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Saikia J, Malik PS, Kumar S, Jain D, Madan K, Bharati SJ, Deo S, Kumar S. Can cell-free DNA (cfDNA) in pleural lavage serve as a predictive and prognostic biomarker among surgically treated Stage I-III a nonsmall cell lung cancer (NSCLC)? A pilot study. J Surg Oncol 2024; 129:1224-1234. [PMID: 38436618 DOI: 10.1002/jso.27610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/16/2024] [Accepted: 02/11/2024] [Indexed: 03/05/2024]
Abstract
BACKGROUND AND OBJECTIVES The role of cell-free DNA (cfDNA) in operable nonsmall cell lung cancer (NSCLC) is unclear. This study was aimed to evaluate the feasibility for identification of cfDNA in pleural lavage fluid and its correlation with plasma in resectable NSCLCs. METHODS Consecutively resected NSCLCs were evaluated for cfDNA levels in preoperative plasma (PLS1), intraoperative pleural-lavage (PLV) and postoperative (at 1 month) plasma sample (PLS2). CfDNA was isolated and measured quantitatively by qPCR in a TaqMan probe-detection approach using the human β-actin gene as the amplifying target. RESULTS All (n = 34) except one were negative for malignant cells in PLV cytology. CfDNA could be isolated from all the three samples (PLS1, PLV, and PLS2) successfully in each patient. The median cfDNA levels in PLS1, PLV and PLS2 were 118 ng/mL (IQR 61-158), 167 ng/mL (IQR 59.9-179.9) and 103 ng/mL (IQR 66.5-125.4) respectively. The median follow-up was 34.1 months (IQR 25.2-41.6). A significant overall-survival (OS) and disease-free survival (DFS) were recorded for patients with cfDNA level cut-offs at 125, 170, and 100 ng/mL, respectively for PLS1, PLV, and PLS2. Patients with raised cfDNA in PLS1 (>125 ng/mL) and PLV (>170 ng/mL) had significantly poorer 2-year OS, p = 0.005 and p = 0.012, respectively. The hazards (OS) were also higher for those with raised cfDNA in PLV (HR = 5.779, 95% CI = 1.162-28.745, p = 0.032). PLV (>170 ng/mL) had increased pleural recurrences (p = 0.021) and correlated significantly with poorer DFS at 2-years (p = 0.001) with increased hazards (HR = 9.767, 95% CI = 2.098-45.451, p = 0.004). Multivariable analysis suggested higher cfDNA in PLV as a poor prognostic factor for both OS and DFS. CONCLUSIONS Among patients with operable NSCLC, it is feasible to identify cfDNA in pleural lavage and correlate PLV cfDNA with pleural recurrences and outcomes.
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Affiliation(s)
- Jyoutishman Saikia
- Department of Surgical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Prabhat S Malik
- Department of Medical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sachin Kumar
- Department of Medical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Department of Pulmonary Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sachidanand Jee Bharati
- Department of Oncoanaesthesia, DR.BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Suryanarayana Deo
- Department of Surgical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Kumar
- Department of Surgical Oncology, DR.BRA-IRCH, All India Institute of Medical Sciences, New Delhi, India
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Wu G, Song M, Wang K, Cui T, Jiao Z, Ji L, Gao X, Wang J, Liu T, Xia X, Fang H, Guan Y, Yi X. DELFMUT: duplex sequencing-oriented depth estimation model for stable detection of low-frequency mutations. Brief Bioinform 2023; 24:bbad277. [PMID: 37539831 DOI: 10.1093/bib/bbad277] [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: 03/12/2023] [Revised: 06/29/2023] [Accepted: 07/13/2023] [Indexed: 08/05/2023] Open
Abstract
Duplex sequencing technology has been widely used in the detection of low-frequency mutations in circulating tumor deoxyribonucleic acid (DNA), but how to determine the sequencing depth and other experimental parameters to ensure the stable detection of low-frequency mutations is still an urgent problem to be solved. The mutation detection rules of duplex sequencing constrain not only the number of mutated templates but also the number of mutation-supportive reads corresponding to each forward and reverse strand of the mutated templates. To tackle this problem, we proposed a Depth Estimation model for stable detection of Low-Frequency MUTations in duplex sequencing (DELFMUT), which models the identity correspondence and quantitative relationships between templates and reads using the zero-truncated negative binomial distribution without considering the sequences composed of bases. The results of DELFMUT were verified by real duplex sequencing data. In the case of known mutation frequency and mutation detection rule, DELFMUT can recommend the combinations of DNA input and sequencing depth to guarantee the stable detection of mutations, and it has a great application value in guiding the experimental parameter setting of duplex sequencing technology.
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Affiliation(s)
- Guiying Wu
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Mengmeng Song
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Ke Wang
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tianyu Cui
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Zicong Jiao
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Liyan Ji
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Xuan Gao
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Jiayin Wang
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Tao Liu
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Xuefeng Xia
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Huan Fang
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
| | - Yanfang Guan
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
- School of Computer Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Xin Yi
- Geneplus-Beijing Institute, Beijing 102206, P. R. China
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Berezina TA, Berezin AE. Cell-free DNA as a plausible biomarker of chronic kidney disease. Epigenomics 2023; 15:879-890. [PMID: 37791402 DOI: 10.2217/epi-2023-0255] [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] [Indexed: 10/05/2023] Open
Abstract
Circulating cell-free DNA (cf-DNA) is released from dead and/or apoptotic leukocytes and due to neutrophil extracellular traps contributing to an inflammatory response. Previous clinical studies have reported that the peak concentrations and dynamic changes of cf-DNA may be used as a noninvasive biomarker of worsening kidney function as well as a guide to the management of kidney allograft rejection. We hypothesized that the pattern and dynamic changes of cf-DNA might be a plausible predictive biomarker for patients at risk of chronic kidney disease (CKD), including individuals with type 2 diabetes mellitus, heart failure, cardiovascular disease and established CKD. Along with it, pre- and posthemodialysis levels of serum cf-DNA appear to be a independent predictor for all-cause mortality in patients with end-stage kidney disease.
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Affiliation(s)
- Tetiana A Berezina
- VitaCenter, Department of Internal Medicine and Nephrology, Zaporozhye, 69000, Ukraine
| | - Alexander E Berezin
- Paracelsus Medical University, Department of Internal Medicine II, Division of Cardiology, Salzburg, 5020, Austria
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Paweletz CP, Heavey GA, Kuang Y, Durlacher E, Kheoh T, Chao RC, Spira AI, Leventakos K, Johnson ML, Ignatius Ou SH, Riely GJ, Anderes K, Yang W, Christensen JG, Jänne PA. Early Changes in Circulating Cell-Free KRAS G12C Predict Response to Adagrasib in KRAS Mutant Non-Small Cell Lung Cancer Patients. Clin Cancer Res 2023; 29:3074-3080. [PMID: 37279096 PMCID: PMC10527102 DOI: 10.1158/1078-0432.ccr-23-0795] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/25/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023]
Abstract
PURPOSE Non-invasive monitoring of circulating tumor DNA (ctDNA) has the potential to be a readily available measure for early prediction of clinical response. Here, we report on early ctDNA changes of KRAS G12C in a Phase 2 trial of adagrasib in patients with advanced, KRAS G12C-mutant lung cancer. EXPERIMENTAL DESIGN We performed serial droplet digital PCR (ddPCR) and plasma NGS on 60 KRAS G12C-mutant patients with lung cancer that participated in cohort A of the KRYSTAL-1 clinical trial. We analyzed the change in ctDNA at 2 specific intervals: Between cycles 1 and 2 and at cycle 4. Changes in ctDNA were compared with clinical and radiographic response. RESULTS We found that, in general, a maximal response in KRAS G12C ctDNA levels could be observed during the initial approximately 3-week treatment period, well before the first scan at approximately 6 weeks. 35 patients (89.7%) exhibited a decrease in KRAS G12C cfDNA >90% and 33 patients (84.6%) achieved complete clearance by cycle 2. Patients with complete ctDNA clearance at cycle 2 showed an improved objective response rate (ORR) compared with patients with incomplete ctDNA clearance (60.6% vs. 33.3%). Furthermore, complete ctDNA clearance at cycle 4 was associated with an improved overall survival (14.7 vs. 5.4 months) and progression-free survival (HR, 0.3). CONCLUSIONS These results support using early plasma response of KRAS G12C assessed at approximately 3 weeks to anticipate the likelihood of a favorable objective clinical response.
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Affiliation(s)
- Cloud P. Paweletz
- Belfer Center of Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Grace A. Heavey
- Belfer Center of Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Yanan Kuang
- Belfer Center of Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115
| | - Emily Durlacher
- Lowe Center for Thoracic Oncology, Dana–Farber Cancer Institute, Boston, MA 02115
| | | | | | | | | | | | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, University of California-Irvine, , Orange, CA 92868
| | - Gregory J. Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, Weill Cornell Medical College, New York, NY 10065
| | | | | | | | - Pasi A. Jänne
- Belfer Center of Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA 02115
- Lowe Center for Thoracic Oncology, Dana–Farber Cancer Institute, Boston, MA 02115
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Lazar J, Antal-Szalmas P, Kurucz I, Ferenczi A, Jozsi M, Tornyi I, Muller M, Fekete JT, Lamont J, FitzGerald P, Gall-Debreceni A, Kadas J, Vida A, Tardieu N, Kieffer Y, Jullien A, Guergova-Kuras M, Hempel W, Kovacs A, Kardos T, Bittner N, Csanky E, Szilasi M, Losonczy G, Szondy K, Galffy G, Csada E, Szalontai K, Somfay A, Malka D, Cottu P, Bogos K, Takacs L. Large scale plasma proteome epitome profiling is an efficient tool for the discovery of cancer biomarkers. Mol Cell Proteomics 2023:100580. [PMID: 37211046 PMCID: PMC10319867 DOI: 10.1016/j.mcpro.2023.100580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 05/15/2023] [Accepted: 05/17/2023] [Indexed: 05/23/2023] Open
Abstract
Current proteomic technologies focus on the quantification of protein levels, while little effort is dedicated to the development of systems approaches to simultaneously monitor proteome variability and abundance. Protein variants may display different immunogenic epitopes detectable by monoclonal antibodies. Epitope variability results from alternative splicing, posttranslational modifications, processing, degradation, and complex formation and possess dynamically changing availability of interacting surface structures frequently serve as reachable epitopes, and often carry different functions. Thus, it is highly likely, that the presence of some of the accessible epitopes correlate with function under physiological and pathological conditions. To enable the exploration of the impact of protein variation on the immunogenic epitome first; here, we present a robust and analytically validated protein epitome profiling (PEP) technology for characterizing immunogenic epitopes of the plasma. To this end we prepared mAb libraries directed against the normalized human plasma proteome as a complex natural immunogen. Resulting hybridoma supernatants were selected for mAb production and the corresponding hybridomas were cloned. Monoclonal antibodies react with single epitopes, thus profiling with the libraries is expected to profile many epitopes which we define by the mimotopes, as we present here. Screening blood plasma samples from control subjects (n = 558) and cancer patients (n = 598) for merely 69 native epitopes displayed by 20 abundant plasma proteins resulted in distinct cancer-specific epitope panels that showed high accuracy (AUC 0.826-0.966) and specificity for lung, breast, and colon cancer. Deeper profiling (≈290 epitopes of approximately 100 proteins) showed unexpected granularity of the epitope-level expression data and detected neutral and lung-cancer associated epitopes of individual proteins. Biomarker epitope panels selected from a pool of 21 epitopes of 12 proteins were validated in independent clinical cohorts. The results demonstrate the value of PEP as a rich and thus far unexplored source of protein biomarkers with diagnostic potential.
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Affiliation(s)
- Jozsef Lazar
- Biosystems International Kft., Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary.
| | - Peter Antal-Szalmas
- University of Debrecen, Faculty of Medicine, Department of Laboratory Medicine, Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary
| | - Istvan Kurucz
- Biosystems International Kft., Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary
| | | | - Mihaly Jozsi
- Eötvös Loránd University, Department of Immunology and MTA-ELTE Complement Research Group, Department of Immunology, Budapest, Hungary
| | - Ilona Tornyi
- Biosystems Immunolab Zrt., Debrecen, Hungary; University of Debrecen, Faculty of Medicine, Department of Human Genetics, Debrecen, Hungary
| | | | | | - John Lamont
- Randox Laboratories Ltd., Crumlin, United Kingdom
| | | | | | - Janos Kadas
- Biosystems International Kft., Debrecen, Hungary
| | - Andras Vida
- University of Debrecen, Faculty of Medicine, Department of Laboratory Medicine, Debrecen, Hungary
| | | | | | | | | | | | | | - Tamas Kardos
- University of Debrecen, Faculty of Medicine, Department of Pulmonology, Debrecen, Hungary
| | - Nora Bittner
- University of Debrecen, Faculty of Medicine, Department of Pulmonology, Debrecen, Hungary
| | - Eszter Csanky
- Miskolc Semmelweis Hospital and University Hospital, Department of Pulmonology, Miskolc, Hungary
| | - Maria Szilasi
- University of Debrecen, Faculty of Medicine, Department of Pulmonology, Debrecen, Hungary
| | - Gyorgy Losonczy
- Semmelweis University, Faculty of Medicine, Department of Pulmonology, Budapest, Hungary
| | - Klara Szondy
- Semmelweis University, Faculty of Medicine, Department of Pulmonology, Budapest, Hungary
| | - Gabriella Galffy
- Semmelweis University, Faculty of Medicine, Department of Pulmonology, Budapest, Hungary
| | - Edit Csada
- Csongrád County Hospital of Chest Diseases, Deszk, Hungary
| | | | - Attila Somfay
- University of Szeged, Faculty of Medicine, Department of Pulmonology, Deszk, Hungary
| | - David Malka
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Paul Cottu
- Department of Medical Oncology, Institut Curie, Paris, France
| | - Krisztina Bogos
- National Koranyi Institute for Pulmonology, Budapest, Hungary
| | - Laszlo Takacs
- Biosystems International Kft., Debrecen, Hungary; Biosystems Immunolab Zrt., Debrecen, Hungary; University of Debrecen, Faculty of Medicine, Department of Human Genetics, Debrecen, Hungary; Biosystems International SAS, Evry, France.
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El Hejjioui B, Bouguenouch L, Melhouf MA, El Mouhi H, Bennis S. Clinical Evidence of Circulating Tumor DNA Application in Aggressive Breast Cancer. Diagnostics (Basel) 2023; 13:470. [PMID: 36766575 PMCID: PMC9914403 DOI: 10.3390/diagnostics13030470] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 12/28/2022] [Accepted: 01/01/2023] [Indexed: 01/31/2023] Open
Abstract
Breast cancer is clinically and biologically heterogeneous and is classified into different subtypes according to the molecular landscape of the tumor. Triple-negative breast cancer is a subtype associated with higher tumor aggressiveness, poor prognosis, and poor response to treatment. In metastatic breast cancer, approximately 6% to 10% of new breast cancer cases are initially staged IV (de novo metastatic disease). The number of metastatic recurrences is estimated to be 20-30% of all existing breast tumor cases, whereby the need to develop specific genetic markers to improve the prognosis of patients suffering from these deadly forms of breast cancer. As an alternative, liquid biopsy methods can minutely identify the molecular architecture of breast cancer, including aggressive forms, which provides new perspectives for more precise diagnosis and more effective therapeutics. This review aimed to summarize the current clinical evidence for the application of circulating tumor DNA in managing breast cancer by detailing the increased usefulness of this biomarker as a diagnostic, prognostic, monitoring, and surveillance marker for breast cancer.
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Affiliation(s)
- Brahim El Hejjioui
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Laila Bouguenouch
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | | | - Hind El Mouhi
- Department of Medical Genetics and Oncogenetics, HASSAN II University Hospital, Fez 30050, Morocco
| | - Sanae Bennis
- Biomedical and Translational Research Laboratory, Faculty of Medicine and Pharmacy, Sidi Mohamed Ben Abdellah University, Fez 30050, Morocco
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Műzes G, Bohusné Barta B, Szabó O, Horgas V, Sipos F. Cell-Free DNA in the Pathogenesis and Therapy of Non-Infectious Inflammations and Tumors. Biomedicines 2022; 10:biomedicines10112853. [PMID: 36359370 PMCID: PMC9687442 DOI: 10.3390/biomedicines10112853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/09/2022] Open
Abstract
The basic function of the immune system is the protection of the host against infections, along with the preservation of the individual antigenic identity. The process of self-tolerance covers the discrimination between self and foreign antigens, including proteins, nucleic acids, and larger molecules. Consequently, a broken immunological self-tolerance results in the development of autoimmune or autoinflammatory disorders. Immunocompetent cells express pattern-recognition receptors on their cell membrane and cytoplasm. The majority of endogenous DNA is located intracellularly within nuclei and mitochondria. However, extracellular, cell-free DNA (cfDNA) can also be detected in a variety of diseases, such as autoimmune disorders and malignancies, which has sparked interest in using cfDNA as a possible biomarker. In recent years, the widespread use of liquid biopsies and the increasing demand for screening, as well as monitoring disease activity and therapy response, have enabled the revival of cfDNA research. The majority of studies have mainly focused on the function of cfDNA as a biomarker. However, research regarding the immunological consequences of cfDNA, such as its potential immunomodulatory or therapeutic benefits, is still in its infancy. This article discusses the involvement of various DNA-sensing receptors (e.g., absent in melanoma-2; Toll-like receptor 9; cyclic GMP-AMP synthase/activator of interferon genes) in identifying host cfDNA as a potent danger-associated molecular pattern. Furthermore, we aim to summarize the results of the experimental studies that we recently performed and highlight the immunomodulatory capacity of cfDNA, and thus, the potential for possible therapeutic consideration.
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Affiliation(s)
| | | | | | | | - Ferenc Sipos
- Correspondence: ; Tel.: +36-20-478-0752; Fax: +36-1-266-0816
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The Overview of Perspectives of Clinical Application of Liquid Biopsy in Non-Small-Cell Lung Cancer. Life (Basel) 2022; 12:life12101640. [PMID: 36295075 PMCID: PMC9604747 DOI: 10.3390/life12101640] [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: 09/20/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 01/19/2023] Open
Abstract
The standard diagnostics procedure for non-small-cell lung cancer (NSCLC) requires a pathological evaluation of tissue samples obtained by surgery or biopsy, which are considered invasive sampling procedures. Due to this fact, re-sampling of the primary tumor at the moment of progression is limited and depends on the patient’s condition, even if it could reveal a mechanism of resistance to applied therapy. Recently, many studies have indicated that liquid biopsy could be provided for the noninvasive management of NSCLC patients who receive molecularly targeted therapies or immunotherapy. The liquid biopsy of neoplastic patients harbors small fragments of circulating-free DNA (cfDNA) and cell-free RNA (cfRNA) secreted to the circulation from normal cells, as well as a subset of tumor-derived circulating tumor cells (CTCs) or circulating tumor DNA (ctDNA). In NSCLC patients, a longitudinal assessment of genetic alterations in “druggable” genes in liquid biopsy might improve the follow-up of treatment efficacy and allow for the detection of an early progression before it is detectable in computed tomography or a clinical image. However, a liquid biopsy may be used to determine a variety of relevant molecular or genetic information for understanding tumor biology and its evolutionary trajectories. Thus, liquid biopsy is currently associated with greater hope for common diagnostic and clinical applications. In this review, we would like to highlight diagnostic challenges in the application of liquid biopsy into the clinical routine and indicate its implications on the metastatic spread of NSCLC or monitoring of personalized treatment regimens.
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Lee IK, Chang JP, Huang WC, Tai CH, Wu HT, Chi CH. Comparative of clinical performance between next-generation sequencing and standard blood culture diagnostic method in patients suffering from sepsis. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:845-852. [PMID: 35995673 DOI: 10.1016/j.jmii.2022.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/08/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Next-generation sequencing (NGS) is a massively unbiased sequencing technology. The objective of this study was to evaluate the performance of NGS-based approach in the detection of microorganisms from septic patients and compare with results of blood culture (BC). METHODS The observational and non-interventional study was conducted from April 2019 to August 2019. RESULTS A total of 96 sets of BC and 48 NGS results obtained from 48 septic patients were analyzed in this study. Thirty-two microorganisms (27 bacteria, 3 fungi and 2 viral) were detected by NGS in 23 (47.9%) patients; and 18 bacteria in 18 (37.5%) patients by BC. Exclusion of skin commensals, the positivity of NGS and BC was 62.5% and 14.5%, respectively (P < 0.001). Microorganisms identified by NGS demonstrated positive agreement with BC in 12 (25%) patients, including concordant results in 11 (22.9%) cases, and discrepancy results in 1 (2%). Of 11 patients with concordant results, 4 had additional microorganisms detected by NGS. NGS-positive but BC-negative was found in 9 (18.7%) patients. Using NGS, difficult-to-culture micro-organisms such as Pneumocystic jirovecii was identified in 2 patients, and Leptospira interrogans in one. Six (12.5%) patients with BC-positive but NGS-negative, whereas skin commensals were isolated in 4 (66.6%) cases. The number of patients that were positive by BC only increase from 29% to 47.9% when combining NGS and BC analyses (P = 0.033). CONCLUSIONS Our study support the advantage of NGS for the diagnosis of infecting microorganisms in sepsis, especially for microorganisms that are currently difficult or impossible to culture.
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Affiliation(s)
- Ing-Kit Lee
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan; School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Jen-Ping Chang
- School of Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Wen-Chi Huang
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Chien-Hsiang Tai
- Division of Infectious Diseases, Department of Internal Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung, Taiwan
| | - Huang-Tu Wu
- Joint Commission of Precision Medicine, Taipei, Taiwan
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Apurva, Kumar A, Dar GM, Sumayya Abdul Sattar R, Verma R, Mahajan B, Singh Saluja S. Molecular markers in cancer. Clin Chim Acta 2022; 532:95-114. [DOI: https:/doi.org/10.1016/j.cca.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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Admission Circulating Cell-Free DNA Levels as a Prognostic Factor in Pediatric Burns. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5004282. [PMID: 35722456 PMCID: PMC9200554 DOI: 10.1155/2022/5004282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 11/17/2022]
Abstract
Background Burn injuries in children are a major physical and psychological trauma, often a severe condition with long-term consequences. Current methods of assessing the extent of burn injuries on admission are inaccurate. Circulating cell-free DNA (cfDNA) is a potential marker of tissue damage that may be useful in burn care. Objective To explore the use of cfDNA admission levels as a prognostic marker of pediatric burn severity and outcome. Methods cfDNA levels of 38 pediatric burn patients (otherwise healthy) and 12 matched pediatric controls (minor elective surgery patients) admitted to our center were quantified by a direct fluorometric assay. Results We found significantly higher admission cfDNA levels in the patient group (median 724 ng/ml, range 44-4405), compared to the control group (median 423 ng/ml, range 206-970, Mann–Whitney, P = 0.03) and a significant difference between cfDNA levels of partial-thickness burns (median 590 ng/ml, range 44-2909) and full-thickness burns (median 2394 ng/ml, range 528-4405, Mann–Whitney, P = 0.01). We also found significant correlations between cfDNA levels and hospitalization duration (Spearman, R = 0.42, P < 0.01) and undergoing surgical procedures (Spearman, R = 0.40, P < 0.01). PICU admission did not correlate to cfDNA levels (Spearman, R = 0.14, P = NS). Discussion. Admission cfDNA levels may be a valuable objective tool for assessing the severity of pediatric burn injuries on admission, including correlations with the length of hospitalization and surgical burden. Conclusion Admission cfDNA levels may be a promising novel pediatric burn assessment method. Further investigation of cfDNA levels in healthy children standardized to age and larger cohorts are needed to establish cfDNA as a valuable prognostic factor for pediatric burn injury.
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Apurva, Kumar A, Mehdi G, Sumayya Abdul Sattar R, Verma R, Mahajan B, Singh Saluja S. Molecular markers in cancer. Clin Chim Acta 2022; 532:95-114. [DOI: 10.1016/j.cca.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/31/2022] [Accepted: 05/31/2022] [Indexed: 12/01/2022]
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Phung Q, Lin MJ, Xie H, Greninger AL. Fragment Size-Based Enrichment of Viral Sequences in Plasma Cell-Free DNA. J Mol Diagn 2022; 24:476-484. [PMID: 35569878 PMCID: PMC9127460 DOI: 10.1016/j.jmoldx.2022.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 12/09/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Sequencing of plasma cell-free DNA (cfDNA) is a promising milieu for broad-based cancer and infectious disease diagnostics. The performance of cfDNA sequencing for infectious disease diagnostics is chiefly limited by inadequate analytical sensitivity. The current study investigated whether the analytical sensitivity of cfDNA sequencing for viral diagnostics could be improved by selective sequencing of short cfDNA fragments, given prior observations of shorter fragment size distribution in microbial and cytomegalovirus-derived cfDNA compared with human-derived cfDNA. It shows that the shorter plasma cfDNA fragment size distribution is a general feature of multiple DNA viruses, including adenovirus [interquartile range (IQR), 87 to 165 bp], herpes simplex virus 2 (IQR, 114 to 195 bp), human herpesvirus 6 (IQR, 145 to 176 bp), and varicella zoster virus (IQR, 98 to 182 bp), compared with human (IQR, 148 to 178 bp). It was used to further optimize a size selection-based cfDNA sequencing method, demonstrating an enrichment of viral sequences up to 16.6-fold, with a median fold enrichment of 6.7×, 4.6×, 2.2×, and 10.3× for adenovirus, herpes simplex virus 2, human herpesvirus 6, and varicella zoster virus, respectively. These findings demonstrate a simple yet scalable method for enhanced detection of DNA viremia that maintains the unbiased nature of cfDNA sequencing.
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Affiliation(s)
- Quynh Phung
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington
| | - Michelle J Lin
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington
| | - Hong Xie
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington Medical Center, Seattle, Washington; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.
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14
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Gonda A, Zhao N, Shah JV, Siebert JN, Gunda S, Inan B, Kwon M, Libutti SK, Moghe PV, Francis NL, Ganapathy V. Extracellular Vesicle Molecular Signatures Characterize Metastatic Dynamicity in Ovarian Cancer. Front Oncol 2021; 11:718408. [PMID: 34868914 PMCID: PMC8637407 DOI: 10.3389/fonc.2021.718408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/29/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Late-stage diagnosis of ovarian cancer, a disease that originates in the ovaries and spreads to the peritoneal cavity, lowers 5-year survival rate from 90% to 30%. Early screening tools that can: i) detect with high specificity and sensitivity before conventional tools such as transvaginal ultrasound and CA-125, ii) use non-invasive sampling methods and iii) longitudinally significantly increase survival rates in ovarian cancer are needed. Studies that employ blood-based screening tools using circulating tumor-cells, -DNA, and most recently tumor-derived small extracellular vesicles (sEVs) have shown promise in non-invasive detection of cancer before standard of care. Our findings in this study show the promise of a sEV-derived signature as a non-invasive longitudinal screening tool in ovarian cancer. METHODS Human serum samples as well as plasma and ascites from a mouse model of ovarian cancer were collected at various disease stages. Small extracellular vesicles (sEVs) were extracted using a commercially available kit. RNA was isolated from lysed sEVs, and quantitative RT-PCR was performed to identify specific metastatic gene expression. CONCLUSION This paper highlights the potential of sEVs in monitoring ovarian cancer progression and metastatic development. We identified a 7-gene panel in sEVs derived from plasma, serum, and ascites that overlapped with an established metastatic ovarian carcinoma signature. We found the 7-gene panel to be differentially expressed with tumor development and metastatic spread in a mouse model of ovarian cancer. The most notable finding was a significant change in the ascites-derived sEV gene signature that overlapped with that of the plasma-derived sEV signature at varying stages of disease progression. While there were quantifiable changes in genes from the 7-gene panel in serum-derived sEVs from ovarian cancer patients, we were unable to establish a definitive signature due to low sample number. Taken together our findings show that differential expression of metastatic genes derived from circulating sEVs present a minimally invasive screening tool for ovarian cancer detection and longitudinal monitoring of molecular changes associated with progression and metastatic spread.
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Affiliation(s)
- Amber Gonda
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Nanxia Zhao
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Jay V. Shah
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Jake N. Siebert
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
- Rutgers-Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, United States
| | - Srujanesh Gunda
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Berk Inan
- School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ, United States
| | - Mijung Kwon
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Steven K. Libutti
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, United States
| | - Prabhas V. Moghe
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
- Department of Chemical and Biochemical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Nicola L. Francis
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
| | - Vidya Ganapathy
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, United States
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Alekseeva L, Mironova N. Role of Cell-Free DNA and Deoxyribonucleases in Tumor Progression. Int J Mol Sci 2021; 22:12246. [PMID: 34830126 PMCID: PMC8625144 DOI: 10.3390/ijms222212246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/30/2022] Open
Abstract
Many studies have reported an increase in the level of circulating cell-free DNA (cfDNA) in the blood of patients with cancer. cfDNA mainly comes from tumor cells and, therefore, carries features of its genomic profile. Moreover, tumor-derived cfDNA can act like oncoviruses, entering the cells of vulnerable organs, transforming them and forming metastatic nodes. Another source of cfDNA is immune cells, including neutrophils that generate neutrophil extracellular traps (NETs). Despite the potential eliminative effect of NETs on tumors, in some cases, their excessive generation provokes tumor growth as well as invasion. Considering both possible pathological contributions of cfDNA, as an agent of oncotransformation and the main component of NETs, the study of deoxyribonucleases (DNases) as anticancer and antimetastatic agents is important and promising. This review considers the pathological role of cfDNA in cancer development and the role of DNases as agents to prevent and/or prohibit tumor progression and the development of metastases.
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Affiliation(s)
| | - Nadezhda Mironova
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia;
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16
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Al Zoughbi W, Fox J, Beg S, Papp E, Hissong E, Ohara K, Keefer L, Sigouros M, Kane T, Bockelman D, Nichol D, Patchell E, Bareja R, Karandikar A, Alnajar H, Cerqueira G, Guthrie VB, Verner E, Manohar J, Greco N, Wilkes D, Tagawa S, Malbari MS, Holcomb K, Eng KW, Shah M, Altorki NK, Sboner A, Nanus D, Faltas B, Sternberg CN, Simmons J, Houvras Y, Molina AM, Angiuoli S, Elemento O, Mosquera JM. Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing. Oncologist 2021; 26:e1971-e1981. [PMID: 34286887 PMCID: PMC8571755 DOI: 10.1002/onco.13905] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Characterization of circulating tumor DNA (ctDNA) has been integrated into clinical practice. Although labs have standardized validation procedures to develop single locus tests, the efficacy of on-site plasma-based next-generation sequencing (NGS) assays still needs to be proved. MATERIALS AND METHODS In this retrospective study, we profiled DNA from matched tissue and plasma samples from 75 patients with cancer. We applied an NGS test that detects clinically relevant alterations in 33 genes and microsatellite instability (MSI) to analyze plasma cell-free DNA (cfDNA). RESULTS The concordance between alterations detected in both tissue and plasma samples was higher in patients with metastatic disease. The NGS test detected 77% of sequence alterations, amplifications, and fusions that were found in metastatic samples compared with 45% of those alterations found in the primary tumor samples (p = .00005). There was 87% agreement on MSI status between the NGS test and tumor tissue results. In three patients, MSI-high ctDNA correlated with response to immunotherapy. In addition, the NGS test revealed an FGFR2 amplification that was not detected in tumor tissue from a patient with metastatic gastric cancer, emphasizing the importance of profiling plasma samples in patients with advanced cancer. CONCLUSION Our validation experience of a plasma-based NGS assay advances current knowledge about translating cfDNA testing into clinical practice and supports the application of plasma assays in the management of oncology patients with metastatic disease. With an in-house method that minimizes the need for invasive procedures, on-site cfDNA testing supplements tissue biopsy to guide precision therapy and is entitled to become a routine practice. IMPLICATIONS FOR PRACTICE This study proposes a solution for decentralized liquid biopsy testing based on validation of a next-generation sequencing (NGS) test that detects four classes of genomic alterations in blood: sequence mutations (single nucleotide substitutions or insertions and deletions), fusions, amplifications, and microsatellite instability (MSI). Although there are reference labs that perform single-site comprehensive liquid biopsy testing, the targeted assay this study validated can be established locally in any lab with capacity to offer clinical molecular pathology assays. To the authors' knowledge, this is the first report that validates evaluating an on-site plasma-based NGS test that detects the MSI status along with common sequence alterations encountered in solid tumors.
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Affiliation(s)
- Wael Al Zoughbi
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Jesse Fox
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Shaham Beg
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Eniko Papp
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Erika Hissong
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
| | - Kentaro Ohara
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Laurel Keefer
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Michael Sigouros
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Troy Kane
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Daniel Bockelman
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Donna Nichol
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Emily Patchell
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
| | - Rohan Bareja
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | | | - Hussein Alnajar
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
| | | | | | - Ellen Verner
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Jyothi Manohar
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Noah Greco
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - David Wilkes
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Scott Tagawa
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | | | - Kevin Holcomb
- Department of Obstetrics and Gynecology, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Kenneth Wha Eng
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Manish Shah
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Nasser K. Altorki
- Division of Thoracic Surgery, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - David Nanus
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Bishoy Faltas
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- Department of Cell and Developmental Biology, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Cora N. Sternberg
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - John Simmons
- Personal Genome Diagnostics Inc.BaltimoreMarylandUSA
| | - Yariv Houvras
- Department of Surgery, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Ana M. Molina
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | | | - Olivier Elemento
- Institute for Computational Biomedicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell MedicineNew YorkNew YorkUSA
- The Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine and New York‐PresbyterianNew YorkNew YorkUSA
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Chae H, Sung PS, Choi H, Kwon A, Kang D, Kim Y, Kim M, Yoon SK. Targeted Next-Generation Sequencing of Plasma Cell-Free DNA in Korean Patients with Hepatocellular Carcinoma. Ann Lab Med 2021; 41:198-206. [PMID: 33063681 PMCID: PMC7591296 DOI: 10.3343/alm.2021.41.2.198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 05/17/2020] [Accepted: 09/19/2020] [Indexed: 01/22/2023] Open
Abstract
Background Hepatocellular carcinoma (HCC) is the second-most-common cause of cancer-related deaths worldwide, and an accurate and non-invasive biomarker for the early detection and monitoring of HCC is required. We assessed pathogenic variants of HCC driver genes in cell-free DNA (cfDNA) from HCC patients who had not undergone systemic therapy. Methods Plasma cfDNA was collected from 20 HCC patients, and deep sequencing was performed using a customized cfDNA next-generation sequencing panel, targeting the major HCC driver genes (TP53, CTNNB1, TERT) that incorporates molecular barcoding. Results In 13/20 (65%) patients, we identified at least one pathogenic variant of two major HCC driver genes (TP53 and CTNNB1), including 16 variants of TP53 and nine variants of CTNNB1. The TP53 and CTNNB1 variants showed low allele frequencies, with median values of 0.17% (range 0.06%–6.99%) and 0.07% (range 0.05%–0.96%), respectively. However, the molecular coverage of variants was sufficient, with median values of 5,543 (range 2,317–9,088) and 7,568 (range 2,400–9,633) for TP53 and CTNNB1 variants, respectively. Conclusions Our targeted DNA sequencing successfully identified low-frequency pathogenic variants in the cfDNA from HCC patients by achieving high coverage of unique molecular families. Our results support the utility of cfDNA analysis to identify somatic gene variants in HCC patients.
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Affiliation(s)
- Hyojin Chae
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Pil Soo Sung
- Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Hayoung Choi
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ahlm Kwon
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Yonggoo Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, College of Medicine, The Catholic University of Korea, Seoul, Korea.,Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Seung Kew Yoon
- Department of Internal Medicine, Seoul St. Mary's Hospital, The Catholic University Liver Research Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
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Ulrich B, Pradines A, Mazières J, Guibert N. Detection of Tumor Recurrence via Circulating Tumor DNA Profiling in Patients with Localized Lung Cancer: Clinical Considerations and Challenges. Cancers (Basel) 2021; 13:cancers13153759. [PMID: 34359659 PMCID: PMC8345193 DOI: 10.3390/cancers13153759] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 12/11/2022] Open
Abstract
Simple Summary Circulating tumor DNA is a novel biomarker with emerging uses in the clinical care of patients with cancer, including non-small-cell lung cancer. Already approved for use in various clinical settings in patients with metastatic non-small-cell lung cancer, recent research has focused on the ability of circulating tumor DNA to predict relapse of patients with localized disease after treatment with curative intent. Identifying patients at increased risk of relapse after treatment with curative intent remains challenging, but several groups have identified circulating tumor DNA kinetics as a potential means of aiding our risk stratification. Herein, we discuss current research that identifies longitudinal circulating tumor DNA kinetics as a highly sensitive and specific marker for relapse. Then, we identify important clinical considerations and challenges for moving forward with further studying and eventually using this biomarker for patients with localized disease in clinic. Abstract Approximately 30% of patients with non-small-cell lung cancer (NSCLC) present with localized/non-metastatic disease and are eligible for surgical resection or other “treatment with curative intent”. Due to the high prevalence of recurrence after treatment, adjuvant therapy is standard care for most patients. The effect of adjuvant chemotherapy is, however, modest, and new tools are needed to identify candidates for adjuvant treatments (chemotherapy, immunotherapy, or targeted therapies), especially since expanded lung cancer screening programs will increase the rate of patients detected with localized NSCLC. Circulating tumor DNA (ctDNA) has shown strong potential to detect minimal residual disease (MRD) and to guide adjuvant therapies. In this manuscript, we review the technical aspects and performances of the main ctDNA sequencing platforms (TRACERx, CAPP-seq) investigated in this purpose, and discuss the potential of this approach to guide or spare adjuvant therapies after definitive treatment of NSCLC.
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Affiliation(s)
- Bryan Ulrich
- Internal Medicine Department, Massachusetts General Hospital, Boston, MA 02114, USA;
| | - Anne Pradines
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (J.M.)
- Medical Laboratory, Claudius Regaud Institute, Toulouse University Cancer Institute (IUCT-O), 31100 Toulouse, France
| | - Julien Mazières
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (J.M.)
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France
| | - Nicolas Guibert
- Cancer Research Centre of Toulouse (CRCT), Inserm, National Scientific Research Centre (CNRS), 31100 Toulouse, France; (A.P.); (J.M.)
- Pulmonology Department, Hôpital Larrey, University Hospital of Toulouse, 31059 Toulouse, France
- Correspondence: ; Tel.: +33-567771836
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Abstract
Cell-free DNA (cfDNA) exists in plasma and can be measured by several techniques. It is now possible to differentiate donor-derived cfDNA (ddcfDNA) from recipient cfDNA in the plasma or urine of solid organ transplant recipients in the absence of donor and recipient genotyping. The assessment of ddcfDNA is being increasingly studied as a noninvasive means of identifying acute rejection (AR) in solid organ transplants, including subclinical AR. We herein review the literature on the correlation of ddcfDNA with AR in kidney transplantation. There have been at least 15 observational studies that have assessed ddcfDNA in urine or plasma using various methodologies with various thresholds for abnormality. Overall, elevated ddcfDNA indicates allograft injury as may occur with AR, infection, or acute tubular injury but may also be found in clinically stable patients with normal histology. Sensitivity is greater for antibody-mediated AR than for cell-mediated AR, and normal levels do not preclude significant cell-mediated rejection. Measurement of ddcfDNA is not a replacement for biopsy that remains the gold standard for diagnosing AR. Serial monitoring of stable patients may allow earlier detection of subclinical AR, but the efficacy of this approach remains to be established. Normal levels should not preclude planned protocol biopsies. There may be roles for following ddcfDNA levels to assess the adequacy of treatment of AR and to guide the intensity of immunosuppression in the individual patient. Randomized controlled trials are necessary to validate the benefit and cost-effectiveness for these various uses. No firm recommendations can be made at this time.
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20
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Laurenzana I, Trino S, Lamorte D, Girasole M, Dinarelli S, De Stradis A, Grieco V, Maietti M, Traficante A, Statuto T, Villani O, Musto P, Sgambato A, De Luca L, Caivano A. Analysis of Amount, Size, Protein Phenotype and Molecular Content of Circulating Extracellular Vesicles Identifies New Biomarkers in Multiple Myeloma. Int J Nanomedicine 2021; 16:3141-3160. [PMID: 33994784 PMCID: PMC8114829 DOI: 10.2147/ijn.s303391] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/11/2021] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Extracellular vesicles (EVs) are naturally secreted cellular lipid bilayer particles, which carry a selected molecular content. Owing to their systemic availability and their role in tumor pathogenesis, circulating EVs (cEVs) can be a valuable source of new biomarkers useful for tumor diagnosis, prognostication and monitoring. However, a precise approach for isolation and characterization of cEVs as tumor biomarkers, exportable in a clinical setting, has not been conclusively established. METHODS We developed a novel and laboratory-made procedure based on a bench centrifuge step which allows the isolation of serum cEVs suitable for subsequent characterization of their size, amount and phenotype by nanoparticle tracking analysis, microscopy and flow cytometry, and for nucleic acid assessment by digital PCR. RESULTS Applied to blood from healthy subjects (HSs) and tumor patients, our approach permitted from a small volume of serum (i) the isolation of a great amount of EVs enriched in small vesicles free from protein contaminants; (ii) a suitable and specific cell origin identification of EVs, and (iii) nucleic acid content assessment. In clonal plasma cell malignancy, like multiple myeloma (MM), our approach allowed us to identify specific MM EVs, and to characterize their size, concentration and microRNA content allowing significant discrimination between MM and HSs. Finally, EV associated biomarkers correlated with MM clinical parameters. CONCLUSION Overall, our cEV based procedure can play an important role in malignancy biomarker discovery and then in real-time tumor monitoring using minimal invasive samples. From a practical point of view, it is smart (small sample volume), rapid (two hours), easy (no specific expertise required) and requirements are widely available in clinical laboratories.
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Affiliation(s)
- Ilaria Laurenzana
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Stefania Trino
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Daniela Lamorte
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Marco Girasole
- Institute for the Study of the Structure of Matter, National Research Council (CNR), Rome, Italy
| | - Simone Dinarelli
- Institute for the Study of the Structure of Matter, National Research Council (CNR), Rome, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Vitina Grieco
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Maddalena Maietti
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Antonio Traficante
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Teodora Statuto
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Oreste Villani
- Hematology and Stem Cell Transplantation Unit, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Pellegrino Musto
- Hematology and Stem Cell Transplantation Unit, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Alessandro Sgambato
- Scientific Direction, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Luciana De Luca
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
| | - Antonella Caivano
- Laboratory of Clinical Research and Advanced Diagnostics, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, PZ, Italy
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Lee SH, Lee EH, Kim EY, Choi YJ, Cha YJ, Chang YS. Biomarkers and diagnostic tools for lung cancer. JOURNAL OF THE KOREAN MEDICAL ASSOCIATION 2021. [DOI: 10.5124/jkma.2021.64.1.66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths in developing to advanced countries worldwide. The incidence rate of lung cancer in Korea has been increasing steadily since 1997. Statistics show that in 2017 alone, the incidence and mortality rates for lung cancer were 52.7 and 34.8 per 100,000 people, respectively, accounting for the highest cause of cancer death in Korea. The process of accurately diagnosing lung cancer consists of several steps, starting with the discovery of pulmonary nodule(s) via a cancer screening test or various other methods followed by the collection of cells or tissues and the identification of target molecules. Thereafter, staging and the development of a therapeutic plan lead to improved clinical outcomes. After the completion of a pilot study, a nationwide lung cancer screening program was introduced in Korea; since 2019, this program has targeted population at high risk for lung cancer: men and women aged 54 to 74 years who had a smoking history of 30 pack-years or more. The frequency of detection of pulmonary nodules is increasing in proportion to the public interest in health and economic growth. In this review, we present diagnostic techniques and biomarkers that are widely used in the medical field in the hope that such information would benefit clinical practice.
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22
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Zhong Y, Xu F, Wu J, Schubert J, Li MM. Application of Next Generation Sequencing in Laboratory Medicine. Ann Lab Med 2021; 41:25-43. [PMID: 32829577 PMCID: PMC7443516 DOI: 10.3343/alm.2021.41.1.25] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/24/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
The rapid development of next-generation sequencing (NGS) technology, including advances in sequencing chemistry, sequencing technologies, bioinformatics, and data interpretation, has facilitated its wide clinical application in precision medicine. This review describes current sequencing technologies, including short- and long-read sequencing technologies, and highlights the clinical application of NGS in inherited diseases, oncology, and infectious diseases. We review NGS approaches and clinical diagnosis for constitutional disorders; summarize the application of U.S. Food and Drug Administration-approved NGS panels, cancer biomarkers, minimal residual disease, and liquid biopsy in clinical oncology; and consider epidemiological surveillance, identification of pathogens, and the importance of host microbiome in infectious diseases. Finally, we discuss the challenges and future perspectives of clinical NGS tests.
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Affiliation(s)
- Yiming Zhong
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
| | - Feng Xu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jinhua Wu
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Jeffrey Schubert
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
| | - Marilyn M. Li
- Department of Pathology & Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA,
USA
- Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA,
USA
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23
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Thakral D, Gupta R, Sahoo RK, Verma P, Kumar I, Vashishtha S. Real-Time Molecular Monitoring in Acute Myeloid Leukemia With Circulating Tumor DNA. Front Cell Dev Biol 2020; 8:604391. [PMID: 33363162 PMCID: PMC7759522 DOI: 10.3389/fcell.2020.604391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/21/2020] [Indexed: 02/06/2023] Open
Abstract
The clonal evolution of acute myeloid leukemia (AML), an oligoclonal hematological malignancy, is driven by a plethora of cytogenetic abnormalities, gene mutations, abnormal epigenetic patterns, and aberrant gene expressions. These alterations in the leukemic blasts promote clinically diverse manifestations with common characteristics of high relapse and drug resistance. Defining and real-time monitoring of a personalized panel of these predictive genetic biomarkers is rapidly being adapted in clinical setting for diagnostic, prognostic, and therapeutic decision-making in AML. A major challenge remains the frequency of invasive biopsy procedures that can be routinely performed for monitoring of AML disease progression. Moreover, a single-site biopsy is not representative of the tumor heterogeneity as it is spatially and temporally constrained and necessitates the understanding of longitudinal and spatial subclonal dynamics in AML. Hematopoietic cells are a major contributor to plasma cell-free DNA, which also contain leukemia-specific aberrations as the circulating tumor-derived DNA (ctDNA) fraction. Plasma cell-free DNA analysis holds immense potential as a minimally invasive tool for genomic profiling at diagnosis as well as clonal evolution during AML disease progression. With the technological advances and increasing sensitivity for detection of ctDNA, both genetic and epigenetic aberrations can be qualitatively and quantitatively evaluated. However, challenges remain in validating the utility of liquid biopsy tools in clinics, and universal recommendations are still awaited towards reliable diagnostics and prognostics. Here, we provide an overview on the scope of ctDNA analyses for prognosis, assessment of response to treatment and measurable residual disease, prediction of disease relapse, development of acquired resistance and beyond in AML.
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Affiliation(s)
- Deepshi Thakral
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Ranjit Kumar Sahoo
- Department of Medical Oncology, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Pramod Verma
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Indresh Kumar
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Sangeeta Vashishtha
- Laboratory Oncology Unit, Dr. BRA IRCH, All India Institute of Medical Sciences, New Delhi, India
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24
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Thakral D, Das N, Basnal A, Gupta R. Cell-free DNA for genomic profiling and minimal residual disease monitoring in Myeloma- are we there yet? AMERICAN JOURNAL OF BLOOD RESEARCH 2020; 10:26-45. [PMID: 32685257 PMCID: PMC7364270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Accepted: 06/11/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Multiple myeloma (MM), a plasma cell neoplasm, afflicts elder individuals accounting for 10% of hematologic malignancies. The MM plasma cells largely reside within the bone marrow niche and are accessible through an invasive bone marrow biopsy, which is challenging during serial monitoring of patients. In this setting, cell free DNA (cfDNA) may have a role to ascertain the molecular aberrations at diagnosis and in assessment of residual disease during therapy. The aim of this review was to explore the utility and current status of cfDNA in MM. METHOD PubMed was searched with terms including cell-free DNA, circulating-tumor DNA, Multiple Myeloma, diagnosis, genomic profiling, Minimal Residual Disease individually or in combination to shortlist the relevant studies. RESULT cfDNA serves as a non-invasive source of tumor-specific molecular biomarker, ctDNA that has immense potential in facilitating management of cancer patients. The mutation detection platforms for ctDNA include hybrid capture and ultra-deep sequencing. Hybrid capture allows full length gene sequencing for mutation and CNV detection. The disease progression can be monitored by profiling prognostic somatic copy number alterations by ultra-low pass whole genome sequencing of ctDNA cost-effectively. Evolution of both the laboratory protocols and bioinformatics tools may further improve the sensitivity of ctDNA detection for better disease management. Only a limited number of studies were available in MM exploring the potential utility of cfDNA. CONCLUSION In this review, we discuss the nuances and challenges associated with molecular evaluation of cfDNA and its potential role in diagnosis and monitoring of treatment response in MM.
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Affiliation(s)
- Deepshi Thakral
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Nupur Das
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Atul Basnal
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
| | - Ritu Gupta
- Laboratory Oncology Unit, Dr BR Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences New Delhi, India
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25
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Sugimori M, Sugimori K, Tsuchiya H, Suzuki Y, Tsuyuki S, Kaneta Y, Hirotani A, Sanga K, Tozuka Y, Komiyama S, Sato T, Tezuka S, Goda Y, Irie K, Miwa H, Miura Y, Ishii T, Kaneko T, Nagahama M, Shibata W, Nozaki A, Maeda S. Quantitative monitoring of circulating tumor DNA in patients with advanced pancreatic cancer undergoing chemotherapy. Cancer Sci 2020; 111:266-278. [PMID: 31746520 PMCID: PMC6942439 DOI: 10.1111/cas.14245] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 11/04/2019] [Accepted: 11/11/2019] [Indexed: 12/14/2022] Open
Abstract
According to cancer genome sequences, more than 90% of cases of pancreatic ductal adenocarcinoma (PDAC) harbor active KRAS mutations. Digital PCR (dPCR) enables accurate detection and quantification of rare mutations. We assessed the dynamics of circulating tumor DNA (ct-DNA) in patients with advanced PDAC undergoing chemotherapy using dPCR. KRAS G12/13 mutation was assayed by dPCR in 47 paired tissue- and ct-DNA samples. The 21 patients were subjected to quantitative ct-DNA monitoring at 4 to 8-week intervals during chemotherapy. KRAS mutation was detected in 45 of those 47 patients using tissue DNA. In the KRAS mutation-negative cases, next-generation sequencing revealed KRAS Q61K and NRAS Q61R mutations. KRAS mutation was detected in 23/45 cases using ct-DNA (liver or lung metastasis, 18/19; mutation allele frequency [MAF], 0.1%-31.7%; peritoneal metastasis, 3/9 [0.1%], locally advanced, 2/17 [0.1%-0.2%]). In the ct-DNA monitoring, the MAF value changed in concordance with the disease state. In the 6 locally advanced cases, KRAS mutation appeared concurrently with liver metastasis. Among the 6 cases with liver metastasis, KRAS mutation disappeared during the duration of stable disease or a partial response, and reappeared at the time of progressive disease. The median progression-free survival was longer in cases in which KRAS mutation disappeared after an initial course of chemotherapy than in those in which it was continuously detected (248.5 vs 50 days, P < .001). Therefore, ct-DNA monitoring enables continuous assessment of disease state and could have prognostic utility during chemotherapy.
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Affiliation(s)
- Makoto Sugimori
- Department of GastroenterologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Kazuya Sugimori
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Hiromi Tsuchiya
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Yoshimasa Suzuki
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Sho Tsuyuki
- Department of GastroenterologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Yoshihiro Kaneta
- Department of GastroenterologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Akane Hirotani
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Katsuyuki Sanga
- Department of GastroenterologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Yuichiro Tozuka
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Satoshi Komiyama
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Takeshi Sato
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Shun Tezuka
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Yoshihiro Goda
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Kuniyasu Irie
- Department of GastroenterologyYokohama City University Graduate School of MedicineYokohamaJapan
| | - Haruo Miwa
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Yuuki Miura
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Tomohiro Ishii
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Takashi Kaneko
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Masatsugu Nagahama
- Department of GastroenterologyShowa University Fujigaoka HospitalYokohamaJapan
| | - Wataru Shibata
- Department of GastroenterologyYokohama City University Graduate School of MedicineYokohamaJapan
- Division of Translational ResearchAdvanced Medical Research CenterYokohama City UniversityYokohamaJapan
| | - Akito Nozaki
- Gastroenterological CenterYokohama City University Medical CenterYokohamaJapan
| | - Shin Maeda
- Department of GastroenterologyYokohama City University Graduate School of MedicineYokohamaJapan
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26
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Zheng H, Wu X, Yin J, Wang S, Li Z, You C. Clinical applications of liquid biopsies for early lung cancer detection. Am J Cancer Res 2019; 9:2567-2579. [PMID: 31911847 PMCID: PMC6943362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 11/15/2019] [Indexed: 06/10/2023] Open
Abstract
Over the past decade, the clinical utility of liquid biopsies in lung cancer has drawn increasing attention. Having been successfully applied in targeted therapy for late stage lung cancer, liquid biopsies are being further investigated regarding their potential role for early detection of lung cancer. Novel biomarkers with high sensitivity and specificity are crucial for identifying patients at early stages as well as for monitoring high-risk populations. A variety of bodily fluids (such as plasma, serum, and sputum) and biomarkers (such as cfDNA, CTCs, gene methylation, and miRNA) have been investigated for their potential role in the diagnosis of lung cancer. In this review, we summarize recent advances in circulating biomarkers regarding the early detection of lung cancer and discuss their potential applications and challenges in clinical settings.
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Affiliation(s)
- Hao Zheng
- Department of Bioinformatics, Lianxi Biotech800 HuanHu Xier Road, Shanghai, China
- Department of Bioinformatics, Novo Vivo Inc435 Tasso St, Palo Alto, CA 94301, USA
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzheng Hospital, Second Military Medical UniversityShanghai, China
| | - Jie Yin
- Purdue University625 Agriculture Mall Dr, West Lafayette, IN 47907, USA
| | - Shuang Wang
- School of Informatics, Computing and Engineering, Indiana University BloomingtonBloomington, IN 47405, USA
- Institutes for Systems Genetics, West China HospitalChengdu, Sichuan, China
- Shanghai Putuo People’s Hospital, Tongji UniversityShanghai, China
- Department of Bioinformatics, Novo Vivo Inc435 Tasso St, Palo Alto, CA 94301, USA
| | - Zhi Li
- Department of Bioinformatics, Lianxi Biotech800 HuanHu Xier Road, Shanghai, China
| | - Changxuan You
- Department of Oncology, Medical Center for Overseas Patient, Nanfang Hospital, Southern Medical UniversityGuangzhou, China
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27
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Locke WJ, Guanzon D, Ma C, Liew YJ, Duesing KR, Fung KYC, Ross JP. DNA Methylation Cancer Biomarkers: Translation to the Clinic. Front Genet 2019; 10:1150. [PMID: 31803237 PMCID: PMC6870840 DOI: 10.3389/fgene.2019.01150] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 10/22/2019] [Indexed: 12/23/2022] Open
Abstract
Carcinogenesis is accompanied by widespread DNA methylation changes within the cell. These changes are characterized by a globally hypomethylated genome with focal hypermethylation of numerous 5’-cytosine-phosphate-guanine-3’ (CpG) islands, often spanning gene promoters and first exons. Many of these epigenetic changes occur early in tumorigenesis and are highly pervasive across a tumor type. This allows DNA methylation cancer biomarkers to be suitable for early detection and also to have utility across a range of areas relevant to cancer detection and treatment. Such tests are also simple in construction, as only one or a few loci need to be targeted for good test coverage. These properties make cancer-associated DNA methylation changes very attractive for development of cancer biomarker tests with substantive clinical utility. Across the patient journey from initial detection, to treatment and then monitoring, there are several points where DNA methylation assays can inform clinical practice. Assays on surgically removed tumor tissue are useful to determine indicators of treatment resistance, prognostication of outcome, or to molecularly characterize, classify, and determine the tissue of origin of a tumor. Cancer-associated DNA methylation changes can also be detected with accuracy in the cell-free DNA present in blood, stool, urine, and other biosamples. Such tests hold great promise for the development of simple, economical, and highly specific cancer detection tests suitable for population-wide screening, with several successfully translated examples already. The ability of circulating tumor DNA liquid biopsy assays to monitor cancer in situ also allows for the ability to monitor response to therapy, to detect minimal residual disease and as an early biomarker for cancer recurrence. This review will summarize existing DNA methylation cancer biomarkers used in clinical practice across the application domains above, discuss what makes a suitable DNA methylation cancer biomarker, and identify barriers to translation. We discuss technical factors such as the analytical performance and product-market fit, factors that contribute to successful downstream investment, including geography, and how this impacts intellectual property, regulatory hurdles, and the future of the marketplace and healthcare system.
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Affiliation(s)
- Warwick J Locke
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Dominic Guanzon
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Chenkai Ma
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Yi Jin Liew
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Konsta R Duesing
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia
| | - Kim Y C Fung
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
| | - Jason P Ross
- Molecular Diagnostics Solutions, CSIRO Health and Biosecurity, North Ryde, NSW, Australia.,Probing Biosystems Future Science Platform, CSIRO Health and Biosecurity, Canberra, ACT, Australia
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28
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Reimers N, Pantel K. Liquid biopsy: novel technologies and clinical applications. Clin Chem Lab Med 2019; 57:312-316. [PMID: 30465714 DOI: 10.1515/cclm-2018-0610] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 10/23/2018] [Indexed: 02/07/2023]
Abstract
"Liquid biopsy" was introduced as a new diagnostic concept in 2010 for the analysis of circulating tumor cells (CTCs) and has been now extended to material (in particular DNA) released by tumor cells in the peripheral blood of cancer patients. Over the past decade, various methods have been developed to detect CTCs and ctDNA in the peripheral blood of cancer patients.
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Affiliation(s)
- Natalie Reimers
- Department of Tumor Biology, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Centre Hamburg-Eppendorf, Martinistr. 52, Hamburg 20246, Germany
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29
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.3] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/19/2019] [Indexed: 12/23/2022] Open
Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies but clinical experience for use of this technology in diagnostic evaluation of infections in immunocompromised hosts is limited. Methods: We conducted an exploratory study using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Pathogen identification by cfDNA NGS demonstrated positive agreement with conventional diagnostic laboratory methods in 7 (70%) cases, including patients with proven/probable invasive aspergillosis, Pneumocystis jirovecii pneumonia, Stenotrophomonas maltophilia bacteremia, Cytomegalovirus and Adenovirus viremia. NGS results were discordant in 3 (30%) cases including two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant in whom cfDNA testing identified the etiological agent of sepsis; and one kidney transplant recipient with invasive aspergillosis who had received >6 months of antifungal therapy prior to NGS testing. Conclusion: These observations support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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Affiliation(s)
- Jose F. Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I. Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D. Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E. Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V. Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V. Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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30
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2019] [Indexed: 03/28/2024] Open
Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies. Methods: Here we report our experience using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Among five hematological malignancy patients, for whom a microbiological diagnosis was established, pathogen identification by cfDNA NGS demonstrated 100% positive agreement with conventional diagnostic laboratory methods. Further, cfDNA identified the etiological agent in two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant. Conclusion: These data support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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Affiliation(s)
- Jose F. Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I. Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D. Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E. Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V. Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V. Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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31
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 11/12/2023] Open
Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies but clinical experience for use of this technology in diagnostic evaluation of infections in immunocompromised hosts is limited. Methods: We conducted an exploratory study using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Pathogen identification by cfDNA NGS demonstrated positive agreement with conventional diagnostic laboratory methods in 7 (70%) cases, including patients with proven/probable invasive aspergillosis, Pneumocystis jirovecii pneumonia, Stenotrophomonas maltophilia bacteremia, Cytomegalovirus and Adenovirus viremia. NGS results were discordant in 3 (30%) cases including two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant in whom cfDNA testing identified the potential etiological agent of sepsis; and one kidney transplant recipient with invasive aspergillosis who had received >6 months of antifungal therapy prior to NGS testing. Conclusion: These observations support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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Affiliation(s)
- Jose F. Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I. Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D. Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E. Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V. Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V. Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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32
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Camargo JF, Ahmed AA, Lindner MS, Morris MI, Anjan S, Anderson AD, Prado CE, Dalai SC, Martinez OV, Komanduri KV. Next-generation sequencing of microbial cell-free DNA for rapid noninvasive diagnosis of infectious diseases in immunocompromised hosts. F1000Res 2019; 8:1194. [PMID: 31814964 PMCID: PMC6883395 DOI: 10.12688/f1000research.19766.4] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 12/14/2022] Open
Abstract
Background: Cell-free DNA (cfDNA) sequencing has emerged as an effective laboratory method for rapid and noninvasive diagnosis in prenatal screening testing, organ transplant rejection screening, and oncology liquid biopsies but clinical experience for use of this technology in diagnostic evaluation of infections in immunocompromised hosts is limited. Methods: We conducted an exploratory study using next-generation sequencing (NGS) for detection of microbial cfDNA in a cohort of ten immunocompromised patients with febrile neutropenia, pneumonia or intra-abdominal infection. Results: Pathogen identification by cfDNA NGS demonstrated positive agreement with conventional diagnostic laboratory methods in 7 (70%) cases, including patients with proven/probable invasive aspergillosis, Pneumocystis jirovecii pneumonia, Stenotrophomonas maltophilia bacteremia, Cytomegalovirus and Adenovirus viremia. NGS results were discordant in 3 (30%) cases including two patients with culture negative sepsis who had undergone hematopoietic stem cell transplant in whom cfDNA testing identified the potential etiological agent of sepsis; and one kidney transplant recipient with invasive aspergillosis who had received >6 months of antifungal therapy prior to NGS testing. Conclusion: These observations support the clinical utility of measurement of microbial cfDNA sequencing from peripheral blood for rapid noninvasive diagnosis of infections in immunocompromised hosts. Larger studies are needed.
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Affiliation(s)
- Jose F Camargo
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | | | - Michele I Morris
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Shweta Anjan
- Infectious Diseases, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Anthony D Anderson
- Department of Pharmacy, University of Miami Sylvester Comprehensive Cancer Center, Miami, FL, 33136, USA
| | - Clara E Prado
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | | | - Octavio V Martinez
- Department of Microbiology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Krishna V Komanduri
- Division of Hematology Oncology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
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Abstract
Since its discovery in human blood plasma about 70 years ago, circulating cell-free DNA (cfDNA) has become an attractive subject of research as noninvasive disease biomarker. The interest in clinical applications has gained an exponential increase, making it a popular and potential target in a wide range of research areas.cfDNA can be found in different body fluids, both in healthy and not healthy subjects. The recent and rapid development of new molecular techniques is promoting the study and the identification of cfDNA, holding the key to minimally invasive diagnostics, improving disease monitoring, clinical decision, and patients' outcome.cfDNA has already given a huge impact on prenatal medicine, and it could become, in the next future, the standard of care also in other fields, from oncology to transplant medicine and cardiovascular diseases.
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Affiliation(s)
- Rossella Ranucci
- Biosciences Laboratory, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Meldola, Italy.
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Ponti G, Manfredini M, Tomasi A. Non-blood sources of cell-free DNA for cancer molecular profiling in clinical pathology and oncology. Crit Rev Oncol Hematol 2019; 141:36-42. [PMID: 31212145 DOI: 10.1016/j.critrevonc.2019.06.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/19/2018] [Accepted: 06/04/2019] [Indexed: 12/12/2022] Open
Abstract
Liquid biopsy can quantify and qualify cell-free (cfDNA) and tumour-derived (ctDNA) DNA fragments in the bloodstream. CfDNA quantification and mutation analysis can be applied to diagnosis, follow-up and therapeutic management as novel oncologic biomarkers. However, some tumor-types release a low amount of DNA into the bloodstream, hampering diagnosis through standard liquid biopsy procedures. Several tumors, as such as brain, kidney, prostate, and thyroid cancer, are in direct contact with other body fluids and may be alternative sources for cfDNA and ctDNA. Non-blood sources of cfDNA/ctDNA useful as novel oncologic biomarkers include cerebrospinal fluids, urine, sputum, saliva, pleural effusion, stool and seminal fluid. Seminal plasma cfDNA, which can be analyzed with cost-effective procedures, may provide powerful information capable to revolutionize prostate cancer (PCa) patient diagnosis and management. In the near future, cfDNA analysis from non-blood biological liquids will become routine clinical practice for cancer patient diagnosis and management.
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Affiliation(s)
- Giovanni Ponti
- Department of Surgical, Medical, Dental & Morphological Sciences with Interest Transplant, Oncological & Regenerative Medicine, Division of Clinical Pathology, University of Modena & Reggio Emilia, Modena, Italy.
| | - Marco Manfredini
- Department of Surgical, Medical, Dental & Morphological Sciences with Interest Transplant, Oncological & Regenerative Medicine, Dermatology Unit, University of Modena & Reggio Emilia, Modena, Italy
| | - Aldo Tomasi
- Department of Surgical, Medical, Dental & Morphological Sciences with Interest Transplant, Oncological & Regenerative Medicine, Division of Clinical Pathology, University of Modena & Reggio Emilia, Modena, Italy
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35
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Park CE, Park SH. Investigation of the Molecular Diagnostic Market in Animals. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2019. [DOI: 10.15324/kjcls.2019.51.1.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Chang-Eun Park
- Department of Biomedical Laboratory Science, Molecular Diagnostics Research Institute, Namseoul University, Cheonan, Korea
| | - Sung-Ha Park
- IVD R&D Group, IVD Business Team, Health and Medical Equipment Division, Samsung Electronics Co., Ltd., Suwon, Korea
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36
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Oh AC, Lee JK, Kim JY, Jin HO, Jung JW, Chang YH, Hong YJ. Utilization of Archived Plasma to Detect Epidermal Growth Factor Receptor Mutation in Non-Small Cell Lung Cancer Patients. Biopreserv Biobank 2019; 17:319-325. [PMID: 30888199 PMCID: PMC6703236 DOI: 10.1089/bio.2018.0126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Precision medicine has received increased attention as an effective approach for the treatment of cancer patients. Because of challenges associated with the availability of archived tissue, liquid biopsies are often performed to detect cancer-specific mutations. One of the major advantages of the liquid biopsy is that the treatment can be monitored longitudinally, even after the tumor tissue is no longer available. In a clinical setting, one component of precision medicine is the detection of cancer-specific mutations using archived samples. In this study, we evaluated the epidermal growth factor receptor (EGFR) mutation status of samples of lung cancer patients stored before introduction of the plasma EGFR test at our institution. The aim of this study was to validate the utility of archived plasma samples for detection of the EGFR mutation in nonsmall cell lung cancer (NSCLC) patients. The Cobas® EGFR Mutation Test v2 was the first liquid biopsy test approved as a companion diagnostic test for patients with NSCLC treated with tyrosine kinase inhibitors. We tested for the EGFR mutation in 116 plasma samples archived in the biobank, and the results were compared with those obtained in the tissue or cytology EGFR mutation test. The EGFR mutation-positive rate from archived plasma was lower than that determined from tissue or cytology at 19.0% and 53.4%, respectively, and the concordance rate between the two tests was 58.6%. Of interest, five (4.3%) samples showed the T790M mutation in the plasma test, whereas this mutation was only detected in two (1.7%) tissue/cytology samples. Five (4.3%) samples were additionally positive in the plasma test. Overall, these results indicate that archived plasma samples can serve as an alternative source for the plasma EGFR mutation test when tissue samples are not available, and can improve precision medicine and long-term follow-up in a noninvasive manner.
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Affiliation(s)
- Ae-Chin Oh
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Jin Kyung Lee
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea.,2KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Ji-Young Kim
- 2KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Hyeon-Ok Jin
- 2KIRAMS Radiation Biobank, Korea Institute of Radiological and Medical Sciences, Seoul, Republic of Korea
| | - Jae Won Jung
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Yoon Hwan Chang
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
| | - Young Jun Hong
- 1Department of Laboratory Medicine, Korea Cancer Center Hospital, Seoul, Republic of Korea
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Reed EK, Steinmark L, Seibert DC, Edelman E. Somatic Testing: Implications for Targeted Treatment. Semin Oncol Nurs 2019; 35:22-33. [PMID: 30660356 DOI: 10.1016/j.soncn.2018.12.009] [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: 10/27/2022]
Abstract
OBJECTIVE To provide an overview of key considerations for somatic testing for the purpose of targeting cancer treatment. DATA SOURCES Literature; research reports. CONCLUSION Genomic testing of cancer cells to identify variants that drive the carcinogenic process is becoming common in clinical settings. Providers and patients need to weigh the potential benefits of testing with technologic and logistic issues. IMPLICATIONS FOR NURSING PRACTICE Testing is available for thousands of genomic variants to identify one or more to guide targeted treatment. Oncology nurses need to understand the benefits and limitations of participating in patient-centered implementation of this testing.
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Ulrich BC, Guibert N. Non-invasive assessment of tumor PD-L1 status with circulating tumor cells. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:S48. [PMID: 30613623 PMCID: PMC6291604 DOI: 10.21037/atm.2018.10.09] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 09/30/2018] [Indexed: 01/20/2023]
Affiliation(s)
| | - Nicolas Guibert
- Thoracic Oncology Department, Larrey Hospital, University Hospital of Toulouse, Toulouse, France
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Abstract
Progress in sensitive analytical approaches has opened new avenues for the detection of cells or products such as circulating cell-free DNA released by tumors. These ‘liquid biopsies’ are being explored in clinical trials for early cancer detection, prediction of recurrent disease, and assessment of therapeutic resistance mechanisms.
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Affiliation(s)
- Anna Babayan
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20246, Hamburg, Germany.
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