department of Pathology, Taizhou People’s Hospital, Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, Jiangsu, PR China
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35
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Edwards RL, Menteer J, Lestz RM, Baxter-Lowe LA. Cell-free DNA as a solid-organ transplant biomarker: technologies and approaches. Biomark Med 2022; 16:401-415. [PMID: 35195028 DOI: 10.2217/bmm-2021-0968] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
High-quality biomarkers that detect emergent graft damage and/or rejection after solid-organ transplantation offer new opportunities to improve post-transplant monitoring, allow early therapeutic intervention and facilitate personalized patient management. Donor-derived cell-free DNA (DD-cfDNA) is a particularly exciting minimally invasive biomarker because it has the potential to be quantitative, time-sensitive and cost-effective. Increased DD-cfDNA has been associated with graft damage and rejection episodes. Efforts are underway to further improve sensitivity and specificity. This review summarizes the procedures used to process and detect DD-cfDNA, measurement of DD-cfDNA in clinical transplantation, approaches for improving sensitivity and specificity and long-term prospects as a transplant biomarker to supplement traditional organ monitoring and invasive biopsies.
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Affiliation(s)
- Rebecca L Edwards
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Jondavid Menteer
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Cardiology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Rachel M Lestz
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA.,Division of Nephrology, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA
| | - Lee Ann Baxter-Lowe
- Department of Pathology & Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, CA 90027, USA.,Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
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36
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Heitz F, Lakis S, Harter P, Heikaus S, Sehouli J, Talwar J, Menon R, Ataseven B, Bertrand M, Schneider S, Mariotti E, Bommert M, Müller JN, Prader S, Leenders F, Hengsbach A, Gloeckner C, Braicu EI, Heukamp LC, du Bois A, Heuckmann JM. Cell-free tumor DNA, CA125 and HE4 for the objective assessment of tumor burden in patients with advanced high-grade serous ovarian cancer. PLoS One 2022; 17:e0262770. [PMID: 35130283 PMCID: PMC8820624 DOI: 10.1371/journal.pone.0262770] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 01/04/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The present prospective study aimed at determining the impact of cell-free tumor DNA (ct-DNA), CA125 and HE4 from blood and ascites for quantification of tumor burden in patients with advanced high-grade serous epithelial ovarian cancer (EOC). METHODS Genomic DNA was extracted from tumor FFPE and ct-DNA from plasma before surgery and on subsequent post-surgical days. Extracted DNA was subjected to hybrid-capture based next generation sequencing. Blood and ascites were sampled before surgery and on subsequent post-surgical days. 20 patients (10 undergoing complete resection (TR0), 10 undergoing incomplete resection (TR>0)) were included. RESULTS The minor allele frequency (MAF) of TP53 mutations in ct-DNA of all patients with TR0 decreased significantly, compared to only one patient with TR>0. It was not possible to distinguish between patients with TR0 and patients with TR>0, using CA125 and HE4 from blood and ascites. CONCLUSIONS Based upon the present findings, ct-DNA assessment in patients with high-grade serous EOC might help to better determine disease burden compared to standard tumor markers. Further studies should prospectively evaluate whether this enhancement of accuracy can help to optimize management of patients with EOC.
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Affiliation(s)
- Florian Heitz
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
- Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Corporate member of Freie Universität Berlin, Berlin, Germany
- Berlin Institute of Health, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Sotirios Lakis
- NEO New Oncology GmbH, Cologne, Germany
- ULTIVUE, Segrate Milan, Italy
| | - Philipp Harter
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | - Sebastian Heikaus
- Evangelische Kliniken Essen-Mitte, Center for Pathology, Essen, Germany
| | - Jalid Sehouli
- Department for Gynecology with the Center for Oncologic Surgery Charité Campus Virchow-Klinikum, Charité–Universitätsmedizin Berlin, Berlin, Germany
- Corporate member of Freie Universität Berlin, Berlin, Germany
- Berlin Institute of Health, Humboldt-Universität zu Berlin, Berlin, Germany
| | | | | | - Beyhan Ataseven
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, Munich, Germany
| | - Miriam Bertrand
- NEO New Oncology GmbH, Cologne, Germany
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Stephanie Schneider
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | | | - Mareike Bommert
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | | | - Sonia Prader
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
- Department of Obstetrics and Gynecology, General Hospital (SABES-ASDAA), Brixen–Bres-sanone, Italy
- Department of Obstetrics and Gynecology, Innsbruck Medical University, Inns-bruck, Austria
| | | | - Alexandra Hengsbach
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
| | | | | | | | - Andreas du Bois
- Evangelische Kliniken Essen-Mitte Klinik für Gynäkologie und gynäkologische Onkologie, Essen, Germany
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Cisneros-Villanueva M, Hidalgo-Pérez L, Rios-Romero M, Cedro-Tanda A, Ruiz-Villavicencio CA, Page K, Hastings R, Fernandez-Garcia D, Allsopp R, Fonseca-Montaño MA, Jimenez-Morales S, Padilla-Palma V, Shaw JA, Hidalgo-Miranda A. Cell-free DNA analysis in current cancer clinical trials: a review. Br J Cancer 2022; 126:391-400. [PMID: 35027672 PMCID: PMC8810765 DOI: 10.1038/s41416-021-01696-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 12/06/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Cell-free DNA (cfDNA) analysis represents a promising method for the diagnosis, treatment selection and clinical follow-up of cancer patients. Although its general methodological feasibility and usefulness has been demonstrated, several issues related to standardisation and technical validation must be addressed for its routine clinical application in cancer. In this regard, most cfDNA clinical applications are still limited to clinical trials, proving its value in several settings. In this paper, we review the current clinical trials involving cfDNA/ctDNA analysis and highlight those where it has been useful for patient stratification, treatment follow-up or development of novel approaches for early diagnosis. Our query included clinical trials, including the terms 'cfDNA', 'ctDNA', 'liquid biopsy' AND 'cancer OR neoplasm' in the FDA and EMA public databases. We identified 1370 clinical trials (FDA = 1129, EMA = 241) involving liquid-biopsy analysis in cancer. These clinical trials show promising results for the early detection of cancer and confirm cfDNA as a tool for real-time monitoring of acquired therapy resistance, accurate disease-progression surveillance and improvement of treatment, situations that result in a better quality of life and extended overall survival for cancer patients.
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Affiliation(s)
- M Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - L Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - M Rios-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - A Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - C A Ruiz-Villavicencio
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - K Page
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Hastings
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - D Fernandez-Garcia
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - R Allsopp
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - M A Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - S Jimenez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - V Padilla-Palma
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico
| | - J A Shaw
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - A Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico, Periférico Sur No. 4809, Col. Arenal Tepepan, Delegación Tlalpan, Ciudad de Mexico, 14610, Mexico City, Mexico.
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38
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Boniface CT, Spellman PT. Blood, Toil, and Taxoteres: Biological Determinates of Treatment-Induce ctDNA Dynamics for Interpreting Tumor Response. Pathol Oncol Res 2022; 28:1610103. [PMID: 35665409 PMCID: PMC9160182 DOI: 10.3389/pore.2022.1610103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 04/29/2022] [Indexed: 11/23/2022]
Abstract
Collection and analysis of circulating tumor DNA (ctDNA) is one of the few methods of liquid biopsy that measures generalizable and tumor specific molecules, and is one of the most promising approaches in assessing the effectiveness of cancer care. Clinical assays that utilize ctDNA are commercially available for the identification of actionable mutations prior to treatment and to assess minimal residual disease after treatment. There is currently no clinical ctDNA assay specifically intended to monitor disease response during treatment, partially due to the complex challenge of understanding the biological sources of ctDNA and the underlying principles that govern its release. Although studies have shown pre- and post-treatment ctDNA levels can be prognostic, there is evidence that early, on-treatment changes in ctDNA levels are more accurate in predicting response. Yet, these results also vary widely among cohorts, cancer type, and treatment, likely due to the driving biology of tumor cell proliferation, cell death, and ctDNA clearance kinetics. To realize the full potential of ctDNA monitoring in cancer care, we may need to reorient our thinking toward the fundamental biological underpinnings of ctDNA release and dissemination from merely seeking convenient clinical correlates.
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Affiliation(s)
- Christopher T. Boniface
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
| | - Paul T. Spellman
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, United States
- *Correspondence: Christopher T. Boniface, ; Paul T. Spellman,
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39
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Deville KA, Seifert ME. Biomarkers of alloimmune events in pediatric kidney transplantation. Front Pediatr 2022; 10:1087841. [PMID: 36741087 PMCID: PMC9895094 DOI: 10.3389/fped.2022.1087841] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/28/2022] [Indexed: 01/21/2023] Open
Abstract
Alloimmune events such as the development of de novo donor-specific antibody (dnDSA), T cell-mediated rejection (TCMR), and antibody-mediated rejection (ABMR) are the primary contributors to kidney transplant failure in children. For decades, a creatinine-based estimated glomerular filtration rate (eGFR) has been the non-invasive gold standard biomarker for detecting clinically significant alloimmune events, but it suffers from low sensitivity and specificity, especially in smaller children and older allografts. Many clinically "stable" children (based on creatinine) will have alloimmune events known as "subclinical acute rejection" (based on biopsy) that merely reflect the inadequacy of creatinine-based estimates for alloimmune injury rather than a distinct phenotype from clinical rejection with allograft dysfunction. The poor biomarker performance of creatinine leads to many unnecessary surveillance and for-cause biopsies that could be avoided by integrating non-invasive biomarkers with superior sensitivity and specificity into current clinical paradigms. In this review article, we will present and appraise the current state-of-the-art in monitoring for alloimmune events in pediatric kidney transplantation. We will first discuss the current clinical standards for assessing the presence of alloimmune injury and predicting long-term outcomes. We will review principles of biomarker medicine and the application of comprehensive metrics to assess the performance of a given biomarker against the current gold standard. We will then highlight novel blood- and urine-based biomarkers (with special emphasis on pediatric biomarker studies) that have shown superior diagnostic and prognostic performance to the current clinical standards including creatinine-based eGFR. Finally, we will review some of the barriers to translating this research and implementing emerging biomarkers into common clinical practice, and present a transformative approach to using multiple biomarker platforms at different times to optimize the detection and management of critical alloimmune events in pediatric kidney transplant recipients.
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Affiliation(s)
- Kyle A Deville
- Division of Pediatric Nephrology, Department of Pediatrics, University of Alabama Heersink School of Medicine, Birmingham, AL, United States
| | - Michael E Seifert
- Division of Pediatric Nephrology, Department of Pediatrics, University of Alabama Heersink School of Medicine, Birmingham, AL, United States
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40
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Sharma M, Verma RK, Kumar S, Kumar V. Computational challenges in detection of cancer using cell-free DNA methylation. Comput Struct Biotechnol J 2021; 20:26-39. [PMID: 34976309 PMCID: PMC8669313 DOI: 10.1016/j.csbj.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.
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Key Words
- Cancer heterogeneity
- Cell free DNA
- Computation
- DMP, Differentially methylated base position
- DMR, Differentially methylated regions
- Diagnosis
- HELP-seq, HpaII-tiny fragment Enrichment by Ligation-mediated PCR sequencing
- MBD-seq, Methyl-CpG Binding Domain Protein Capture Sequencing
- MCTA-seq, Methylated CpG tandems amplification and sequencing
- MSCC, Methylation Sensitive Cut Counting
- MSRE, methylation sensitive restriction enzymes
- MeDIP-seq, Methylated DNA Immunoprecipitation Sequencing
- RRBS, Reduced-Representation Bisulfite Sequencing
- WGBS, Whole Genome Bisulfite Sequencing
- cfDNA, cell free DNA
- ctDNA, circulating tumor DNA
- dPCR, digital polymerase chain reaction
- ddMCP, droplet digital methylation-specific PCR
- ddPCR, droplet digital polymerase chain reaction
- scCGI, methylated CGIs at single cell level
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Affiliation(s)
- Madhu Sharma
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Rohit Kumar Verma
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Sunil Kumar
- Department of Surgical oncology, All India Institute of Medical sciences, New Delhi 110029, India
| | - Vibhor Kumar
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
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41
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Mika T, Thomson J, Nilius-Eliliwi V, Vangala D, Baraniskin A, Wulf G, Klein-Scory S, Schroers R. Quantification of cell-free DNA for the analysis of CD19-CAR-T cells during lymphoma treatment. Mol Ther Methods Clin Dev 2021; 23:539-550. [PMID: 34853800 PMCID: PMC8606297 DOI: 10.1016/j.omtm.2021.10.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/21/2021] [Accepted: 10/26/2021] [Indexed: 11/25/2022]
Abstract
Chimeric antigen receptor (CAR)-T cells are increasingly used for the treatment of hematologic malignancies. Treatment success relies highly upon sufficient expansion of CAR-T effector cells. Accordingly, longitudinal quantification of CAR-T cells during therapy is clinically important. Techniques to quantify CAR-T cells in patient blood samples are based on flow cytometry and PCR. However, cellular kinetics of CAR-T cells are very complex and under current investigation. In this study, feasibility of CAR-T cell quantification by cell-free DNA (cfDNA) was analyzed. cfDNA isolated from 74 blood samples of 12 patients during lymphoma treatment with the anti-CD19 CAR-T cell product axicabtagene ciloleucel (axi-cel) were analyzed. Concentrations of cfDNA specific for the CAR-T gene construct (cfCAR-DNA) and a reference gene were quantified by a newly designed digital-droplet PCR (ddPCR) assay. Detection and quantification of cfCAR-DNA was feasible and reliable for all patients included. Relative quantification of cfCAR-DNA compared to a reference gene, suitable for genomic DNA analysis, was heterogeneous in treatment responders and non-responders. In contrast, parallel analyses of cfCAR-DNA and reference cfDNA in a patient-specific approach gave insight into active lymphoma killing and treatment responses. In summary, plasma cfDNA determination in lymphoma patients is a promising tool for future clinical decision making.
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42
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Schobers G, Koeck R, Pellaers D, Stevens SJC, Macville MVE, Paulussen ADC, Coonen E, van den Wijngaard A, de Die-Smulders C, de Wert G, Brunner HG, Zamani Esteki M. Liquid biopsy: state of reproductive medicine and beyond. Hum Reprod 2021; 36:2824-2839. [PMID: 34562078 PMCID: PMC8523207 DOI: 10.1093/humrep/deab206] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 08/06/2021] [Indexed: 01/23/2023] Open
Abstract
Liquid biopsy is the process of sampling and analyzing body fluids, which enables non-invasive monitoring of complex biological systems in vivo. Liquid biopsy has myriad applications in health and disease as a wide variety of components, ranging from circulating cells to cell-free nucleic acid molecules, can be analyzed. Here, we review different components of liquid biopsy, survey state-of-the-art, non-invasive methods for detecting those components, demonstrate their clinical applications and discuss ethical considerations. Furthermore, we emphasize the importance of artificial intelligence in analyzing liquid biopsy data with the aim of developing ethically-responsible non-invasive technologies that can enhance individualized healthcare. While previous reviews have mainly focused on cancer, this review primarily highlights applications of liquid biopsy in reproductive medicine.
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Affiliation(s)
- Gaby Schobers
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rebekka Koeck
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Dominique Pellaers
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Merryn V E Macville
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Aimée D C Paulussen
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Edith Coonen
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Center for Reproductive Medicine, Maastricht University Medical Centre+, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Arthur van den Wijngaard
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands
| | - Christine de Die-Smulders
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Guido de Wert
- Faculty of Health, Medicine and Life Sciences, Department of Health, Ethics and Society, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Masoud Zamani Esteki
- Department of Clinical Genetics, Maastricht University Medical Centre+, Maastricht, The Netherlands.,Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
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Morais M, Pinto DM, Machado JC, Carneiro S. ctDNA on liquid biopsy for predicting response and prognosis in locally advanced rectal cancer: A systematic review. Eur J Surg Oncol 2021; 48:218-227. [PMID: 34511270 DOI: 10.1016/j.ejso.2021.08.034] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 08/31/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The management of locally advanced rectal cancer (LARC) requires a multidisciplinary approach, with an increasing interest for non-operative strategies. Liquid biopsy for obtaining circulating tumor DNA (ctDNA) can provide information on neoadjuvant chemoradiotherapy (nCRT) pathological response and cancer-specific prognosis, and therefore might be a promising guide for these treatments. METHODS A systematic review of the studies available in literature has been performed to assess the role of ctDNA as a predictive and prognostic biomarker in LARC patients. RESULTS We retrieved 21 publications, of which 17 full-text articles and 4 abstracts. Results have been labelled into two groups: predictive and prognostic. Data about the usefulness of liquid biopsy in this setting is still inconclusive. However, baseline higher levels of longer fragments of cell-free DNA and integrity index, tumor-specific mutations and certain methylated genes could predict non-responders. Also, undetectable baseline ctDNA and decrease of common rectal cancer mutations throughout treatment (dynamic monitoring) were predictive factors of pathological complete response. The continuous detection of ctDNA in different timepoints of treatment (minimal residual disease) was consistently associated with worse prognosis. CONCLUSIONS ctDNA is a promising biomarker that could assist predicting treatment response to nCRT and prognosis in patients with LARC. The ideal methods and timings for the liquid biopsy still have to be defined.
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Affiliation(s)
- Marina Morais
- Surgery Department, Hospital Pedro Hispano, Matosinhos, Portugal; Surgery Department, Faculty of Medicine, University of Porto, Porto, Portugal.
| | - Diogo Melo Pinto
- Surgery Department, Hospital Pedro Hispano, Matosinhos, Portugal
| | - José Carlos Machado
- I3S - Institute for Research and Innovation in Health and IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal; Pathology Department, Faculty of Medicine, University of Porto, Porto, Portugal
| | - Silvestre Carneiro
- Surgery Department, Faculty of Medicine, University of Porto, Porto, Portugal; Surgery Department, Centro Hospitalar de São João, Porto, Portugal
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44
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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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45
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Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A. Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA. Front Genet 2021; 12:671057. [PMID: 34386036 PMCID: PMC8353442 DOI: 10.3389/fgene.2021.671057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.
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Affiliation(s)
- Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, United States
| | - A. Patrick McDeed
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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Le Guin CHD, Bornfeld N, Bechrakis NE, Jabbarli L, Richly H, Lohmann DR, Zeschnigk M. Early detection of metastatic uveal melanoma by the analysis of tumor-specific mutations in cell-free plasma DNA. Cancer Med 2021; 10:5974-5982. [PMID: 34291585 PMCID: PMC8419753 DOI: 10.1002/cam4.4153] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 12/16/2022] Open
Abstract
Background Eye salvaging therapy of malignant melanomas of the uvea can preserve the eye in most cases, but still about half of patients die from metastatic disease. Previous analyses of cell‐free DNA from plasma had shown detectable levels of tumor‐specific GNAQ/GNA11 mutations in patients with the clinical diagnosis of progressive disease. However, data on the time span that elapses from the detection of ctDNA in plasma to the clinical detection of metastases (diagnostic lead time) are missing. Methods We examined 135 patients with uveal melanoma. Cell‐free DNA was isolated from a total of 807 blood samples which were taken over a period of up to 41 months and analyzed for the presence of GNAQ/GNA11 mutations by deep amplicon sequencing. Results Twenty‐one of the 135 patients developed metastases or recurrence. A ctDNA signal was identified in the plasma of 17 of the 21 patients. In 10 patients, this ctDNA signal preceded the clinical diagnosis of metastasis by 2–10 months. In 10 other patients, a ctDNA signal was only detected in samples obtained shortly before or after radiotherapy. The presence of a ctDNA signal in 16 of the remaining 125 patients was linked to clinical manifestation of metastases (n = 14) or tumor recurrence (n = 2) with a sensitivity and specificity of 80% and 96%, respectively. Conclusion Detection of ctDNA in plasma can provide a diagnostic lead time over the clinical diagnosis of metastases or tumor recurrence. Longer lead times are to be expected if intervals between sampling are shortened.
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Affiliation(s)
- Claudia H D Le Guin
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Norbert Bornfeld
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nikolaos E Bechrakis
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Leyla Jabbarli
- Department of Ophthalmology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Heike Richly
- Department of Medical Oncology, West German Cancer Center, University Duisburg-Essen, Essen, Germany
| | - Dietmar R Lohmann
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Michael Zeschnigk
- Institute of Human Genetics, University Hospital Essen, University Duisburg-Essen, Essen, Germany
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47
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The landscape of copy number variations in classical Hodgkin lymphoma: a joint KU Leuven and LYSA study on cell-free DNA. Blood Adv 2021; 5:1991-2002. [PMID: 33843986 DOI: 10.1182/bloodadvances.2020003039] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/02/2021] [Indexed: 12/20/2022] Open
Abstract
The low abundance of Hodgkin/Reed-Sternberg (HRS) cells in lymph node biopsies in classical Hodgkin lymphoma (cHL) complicates the analysis of somatic genetic alterations in HRS cells. As circulating cell-free DNA (cfDNA) contains circulating tumor DNA (ctDNA) from HRS cells, we prospectively collected cfDNA from 177 patients with newly diagnosed, mostly early-stage cHL in a monocentric study at Leuven, Belgium (n = 59) and the multicentric BREACH study by Lymphoma Study Association (n = 118). To catalog the patterns and frequencies of genomic copy number aberrations (CNAs), cfDNA was sequenced at low coverage (0.26×), and data were analyzed with ichorCNA to yield read depth-based copy number profiles and estimated clonal fractions in cfDNA. At diagnosis, the cfDNA concentration, estimated clonal fraction, and ctDNA concentration were significantly higher in cHL cases than controls. More than 90% of patients exhibited CNAs in cfDNA. The most frequent gains encompassed 2p16 (69%), 5p14 (50%), 12q13 (50%), 9p24 (50%), 5q (44%), 17q (43%), 2q (41%). Losses mostly affected 13q (57%), 6q25-q27 (55%), 4q35 (50%), 11q23 (44%), 8p21 (43%). In addition, we identified loss of 3p13-p26 and of 12q21-q24 and gain of 15q21-q26 as novel recurrent CNAs in cHL. At diagnosis, ctDNA concentration was associated with advanced disease, male sex, extensive nodal disease, elevated erythrocyte sedimentation rate, metabolic tumor volume, and HRS cell burden. CNAs and ctDNA rapidly diminished upon treatment initiation, and persistence of CNAs was associated with increased probability of relapse. This study endorses the development of ctDNA as gateway to the HRS genome and substrate for early disease response evaluation.
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48
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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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49
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Koval AP, Blagodatskikh KA, Kushlinskii NE, Shcherbo DS. The Detection of Cancer Epigenetic Traces in Cell-Free DNA. Front Oncol 2021; 11:662094. [PMID: 33996585 PMCID: PMC8118693 DOI: 10.3389/fonc.2021.662094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/12/2021] [Indexed: 12/23/2022] Open
Abstract
Nucleic acid fragments found in blood circulation originate mostly from dying cells and carry signs pointing to specific features of the parental cell types. Deciphering these clues may be transformative for numerous research and clinical applications but strongly depends on the development and implementation of robust analytical methods. Remarkable progress has been achieved in the reliable detection of sequence alterations in cell-free DNA while decoding epigenetic information from methylation and fragmentation patterns requires more sophisticated approaches. This review discusses the currently available strategies for detecting and analyzing the epigenetic marks in the liquid biopsies.
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Affiliation(s)
- Anastasia P Koval
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Konstantin A Blagodatskikh
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Nikolay E Kushlinskii
- Laboratory of Clinical Biochemistry, N.N. Blokhin Cancer Research Medical Center of Oncology, Moscow, Russia
| | - Dmitry S Shcherbo
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Moscow, Russia
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50
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Andargie TE, Tsuji N, Seifuddin F, Jang MK, Yuen PS, Kong H, Tunc I, Singh K, Charya A, Wilkins K, Nathan S, Cox A, Pirooznia M, Star RA, Agbor-Enoh S. Cell-free DNA maps COVID-19 tissue injury and risk of death and can cause tissue injury. JCI Insight 2021; 6:147610. [PMID: 33651717 PMCID: PMC8119224 DOI: 10.1172/jci.insight.147610] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/02/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION The clinical course of coronavirus 2019 (COVID-19) is heterogeneous, ranging from mild to severe multiorgan failure and death. In this study, we analyzed cell-free DNA (cfDNA) as a biomarker of injury to define the sources of tissue injury that contribute to such different trajectories. METHODS We conducted a multicenter prospective cohort study to enroll patients with COVID-19 and collect plasma samples. Plasma cfDNA was subject to bisulfite sequencing. A library of tissue-specific DNA methylation signatures was used to analyze sequence reads to quantitate cfDNA from different tissue types. We then determined the correlation of tissue-specific cfDNA measures to COVID-19 outcomes. Similar analyses were performed for healthy controls and a comparator group of patients with respiratory syncytial virus and influenza. RESULTS We found markedly elevated levels and divergent tissue sources of cfDNA in COVID-19 patients compared with patients who had influenza and/or respiratory syncytial virus and with healthy controls. The major sources of cfDNA in COVID-19 were hematopoietic cells, vascular endothelium, hepatocytes, adipocytes, kidney, heart, and lung. cfDNA levels positively correlated with COVID-19 disease severity, C-reactive protein, and D-dimer. cfDNA profile at admission identified patients who subsequently required intensive care or died during hospitalization. Furthermore, the increased cfDNA in COVID-19 patients generated excessive mitochondrial ROS (mtROS) in renal tubular cells in a concentration-dependent manner. This mtROS production was inhibited by a TLR9-specific antagonist. CONCLUSION cfDNA maps tissue injury that predicts COVID-19 outcomes and may mechanistically propagate COVID-19–induced tissue injury. FUNDING Intramural Targeted Anti–COVID-19 grant, NIH.
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Affiliation(s)
- Temesgen E Andargie
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA.,Department of Biology, Howard University, Washington DC, USA
| | - Naoko Tsuji
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | | | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Peter St Yuen
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | - Ilker Tunc
- Bioinformatics and Computation Core, NHLBI, Maryland, USA
| | - Komudi Singh
- Bioinformatics and Computation Core, NHLBI, Maryland, USA
| | - Ananth Charya
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA
| | | | - Steven Nathan
- Advanced Lung Disease and Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia, USA
| | - Andrea Cox
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Robert A Star
- Renal Diagnostics and Therapeutics Unit, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), NIH, Bethesda, Maryland, USA
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation (GRAfT) and Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute (NHLBI), NIH, Bethesda, Maryland, USA.,Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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