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Scimia M, Pepe F, Russo G, Palumbo L, Malapelle U, Chuang R, Scimia S, Sha M, Tanaka H, Shen S, Chen D, Troncone G, Bianco MA. The Impact of potential 'confounders' on the diagnostic sensitivity of circulating free DNA in management of FIT+ patients: a pilot study. J Clin Pathol 2024; 77:557-560. [PMID: 38649261 PMCID: PMC11287558 DOI: 10.1136/jcp-2024-209527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/29/2024] [Indexed: 04/25/2024]
Abstract
Cell-free DNA (cfDNA) has long been established as a useful diagnostic and prognostic tool in a variety of clinical settings, ranging from infectious to cardiovascular and neoplastic diseases. However, non-neoplastic diseases can act as confounders impacting on the amount of cfDNA shed in bloodstream and on technical feasibility of tumour derived free circulating nucleic acids selecting patients with cancer. Here, we investigated the potential impact of other pathological processes in the clinical stratification of 637 FIT+ patients. A single and multiple logistic regression yielded similar results. Crude sensitivity was 75.9% versus adjusted sensitivity of 74.1%, relative risk 0.9761 (0.8516 to 1.1188), risk difference 0.0181 (-0.0835 to 0.1199) and OR 0.9079 (0.5264 to 1.5658). Potential confounding effect from other source of cfDNA plays a pivotal role in the clinical stratification of FIT+ patients.
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Affiliation(s)
| | - Francesco Pepe
- Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Russo
- Public Health, University of Naples Federico II, Naples, Italy
| | - Lucia Palumbo
- Public Health, University of Naples Federico II, Naples, Italy
| | | | | | | | | | | | - Shuo Shen
- DiaCarta Inc, Richmond, Virginia, USA
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Sawai A, Shida T, Hoshikawa Y, Hatanaka S, Ueda M, Kato Y, Tokinoya K, Natsui H, Kawakami Y, Takekoshi K. Effect of acute moderate-intensity cycling on cfDNA levels considering menstrual cycle phases. Front Sports Act Living 2024; 6:1322295. [PMID: 38348376 PMCID: PMC10859457 DOI: 10.3389/fspor.2024.1322295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/15/2024] [Indexed: 02/15/2024] Open
Abstract
Introduction We aimed to determine the effects of exercise on cell-free DNA (cfDNA) levels and concentration changes during the menstrual cycle in participants with regular menstrual cycles and no exercise habits. Methods Eleven sedentary female students with regular menstrual cycles and ovulation performed bicycle exercises at 60% VO2max for 30 min during the menstrual, ovulatory, and luteal phases. Blood samples were collected before (Pre), immediately after (Post 0), 30 min after (Post 30), and 60 min after (Post 60) exercise. Blood concentrations of ovarian hormones, cfDNA, prostaglandin F2a (PGF2α), interleukin-6 (IL-6), and aromatase were evaluated. Results Based on the concentration of ovarian hormones, seven individuals were finally analyzed. No significant phase difference was observed in cfDNA across all time points. cfDNA (menstrual phase: p = 0.028, ovulatory phase: p = 0.018, and luteal phase: p = 0.048) and aromatase concentrations (menstrual phase: p = 0.040, ovulatory phase: p = 0.039, and luteal phase: p = 0.045) significantly increased from Pre to Post 0 in all phases. Serum estradiol (E2) levels were significantly higher in the luteal phase at all time points than in the menstrual phase (Pre: p < 0.001, Post 0: p < 0.001, Post 30: p = 0.005, and Post 60: p = 0.011); however, serum progesterone (P4) levels were significantly higher in the luteal phase at all time points than in the menstrual (Pre: p < 0.001, Post 0: p < 0.001, Post 30: p < 0.001, and Post 60: p < 0.001) and ovulatory phases (Pre: p = 0.005, Post 0: p = 0.005, Post 30: p = 0.003, and Post 60: p = 0.003). E2 levels significantly increased from Pre to Post 0 in the ovulatory and luteal phases, whereas P4 levels increased in the luteal phase. Progesterone to estradiol level ratio (P4/E2) changes from Pre to Post 0 (%baseline) during the luteal phase were significantly negatively correlated (r = -0.82, p = 0.046) with the changes in cfDNA from Pre to Post 0. Furthermore, the repeated measures correlation between P4/E2 and cfDNA level showed a significant negative correlation in ovulatory and luteal phases. Discussion The results indicate that while resting cfDNA levels are unlikely to be affected by a woman's menstrual cycle, the increase in cfDNA after exercise is higher in the ovulatory phase (when only E2 increases) and lower in the luteal phase (when E2 and P4 increase with exercise) compared to that in the menstrual phase (when E2 and P4 are in low levels), suggesting the contribution of increased ovarian hormone levels after exercise.
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Affiliation(s)
- Akemi Sawai
- Research Institute of Physical Fitness, Japan Women’s College of Physical Education, Setagaya City, Japan
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
| | - Takashi Shida
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
- Research Team for Promoting Independence and Mental Health, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi City, Japan
| | - Yoshihiro Hoshikawa
- Department of Sports Science, Japan Women’s College of Physical Education, Setagaya City, Japan
| | - Sho Hatanaka
- Research Team for Promoting Independence and Mental Health, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi City, Japan
| | - Mashiro Ueda
- Master’s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba City, Japan
| | - Yuri Kato
- Master’s Program in Medical Sciences, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba City, Japan
| | - Katsuyuki Tokinoya
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
- Embodied Wisdom Division, Center for Liberal Education and Learning, Sophia University, Chiyoda City, Japan
| | - Hiroaki Natsui
- Department of Sports and Health Science, Japan Women’s College of Physical Education, Setagaya City, Japan
| | - Yasushi Kawakami
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
| | - Kazuhiro Takekoshi
- Department of Clinical Laboratory, Faculty of Medicine, University of Tsukuba, Tsukuba City, Japan
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Drag MH, Debes KP, Franck CS, Flethøj M, Lyhne MK, Møller JE, Ludvigsen TP, Jespersen T, Olsen LH, Kilpeläinen TO. Nanopore sequencing reveals methylation changes associated with obesity in circulating cell-free DNA from Göttingen Minipigs. Epigenetics 2023; 18:2199374. [PMID: 37032646 PMCID: PMC10088973 DOI: 10.1080/15592294.2023.2199374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/29/2023] [Accepted: 03/08/2023] [Indexed: 04/11/2023] Open
Abstract
Profiling of circulating cell-free DNA (cfDNA) by tissue-specific base modifications, such as 5-methylcytosines (5mC), may enable the monitoring of ongoing pathophysiological processes. Nanopore sequencing allows genome-wide 5mC detection in cfDNA without bisulphite conversion. The aims of this study were: i) to find differentially methylated regions (DMRs) of cfDNA associated with obesity in Göttingen minipigs using Nanopore sequencing, ii) to validate a subset of the DMRs using methylation-specific PCR (MSP-PCR), and iii) to compare the cfDNA DMRs with those from whole blood genomic DNA (gDNA). Serum cfDNA and gDNA were obtained from 10 lean and 7 obese Göttingen Minipigs both with experimentally induced myocardial infarction and sequenced using Oxford Nanopore MinION. A total of 1,236 cfDNA DMRs (FDR<0.01) were associated with obesity. In silico analysis showed enrichment of the adipocytokine signalling, glucagon signalling, and cellular glucose homoeostasis pathways. A strong cfDNA DMR was discovered in PPARGC1B, a gene linked to obesity and type 2 diabetes. The DMR was validated using MSP-PCR and correlated significantly with body weight (P < 0.05). No DMRs intersected between cfDNA and gDNA, suggesting that cfDNA originates from body-wide shedding of DNA. In conclusion, nanopore sequencing detected differential methylation in minute quantities (0.1-1 ng/µl) of cfDNA. Future work should focus on translation into human and comparing 5mC from somatic tissues to pinpoint the exact location of pathology.
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Affiliation(s)
- Markus Hodal Drag
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Conservation, Copenhagen Zoo, Frederiksberg, Denmark
| | | | - Clara Sandkamm Franck
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mette Flethøj
- Research & Early Development, Novo Nordisk A/S, Måløv, Denmark
| | - Mille Kronborg Lyhne
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jacob Eifer Møller
- Department of Cardiology, Copenhagen University Hospital and Odense University Hospital, Odense, Denmark
| | | | - Thomas Jespersen
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lisbeth Høier Olsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O. Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Panizzi L, Dittmer KE, Vignes M, Doucet JS, Gedye K, Waterland MR, Rogers CW, Sano H, McIlwraith CW, Riley CB. Plasma and Synovial Fluid Cell-Free DNA Concentrations Following Induction of Osteoarthritis in Horses. Animals (Basel) 2023; 13:ani13061053. [PMID: 36978592 PMCID: PMC10044647 DOI: 10.3390/ani13061053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/03/2023] [Accepted: 03/11/2023] [Indexed: 03/17/2023] Open
Abstract
Biomarkers for osteoarthritis (OA) in horses have been extensively investigated, but translation into clinical use has been limited due to cost, limited sensitivity, and practicality. Identifying novel biomarkers that overcome these limitations could facilitate early diagnosis and therapy. This study aimed to compare the concentrations of synovial fluid (SF) and plasma cell-free DNA (cfDNA) over time in control horses with those with induced carpal OA. Following an established model, unilateral carpal OA was induced in 9 of 17 healthy Thoroughbred fillies, while the remainder were sham-operated controls. Synovial fluid and plasma samples were obtained before induction of OA (Day 0) and weekly thereafter until Day 63, and cfDNA concentrations were determined using fluorometry. The SF cfDNA concentrations were significantly higher for OA joints than for sham-operated joints on Days 28 (median 1430 μg/L and 631 μg/L, respectively, p = 0.017) and 63 (median 1537 μg/L and 606 μg/L, respectively, p = 0.021). There were no significant differences in plasma cfDNA between the OA and the sham groups after induction of carpal OA. Plasma cfDNA measurement is not sufficiently sensitive for diagnostic purposes in this induced model of OA. Synovial fluid cfDNA measurement may be used as a biomarker to monitor early disease progression in horses with OA.
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Affiliation(s)
- Luca Panizzi
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
- Correspondence:
| | - Keren E. Dittmer
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
| | - Matthieu Vignes
- School of Mathematical and Computational Sciences, College of Science, Massey University, Palmerston North 4442, New Zealand;
| | - Jennie S. Doucet
- Department of Biology, Faculty of Science, University of Waterloo, Waterloo, ON N2L 3G1, Canada;
| | - Kristene Gedye
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
| | - Mark R. Waterland
- School of Natural Sciences, College of Science, Massey University, Palmerston North 4442, New Zealand;
| | - Chris W. Rogers
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
- School of Agriculture and Environment, College of Science, Massey University, Palmerston North 4442, New Zealand
| | - Hiroki Sano
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
| | - C. Wayne McIlwraith
- Orthopaedic Research Center, C. Wayne McIlwraith Translational Medicine Institute, School of Veterinary Medicine, Colorado State University, Fort Collins, CO 80523-1601, USA;
| | - Christopher B. Riley
- School of Veterinary Science, College of Science, Massey University, Palmerston North 4442, New Zealand; (K.E.D.); (K.G.); (C.W.R.); (H.S.); (C.B.R.)
- Department of Clinical Sciences, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
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Martínez de Toda I, González-Sánchez M, Díaz-Del Cerro E, Valera G, Carracedo J, Guerra-Pérez N. Sex differences in markers of oxidation and inflammation. Implications for ageing. Mech Ageing Dev 2023; 211:111797. [PMID: 36868323 DOI: 10.1016/j.mad.2023.111797] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 02/28/2023] [Indexed: 03/05/2023]
Abstract
Sexual dimorphism is a key factor to consider in the ageing process given the impact that it has on life expectancy. The oxidative-inflammatory theory of ageing states that the ageing process is the result of the establishment of oxidative stress which, due to the interplay of the immune system, translates into inflammatory stress, and that both processes are responsible for the damage and loss of function of an organism. We show that there are relevant gender differences in a number of oxidative and inflammatory markers and propose that they may account for the differential lifespan between sexes, given that males display, in general, higher oxidation and basal inflammation. In addition, we explain the significant role of circulating cell-free DNA as a marker of oxidative damage and an inductor of inflammation, connecting both processes and having the potential to become a useful ageing marker. Finally, we discuss how oxidative and inflammatory changes take place differentially with ageing in each sex, which could also have an impact on the sex-differential lifespan. Further research including sex as an essential variable is needed to understand the grounds of sex differences in ageing and to better comprehend ageing itself.
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Affiliation(s)
- Irene Martínez de Toda
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Mónica González-Sánchez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain.
| | - Estefanía Díaz-Del Cerro
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Gemma Valera
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Julia Carracedo
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
| | - Natalia Guerra-Pérez
- Department of Genetics, Physiology, and Microbiology. Unit of Animal Physiology, Faculty of Biology, Complutense University of Madrid, 28040 Madrid, Spain; Instituto de Investigación Sanitaria Hospital 12 de Octubre (imas12), 28041 Madrid, Spain.
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Sayal L, Hamadah O, AlMasri A, Idrees M, Kassem I, Habbal W, Alsalamah B, Kujan O. Salivary-Based Cell-Free Mitochondrial DNA Level Is an Independent Prognostic Biomarker for Patients with Head and Neck Squamous Cell Carcinoma. J Pers Med 2023; 13:jpm13020301. [PMID: 36836535 PMCID: PMC9958681 DOI: 10.3390/jpm13020301] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Changes in the copy numbers of cell-free nuclear DNA (cf-nDNA) and cell-free mitochondrial DNA (cf-mtDNA) have shown promising diagnostic utilities among patients with head and neck squamous cell carcinoma (HNSCC). Considering the absence of objective prognostic tools for HNSCC surveillance, this study aimed to assess the utility of saliva-based cf-nDNA and cf-mtDNA in predicting the overall survival of patients with HNSCC. The study included ninety-four patients with a confirmed HNSCC diagnosis with a mean follow-up time of 32.04 months (±19.1). A saliva-based liquid biopsy was collected from each patient. A multiplex quantitative PCR was used to determine the absolute number of cf-nDNA and cf-mtDNA. The Kaplan-Meier estimator and Cox proportional hazards regression models were used to assess overall survival. The absolute copy numbers of cf-nDNA and cf-mtDNA were statistically significantly higher among the deceased patients than among the censored ones (p < 0.05). Individuals with elevated levels of cf-nDNA or cf-mtDNA were associated with a significantly poorer overall survival (p ≤ 0.05). A univariate analysis showed that only the absolute copy number of cf-mtDNA was the sole predictor of overall survival. However, the multivariate analysis showed that all the absolute copy numbers of cf-nDNA, the absolute copy numbers of cf-mtDNA, and the stage of HNSCC were predictors of overall survival. Our study confirms that saliva is a reliable and non-invasive source of data that can be used to predict the overall survival of patients with HNSCC, where cf-mtDNA levels act as the sole predictor.
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Affiliation(s)
- Lana Sayal
- Department of Oral Medicine, The Faculty of Dental Medicine, Damascus University, Damascus P.O. Box 30621, Syria
| | - Omar Hamadah
- Department of Oral Medicine, The Faculty of Dental Medicine, Damascus University, Damascus P.O. Box 30621, Syria
| | - Aroub AlMasri
- Biomedical Department, National Commission for Biotechnology, Damascus P.O. Box 31902, Syria
| | - Majdy Idrees
- UWA Dental School, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Issam Kassem
- Faculty of Science, Damascus University, Damascus P.O. Box 30621, Syria
| | - Wafa Habbal
- Clinical Laboratories Department, Al-Assad Hospital, Damascus P.O. Box 10769, Syria
| | - Buthainah Alsalamah
- Department of Molecular Biology, National Commission for Biotechnology, Damascus P.O. Box 31902, Syria
| | - Omar Kujan
- UWA Dental School, The University of Western Australia, Nedlands, WA 6009, Australia
- Correspondence: ; Tel.: +61-8-6457-7649
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Bryzgunova O, Bondar A, Ruzankin P, Tarasenko A, Zaripov M, Kabilov M, Laktionov P. Locus-Specific Bisulfate NGS Sequencing of GSTP1, RNF219, and KIAA1539 Genes in the Total Pool of Cell-Free and Cell-Surface-Bound DNA in Prostate Cancer: A Novel Approach for Prostate Cancer Diagnostics. Cancers (Basel) 2023; 15:cancers15020431. [PMID: 36672380 PMCID: PMC9856824 DOI: 10.3390/cancers15020431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/27/2022] [Accepted: 12/27/2022] [Indexed: 01/11/2023] Open
Abstract
The locus-specific methylation of three genes (GSTP1, RNF219, and KIAA1539, also known as FAM214B) in the total pool of blood cell-free DNA, including cell-free DNA from plasma and cell-surface-bound DNA, of patients with prostate cancer and healthy donors was studied on the MiSeq platform. Our study found a higher methylation index of loci for total cell-free DNA compared with cell-free DNA. For total cell-free DNA, the methylation of GSTP1 in each of the 11 positions provided a complete separation of cancer patients from healthy donors, whereas for cell-free DNA, there were no positions in the three genes allowing for such separation. Among the prostate cancer patients, the minimum proportion of GSTP1 genes methylated in any of the 17 positions was 12.1% of the total circulated DNA fragments, and the minimum proportion of GSTP1 genes methylated in any of the 11 diagnostically specific positions was 8.4%. Total cell-free DNA was shown to be more convenient and informative as a source of methylated DNA molecules circulating in the blood than cell-free DNA.
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Affiliation(s)
- Olga Bryzgunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Correspondence: ; Tel.: +7-383-363-51-44; Fax: +7-383-363-51-53
| | - Anna Bondar
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Ruzankin
- Sobolev Institute of Mathematics, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton Tarasenko
- Sobolev Institute of Mathematics, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Department of Mathematics and Mechanics, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Marat Zaripov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Pavel Laktionov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Zangouei AS, Zangoue M, Taghehchian N, Zangooie A, Rahimi HR, Saburi E, Alavi MS, Moghbeli M. Cell cycle related long non-coding RNAs as the critical regulators of breast cancer progression and metastasis. Biol Res 2023; 56:1. [PMID: 36597150 PMCID: PMC9808980 DOI: 10.1186/s40659-022-00411-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 12/29/2022] [Indexed: 01/04/2023] Open
Abstract
Cell cycle is one of the main cellular mechanisms involved in tumor progression. Almost all of the active molecular pathways in tumor cells directly or indirectly target the cell cycle progression. Therefore, it is necessary to assess the molecular mechanisms involved in cell cycle regulation in tumor cells. Since, early diagnosis has pivotal role in better cancer management and treatment, it is required to introduce the non-invasive diagnostic markers. Long non-coding RNAs (LncRNAs) have higher stability in body fluids in comparison with mRNAs. Therefore, they can be used as efficient non-invasive markers for the early detection of breast cancer (BCa). In the present review we have summarized all of the reported lncRNAs involved in cell cycle regulation in BCa. It has been reported that lncRNAs mainly affect the cell cycle in G1/S transition through the CCND1/CDK4-6 complex. Present review paves the way of introducing the cell cycle related lncRNAs as efficient markers for the early detection of BCa.
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Affiliation(s)
- Amir Sadra Zangouei
- grid.411583.a0000 0001 2198 6209Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Malihe Zangoue
- grid.411701.20000 0004 0417 4622Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran ,grid.411701.20000 0004 0417 4622Department of Anesthesiology, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | - Negin Taghehchian
- grid.411583.a0000 0001 2198 6209Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Zangooie
- grid.411701.20000 0004 0417 4622Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran ,grid.411701.20000 0004 0417 4622Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran
| | - Hamid Reza Rahimi
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Saburi
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahya Sadat Alavi
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- grid.411583.a0000 0001 2198 6209Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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9
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Takousis P, Devonshire AS, Redshaw N, von Baumgarten L, Whale AS, Jones GM, Fernandez-Gonzalez A, Martin J, Foy CA, Alexopoulos P, Huggett JF, Perneczky R. A standardised methodology for the extraction and quantification of cell-free DNA in cerebrospinal fluid and application to evaluation of Alzheimer's disease and brain cancers. N Biotechnol 2022; 72:97-106. [PMID: 36202346 DOI: 10.1016/j.nbt.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 09/23/2022] [Accepted: 10/01/2022] [Indexed: 11/27/2022]
Abstract
Cerebrospinal fluid (CSF) is a source of diagnostic biomarkers for a range of neurological conditions. Cell-free DNA (cfDNA) is detected in CSF and differences in the concentration of cell-free mitochondrial DNA have been reported in studies of neurodegenerative disorders including Alzheimer's disease (AD). However, the influence of pre-analytical steps has not been investigated for cfDNA in CSF and there is no standardised approach for quantification of total cfDNA (copies of nuclear genome or mitochondria-derived gene targets). In this study, the suitability of four extraction methods was evaluated: QIAamp Circulating Nucleic Acid (Qiagen), Quick-cfDNA Serum & Plasma (Zymo), NucleoSnap® DNA Plasma (Macherey-Nagel) and Plasma/Serum Circulating DNA Purification Mini (Norgen) kits, for cfDNA extraction from CSF of controls and AD dementia patients, utilising a spike-in control for extraction efficiency and fragment size. One of the optimal extraction methods was applied to a comparison of cfDNA concentrations in CSF from control subjects, AD dementia and primary and secondary brain tumour patients. Extraction efficiency based on spike-in recovery was similar in all three groups whilst both endogenous mitochondrial and nucleus-derived cfDNA was significantly higher in CSF from cancer patients compared to control and AD groups, which typically contained < 100 genome copies/mL. This study shows that it is feasible to measure low concentration nuclear and mitochondrial gene targets in CSF and that normalisation of extraction yield can help control pre-analytical variability influencing biomarker measurements.
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Affiliation(s)
- Petros Takousis
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK
| | - Alison S Devonshire
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK.
| | - Nicholas Redshaw
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Louisa von Baumgarten
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany; Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany
| | - Alexandra S Whale
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Gerwyn M Jones
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Ana Fernandez-Gonzalez
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Jan Martin
- Department of Anaesthesiology and Intensive Care Medicine, Technical University Munich, Munich, Germany
| | - Carole A Foy
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Panagiotis Alexopoulos
- Department of Psychiatry, University of Patras, Rion Patras, Greece; Department of Psychiatry and Psychotherapy, Technical University Munich, Munich, Germany
| | - Jim F Huggett
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Robert Perneczky
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK; Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
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Xie Y, Xu X, Lin J, Xu Y, Wang J, Ren Y, Wu A. Effective Separation of Cancer-Derived Exosomes in Biological Samples for Liquid Biopsy: Classic Strategies and Innovative Development. GLOBAL CHALLENGES (HOBOKEN, NJ) 2022; 6:2100131. [PMID: 36176940 PMCID: PMC9463520 DOI: 10.1002/gch2.202100131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/28/2022] [Indexed: 05/26/2023]
Abstract
Liquid biopsy has remarkably facilitated clinical diagnosis and surveillance of cancer via employing a non-invasive way to detect cancer-derived components, such as circulating tumor DNA and circulating tumor cells from biological fluid samples. The cancer-derived exosomes, which are nano-sized vesicles secreted by cancer cells have been investigated in liquid biopsy as their important roles in intracellular communication and disease development have been revealed. Given the challenges posed by the complicated humoral microenvironment, which contains a variety of different cells and macromolecular substances in addition to the exosomes, it has attracted a large amount of attention to effectively isolate exosomes from collected samples. In this review, the authors aim to analyze classic strategies for separation of cancer-derived exosomes, giving an extensive discussion of advantages and limitations of these methods. Furthermore, the innovative multi-strategy methods to realize efficient isolation of cancer-derived exosomes in practical applications are also presented. Additionally, the possible development trends of exosome separation in to the future is discussed in this review.
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Affiliation(s)
- Yujiao Xie
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
- Research Group for Fluids and Thermal EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Department of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
| | - Xiawei Xu
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
- Research Group for Fluids and Thermal EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Department of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
| | - Jie Lin
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
| | - Yanping Xu
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
| | - Jing Wang
- Department of Electrical and Electronic EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Key Laboratory of More Electric Aircraft Technology of Zhejiang ProvinceUniversity of Nottingham Ningbo ChinaNingbo315100China
- Nottingham Ningbo China Beacons of Excellence Research and Innovation InstituteNingbo315040China
| | - Yong Ren
- Research Group for Fluids and Thermal EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Department of MechanicalMaterials and Manufacturing EngineeringUniversity of Nottingham Ningbo ChinaNingbo315100China
- Nottingham Ningbo China Beacons of Excellence Research and Innovation InstituteNingbo315040China
- Key Laboratory of Carbonaceous Wastes Processing and Process Intensification Research of Zhejiang ProvinceUniversity of Nottingham Ningbo ChinaNingbo315100China
| | - Aiguo Wu
- Cixi Institute of Biomedical EngineeringInternational Cooperation Base of Biomedical MaterialsTechnology and ApplicationChinese Academy of Science (CAS) Key Laboratory of Magnetic Materials and Devices and Zhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201P. R. China
- Advanced Energy Science and Technology Guangdong LaboratoryHuizhou516000P. R. China
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11
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Mitchell MI, Ma J, Carter CL, Loudig O. Circulating Exosome Cargoes Contain Functionally Diverse Cancer Biomarkers: From Biogenesis and Function to Purification and Potential Translational Utility. Cancers (Basel) 2022; 14:3350. [PMID: 35884411 PMCID: PMC9318395 DOI: 10.3390/cancers14143350] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/01/2022] [Accepted: 07/07/2022] [Indexed: 12/12/2022] Open
Abstract
Although diagnostic and therapeutic treatments of cancer have tremendously improved over the past two decades, the indolent nature of its symptoms has made early detection challenging. Thus, inter-disciplinary (genomic, transcriptomic, proteomic, and lipidomic) research efforts have been focused on the non-invasive identification of unique "silver bullet" cancer biomarkers for the design of ultra-sensitive molecular diagnostic assays. Circulating tumor biomarkers, such as CTCs and ctDNAs, which are released by tumors in the circulation, have already demonstrated their clinical utility for the non-invasive detection of certain solid tumors. Considering that exosomes are actively produced by all cells, including tumor cells, and can be found in the circulation, they have been extensively assessed for their potential as a source of circulating cell-specific biomarkers. Exosomes are particularly appealing because they represent a stable and encapsulated reservoir of active biological compounds that may be useful for the non-invasive detection of cancer. T biogenesis of these extracellular vesicles is profoundly altered during carcinogenesis, but because they harbor unique or uniquely combined surface proteins, cancer biomarker studies have been focused on their purification from biofluids, for the analysis of their RNA, DNA, protein, and lipid cargoes. In this review, we evaluate the biogenesis of normal and cancer exosomes, provide extensive information on the state of the art, the current purification methods, and the technologies employed for genomic, transcriptomic, proteomic, and lipidomic evaluation of their cargoes. Our thorough examination of the literature highlights the current limitations and promising future of exosomes as a liquid biopsy for the identification of circulating tumor biomarkers.
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Affiliation(s)
- Megan I Mitchell
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Claire L Carter
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
| | - Olivier Loudig
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ 07110, USA
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12
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Ha SM, Kim HK, Kim Y, Noh DY, Han W, Chang JM. Diagnostic performance improvement with combined use of proteomics biomarker assay and breast ultrasound. Breast Cancer Res Treat 2022; 192:541-552. [PMID: 35084623 DOI: 10.1007/s10549-022-06527-1] [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: 10/28/2021] [Accepted: 01/16/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE To investigate the combined use of blood-based 3-protein signature and breast ultrasound (US) for validating US-detected lesions. METHODS From July 2011 to April 2020, women who underwent whole-breast US within at least 6 months from sampling period were retrospectively included. Blood-based 3-protein signature (Mastocheck®) value and US findings were evaluated. Following outcome measures were compared between US alone and the combination of Mastocheck® value with US: sensitivity, specificity, positive predictive value (PPV), negative predictive value, area under the receiver operating characteristic curve (AUC), and biopsy rate. RESULTS Among the 237 women included, 59 (24.9%) were healthy individuals and 178 (75.1%) cancer patients. Mean size of cancers was 1.2 ± 0.8 cm. Median value of Mastocheck® was significantly different between nonmalignant (- 0.24, interquartile range [IQR] - 0.48, - 0.03) and malignant lesions (0.55, IQR - 0.03, 1.42) (P < .001). Utilizing Mastocheck® value with US increased the AUC from 0.67 (95% confidence interval [CI] 0.61, 0.73) to 0.81 (95% CI 0.75, 0.88; P < .001), and specificity from 35.6 (95% CI 23.4, 47.8) to 64.4% (95% CI 52.2, 76.6; P < .001) without loss in sensitivity. PPV was increased from 82.2 (95% CI 77.1, 87.3) to 89.3% (95% CI 85.0, 93.6; P < .001), and biopsy rate was significantly decreased from 79.3 (188/237) to 72.1% (171/237) (P < .001). Consistent improvements in specificity, PPV, and AUC were observed in asymptomatic women, in women with dense breast, and in those with normal/benign mammographic findings. CONCLUSION Mastocheck® is an effective tool that can be used with US to improve diagnostic specificity and reduce false-positive findings and unnecessary biopsies.
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Affiliation(s)
- Su Min Ha
- Department of Radiology, Seoul National University College of Medicine and Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea
| | - Hong-Kyu Kim
- Department of Surgery, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
| | - Yumi Kim
- Department of Surgery, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
- Department of Surgery, CHA University Gangnam Medical Center, Seoul, Republic of Korea
| | - Dong-Young Noh
- Department of Surgery, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
- Department of Surgery, CHA University Gangnam Medical Center, Seoul, Republic of Korea
| | - Wonshik Han
- Department of Surgery, Seoul National University College of Medicine and Seoul National University Hospital, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
| | - Jung Min Chang
- Department of Radiology, Seoul National University College of Medicine and Seoul National University Hospital, 101 Daehak-ro, Jongno-gu, Seoul, 110-744, Republic of Korea.
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13
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Tay TKY, Tan PH. Liquid Biopsy in Breast Cancer: A Focused Review. Arch Pathol Lab Med 2021; 145:678-686. [PMID: 32045277 DOI: 10.5858/arpa.2019-0559-ra] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2019] [Indexed: 01/27/2023]
Abstract
CONTEXT.— The role of liquid biopsy in cancer management has been gaining increased prominence in the past decade, with well-defined clinical applications now being established in lung cancer. Recently, the US Food and Drug Administration also approved the Therascreen PIK3CA RGQ polymerase chain reaction assay as a companion diagnostic assay to detect PIK3CA mutations in breast cancer for both tissue and liquid biopsies, bringing the role of liquid biopsy in breast cancer management to the fore. Its utility in other aspects of breast cancer, however, is yet to be clearly defined. OBJECTIVE.— To review the studies that looked at liquid biopsies in breast cancer and examine their potential for clinical application in the areas of early diagnosis, prognostication, monitoring disease response, detecting minimal residual disease, and predicting risk of progression or relapse. We focus mainly on circulating tumor cells and circulating tumor DNA. DATA SOURCES.— Peer-reviewed articles in PubMed. CONCLUSIONS.— Liquid biopsies in breast cancers have yielded promising results, especially in the areas of monitoring treatment response and predicting disease progression or relapse. With further study, and hopefully coupled with continued improvements in technologies that isolate tumor-derived materials, liquid biopsies may go on to play a greater role in the breast cancer clinic.
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Affiliation(s)
- Timothy Kwang Yong Tay
- From the Department of Anatomical Pathology (Tay, Tan), Singapore General Hospital, Singapore
| | - Puay Hoon Tan
- From the Department of Anatomical Pathology (Tay, Tan), Singapore General Hospital, Singapore.,The Division of Pathology (Tan), Singapore General Hospital, Singapore
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14
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Hepatitis C Virus Clearance by Direct-Acting Antivirals Agents Improves Endothelial Dysfunction and Subclinical Atherosclerosis: HEPCAR Study. Clin Transl Gastroenterol 2021; 11:e00203. [PMID: 32955194 PMCID: PMC7431267 DOI: 10.14309/ctg.0000000000000203] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
INTRODUCTION Hepatitis C virus (HCV) infection has been related to increased cardiovascular (CV) risk. The aim of this study was to analyze the impact of sustained virological response (SVR) on endothelial dysfunction and subclinical atherosclerosis in patients with hepatitis C virus treated with direct-acting antiviral agents. METHODS A total of 114 patients were prospectively recruited and underwent CV risk assessment including (i) endothelial dysfunction determined through laser Doppler flowmetry and (ii) subclinical atherosclerosis, elucidated by the ankle-brachial index (ABI). Atherogenic lipid profile (total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol, and triglycerides); markers of oxidative stress (oxidized low-density lipoprotein antibodies [OLAbs]), soluble markers of adhesion (vascular cell adhesion molecule [VCAM], e-selectin, and soluble markers of angiogenesis; and vascular endothelial growth factor, endothelial [EMPs] and platelet [PMPs] apoptotic microparticles, and cell-free DNA [cfDNA]) were measured. All determinations were performed at baseline, 12 weeks (SVR time), and 1 year after treatment. RESULTS In patients with endothelial dysfunction, area of hyperemia improved after virus clearance (P = 0.013) and was related to significant decrease in VCAM, e-selectin (P < 0.001), and cfDNA (P = 0.017) and to increased OLAb levels (P = 0.001). In patients with subclinical atherosclerosis at baseline, a significantly improved ABI was seen after HCV clearance (P < 0.001). Levels of both EMPs and PMPs also decreased after SVR and at follow-up (P = 0.006 and P = 0.002, respectively). DISCUSSION HCV clearance improved not only liver function but also endothelial dysfunction and subclinical atherosclerosis promoted by decrease in levels of VCAM, e-selectin, cfDNA, and PMPs and EMPs.
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15
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Kim JJ, Park K, Han YR, Kim SH, Oh SB, Oh SY, Hong YJ, Yun MS. Verification of performance of a direct fluorescent assay for cell-free DNA quantification, stability according to pre-analytical storage conditions, and the effect of freeze-thawing. Biomed Rep 2021; 15:68. [PMID: 34257964 PMCID: PMC8243239 DOI: 10.3892/br.2021.1444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/07/2021] [Indexed: 12/15/2022] Open
Abstract
A simple fluorescence-based cell-free DNA (CFD) assay has been previously developed that can directly measure nucleic acids without prior DNA extraction and amplification. However, studies on fluorescence-based CFD are lacking. In particular, there is no known information regarding the stability with regard to pre-analytical storage conditions in relation to time and temperature, or on the influence of freeze-thawing. Plasma was directly assayed to measure CFD using PicoGreen™ reagent. Standard linearity and accuracy were confirmed using salmon sperm DNA. Whole blood was left at room temperature (RT) and at 4˚C, and then plasma was separated. The CFD was also measured using thawed plasma after 1 week of freezing. As a correlation with a sperm DNA concentration, CFD demonstrated linearity over a wide range of concentrations, with a 0.998 correlation coefficient. The CFD level showed a change of up to 2.5 µg/ml according to pre-analytical storage time, and the changes were not consistent over time. The CFD values at RT after 1 h were similar to the baseline values, and the relative standard deviation was lowest under this condition. The CFD values between 4˚C and RT were similar over all time periods assessed. After freeze-thawing, the change in CFD value was reduced compared to that before freezing. The present study showed that CFD measurements using plasma processed within 1 h were optimal. Additionally, the effects of substantial changes according to storage conditions were reduced after freeze-thawing, and thus studies using stored samples is viable and relevant.
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Affiliation(s)
- Jae-Joon Kim
- Medical Oncology and Hematology, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Kwonoh Park
- Medical Oncology and Hematology, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Yu Ran Han
- Bionoxx Inc., Seongnam-si, Gyeonggi, Gyeongsangnam-do 50612, Republic of Korea
| | - Syed Hyun Kim
- Bionoxx Inc., Seongnam-si, Gyeonggi, Gyeongsangnam-do 50612, Republic of Korea
| | - Sang-Bo Oh
- Medical Oncology and Hematology, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - So Yeon Oh
- Medical Oncology and Hematology, Department of Internal Medicine, Pusan National University Yangsan Hospital, Yangsan-si, Gyeongsangnam-do 50612, Republic of Korea
| | - Yun Jeong Hong
- Department of Neurology, Uijeongbu St. Mary's Hospital, Catholic University of Korea, Seoul Special City, Gyeongsangnam-do 50612, Republic of Korea
| | - Mi Sook Yun
- Division of Biostatistics, Research Institute for Convergence of Biomedical Science and Technology, Pusan National University Yangsan Hospital, Yangsan-si, Gyeongsangnam-do 50612, Republic of Korea
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Practices and expectations on the use of circulating tumor DNA in colorectal cancer patients: A bi-national AGEO/AIOM/GERCOR/FFCD/FRENCH survey. Clin Res Hepatol Gastroenterol 2021; 45:101681. [PMID: 33785445 DOI: 10.1016/j.clinre.2021.101681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 03/22/2021] [Indexed: 02/04/2023]
Abstract
BACKGROUND Increasing evidence shows that circulating tumor DNA (ctDNA) is a valuable tool in providing molecular, prognostic, predictive and dynamic information in colorectal cancer (CRC) patients. This study aimed to make a picture of knowledge, practice, attitudes and expectations about ctDNA in CRC patients. MATERIAL AND METHODS An online CRC-ctdna survey was distributed from November 2019 to January 2020 to French and Italian cooperative and scientific groups of Hepato-Gastroenterologists (HGE), Medical Oncologists (MO), Radiotherapists (RT) and Digestive Surgeons (DS). RESULTS Overall, 307 physicians completed the survey (57% Italian; 43% French). Most of them were MO (62%) and HGE (24%). Affiliations were University Hospital (48%), Cancer Center (21%), General Hospital (21%) and Private Hospital (10%). Notably, half of respondents declared to have access to ctDNA in their daily practice. Of them, 53% uses ctDNA to assess RAS/BRAF status only, 46% for RAS/BRAF with other mutations and 1% only for other mutations. MO and HGE identified quick RAS profiling (P = 0.031) as the main reason of interest in the use of ctDNA. Physicians from University Hospitals and Cancer Centers prescribed more ctDNA (P < 0.001) and more often in house (P < 0.001). The main future expectations concerning ctDNA were to guide therapeutic strategies in metastatic (78%) and adjuvant (73%) settings, and to better/quicker profile disease at baseline (56%). CONCLUSION Half of participants can order ctDNA in their daily practice. Molecular profiling of metastatic patients remains the main goal of ctDNA use and ctDNA-based therapeutic strategies are an expectation for the future in both adjuvant and metastatic settings.
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Self-rated health in individuals with and without disease is associated with multiple biomarkers representing multiple biological domains. Sci Rep 2021; 11:6139. [PMID: 33731775 PMCID: PMC7969614 DOI: 10.1038/s41598-021-85668-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/01/2021] [Indexed: 12/18/2022] Open
Abstract
Self-rated health (SRH) is one of the most frequently used indicators in health and social research. Its robust association with mortality in very different populations implies that it is a comprehensive measure of health status and may even reflect the condition of the human organism beyond clinical diagnoses. Yet the biological basis of SRH is poorly understood. We used data from three independent European population samples (N approx. 15,000) to investigate the associations of SRH with 150 biomolecules in blood or urine (biomarkers). Altogether 57 biomarkers representing different organ systems were associated with SRH. In almost half of the cases the association was independent of disease and physical functioning. Biomarkers weakened but did not remove the association between SRH and mortality. We propose three potential pathways through which biomarkers may be incorporated into an individual’s subjective health assessment, including (1) their role in clinical diseases; (2) their association with health-related lifestyles; and (3) their potential to stimulate physical sensations through interoceptive mechanisms. Our findings indicate that SRH has a solid biological basis and it is a valid but non-specific indicator of the biological condition of the human organism.
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18
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Drag MH, Kilpeläinen TO. Cell-free DNA and RNA-measurement and applications in clinical diagnostics with focus on metabolic disorders. Physiol Genomics 2020; 53:33-46. [PMID: 33346689 DOI: 10.1152/physiolgenomics.00086.2020] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Circulating cell-free DNA (cfDNA) and RNA (cfRNA) hold enormous potential as a new class of biomarkers for the development of noninvasive liquid biopsies in many diseases and conditions. In recent years, cfDNA and cfRNA have been studied intensely as tools for noninvasive prenatal testing, solid organ transplantation, cancer screening, and monitoring of tumors. In obesity, higher cfDNA concentration indicates accelerated cellular turnover of adipocytes during expansion of adipose mass and may be directly involved in the development of adipose tissue insulin resistance by inducing inflammation. Furthermore, cfDNA and cfRNA have promising diagnostic value in a range of obesity-related metabolic disorders, such as nonalcoholic fatty liver disease, type 2 diabetes, and diabetic complications. Here, we review the current and future applications of cfDNA and cfRNA within clinical diagnostics, discuss technical and analytical challenges in the field, and summarize the opportunities of using cfDNA and cfRNA in the diagnostics and prognostics of obesity-related metabolic disorders.
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Affiliation(s)
- Markus H Drag
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tuomas O Kilpeläinen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Fiste O, Liontos M, Koutsoukos K, Terpos E, Dimopoulos MA, Zagouri F. Circulating tumor DNA-based predictive biomarkers in breast cancer clinical trials: a narrative review. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1603. [PMID: 33437802 PMCID: PMC7791253 DOI: 10.21037/atm-20-1175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 09/06/2020] [Indexed: 12/31/2022]
Abstract
Breast carcinoma is the most frequent and the second leading cause of cancer mortality in women worldwide. Current treatment decisions are based on tumor profiling of the initial tissue biopsy. Cancer though evolves both spatially and temporarily in a significant percentage of patients during treatment. However, sequential biopsies from the primary tumor or its metastatic sites are not either convenient or feasible in the majority of cases. In the era of precision medicine, analysis of circulating blood-based biomarkers in the field of liquid biopsies provides an insight into the dynamic molecular profiling of the primary tumor and its metastases, in a relatively non-invasive way. The latter permits not only patient stratification but also longitudinal evaluation of treatment response, when incorporated into clinical trials. This review summarizes the results from recent and ongoing circulating tumor DNA (ctDNA)-based biomarker-driven clinical trials, with respect to ctDNA analysis' predictive role, both in adjuvant, neo-adjuvant, and metastatic setting. Furthermore, current challenges in ctDNA analysis applications are critically discussed, including pre-analytical and analytical issues, and future perspectives in this field, through the conduct of well-designed, multicenter, randomized, large-scale, biomarker-stratified trials, with robust statistical methods. Despite in its infancy, ctDNA analysis holds great promise as a minimally invasive tool regarding tailored, personalized treatment guidance for breast cancer patients.
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Affiliation(s)
- Oraianthi Fiste
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Michael Liontos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Konstantinos Koutsoukos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Meletios A Dimopoulos
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
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Plasma Cell-Free Human Papillomavirus Oncogene E6 and E7 DNA Predicts Outcome in Oropharyngeal Squamous Cell Carcinoma. J Mol Diagn 2020; 22:1333-1343. [PMID: 32822851 DOI: 10.1016/j.jmoldx.2020.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 07/30/2020] [Accepted: 08/03/2020] [Indexed: 12/24/2022] Open
Abstract
Persistent human papillomavirus (HPV) infection is associated with the development of oropharyngeal squamous cell carcinoma (OPSCC), and increasing incidences of OPSCC are reported. The generally favorable treatment outcome in patients with HPV-driven OPSCC has brought de-escalation of treatment into discussion. Nevertheless, 13% to 25% develop a relapse within two years after current standard treatment. New biomarkers are urgently required to monitor therapy response, tumor burden, and minimal residual disease during follow-up. This observational study examined 50 patients with OPSCC to investigate plasma cell-free (cf) HPV-DNA derived from tumor cells before therapy and during follow-up. Real-time PCR was applied to quantify the DNA concentration of HPV oncogenes E6 and E7. A total of 85.7% of pretreatment samples from patients with HPV-driven OPSCC (n = 28) were positive for at least one marker, and cfHPV-DNA concentration increased with tumor size. Virtually no signals were detected in HPV-negative OPSCC patients (n = 20; P ≤ 0.001). Patients without clinical evidence of recurrence had significantly reduced cfHPV-DNA concentrations after therapy (P ≤ 0.001). Conversely, cfHPV-DNA levels increased or remained above threshold in five patients who had residual disease or developed recurrence. In conclusion, plasma cfHPV-DNA detection correlates with the clinical course of disease in patients with HPV-driven OPSCC. Consequently, extensive clinical investigation should be considered if cfHPV-DNA is detected during follow-up of patients with HPV-driven OPSCC.
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21
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Ewing sarcoma family of tumors-derived small extracellular vesicle proteomics identify potential clinical biomarkers. Oncotarget 2020; 11:2995-3012. [PMID: 32821345 PMCID: PMC7415402 DOI: 10.18632/oncotarget.27678] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Accepted: 06/20/2020] [Indexed: 01/03/2023] Open
Abstract
PURPOSE Ewing Sarcoma Family of Tumors (ESFT), the second most common pediatric osseous malignancy, are characterized by the pathognomonic chromosomal EWS-ETS translocation. Outside of tumor biopsy, no clinically relevant ESFT biomarkers exist. Additionally, tumor burden assessment at diagnosis, monitoring of disease responsiveness to therapy, and detection of disease recurrence are limited to radiographic imaging. To identify new, clinically relevant biomarkers we evaluated the proteome of a subset of ESFT-derived small extracellular vesicles (sEVs). MATERIALS AND METHODS We performed the first high quality proteomic study of ESFT-derived sEVs from 5 ESFT cell lines representing the most common EWS-ETS fusion types and identified 619 proteins composing the core ESFT sEV proteome. We compared these core proteins to databases of common plasma-based proteins and sEV-associated proteins found within healthy plasma to identify proteins unique or enriched within ESFT. RESULTS From these analyses, two membrane bound proteins with biomarker potential were selected, CD99/MIC2 and NGFR, to develop a liquid-based assay enriching of ESFT-associated sEVs and detection of sEV mRNA cargo (i.e., EWS-ETS transcripts). We employed this immuno-enrichment approach to diagnosis of ESFT utilizing plasma (250 μl) from both localized and metastatic ESFT pediatric patients and cancer-free controls, and showed significant diagnostic power [AUC = 0.92, p = 0.001 for sEV numeration, with a PPV = 1.00, 95% CI = (0.63, 1.00) and a NPV = 0.67, 95% CI = (0.30, 0.93)]. CONCLUSIONS In this study, we demonstrate utilization of circulating ESFT-associated sEVs in pediatric patients as a source of minimally invasive diagnostic and potentially prognostic biomarkers.
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22
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Liao H, Li H. Advances in the Detection Technologies and Clinical Applications of Circulating Tumor DNA in Metastatic Breast Cancer. Cancer Manag Res 2020; 12:3547-3560. [PMID: 32547192 PMCID: PMC7244344 DOI: 10.2147/cmar.s249041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/16/2020] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) represents the most commonly diagnosed cancer among females worldwide. Although targeted therapy has greatly improved the efficacy of treating BC, a large proportion of BC patients eventually develop recurrence or metastasis. Traditional invasive tumor tissue biopsy is short of comprehensiveness in tumor assessment due to heterogeneity. Liquid biopsy, an attractive non-invasive approach mainly including circulating tumor cell and circulating tumor DNA (ctDNA), has been widely utilized in a variety of cancers with the advances of sequencing technologies in recent years. The ctDNA that is found circulating in body fluids refers to DNA released from tumor cells and has shown clinical utility in metastatic breast cancer (MBC). With the results of genomic variants detection, ctDNA could be used to predict clinical outcomes, monitor disease progression, and guide treatment for patients with MBC. Moreover, the drug resistance problem may be addressed by ctDNA detection. In this review, we summarized the technological developments and clinical applications of ctDNA in MBC.
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Affiliation(s)
- Hao Liao
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
| | - Huiping Li
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing 100142, People's Republic of China
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23
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Alghofaili L, Almubarak H, Gassem K, Islam SS, Coskun S, Kaya N, Karakas B. Cell-free DNA levels of twins and sibling pairs indicate individuality and possible use as a personalized biomarker. PLoS One 2019; 14:e0223470. [PMID: 31600277 PMCID: PMC6786590 DOI: 10.1371/journal.pone.0223470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/22/2019] [Indexed: 01/01/2023] Open
Abstract
Cell-free DNA (cfDNA) in the human blood circulation has been under investigation since its initial observation in 1948. Plasma cfDNA is known to be significantly elevated in diseased people. Due to possible variation in the population, evaluating cfDNA as a non-invasive biomarker at disease onset alone may not be sensitive enough to accurately diagnose diseases, particularly early stage cancers on a personal level. To understand the factors that define the cfDNA levels on the personal level and for better use as a non-invasive biomarker, we isolated cfDNA from the plasma of healthy individuals with varying degrees of genetic and/or environmental similarities (monozygotic twins, dizygotic twins, sibling pairs, and unrelated individuals) as well as from patients with varying stages of breast and ovarian cancer undergoing treatment. Cell-free DNA levels were quantified by a fluorometer (ng/ml) and/or real-time PCR (copies/ml). The associations between individuals with various degrees of genetic and/or environmental similarities and their plasma cfDNA levels were evaluated. The ACE model (A = additive genetic, C = common environment, and E = specific environmental factors) was used to determine the proportion of each factor on the cfDNA levels. We found a high correlation (r = 0.77; p < 0.0001) in plasma cfDNA levels between monozygotic twins (n = 39). However, the correlation was gradually reduced to moderate (r = 0.47; p = 0.016) between dizygotic twins (n = 13) and low correlation (r = 0.28; p = 0.043) between sibling pairs (n = 26). The ACE model analysis showed that the plasma cfDNA level of a given healthy individual is influenced both by genetic and the environmental components in similar proportions (53% and 47%, respectively; A = 53%, C = 22.5%, E = 24.5%). Moreover, while age had no effect, gender significantly influenced the individual’s plasma cfDNA level. As expected, cfDNA levels were significantly higher in both breast (n = 26) (p<0.0001) and ovarian (n = 64) (p<0.0001) cancer patients compared to the healthy individuals. Our study demonstrated that both genome and environmental factors modulate the individual’s cfDNA level suggesting that its diagnostic sensitivity may be improved only if the person’s cfDNA level is known prior to disease presentation.
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Affiliation(s)
- Lamyaa Alghofaili
- Translational Cancer Research Section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.,Alfaisal University Medical School, Riyadh, Saudi Arabia
| | - Hannah Almubarak
- Translational Cancer Research Section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Khawlah Gassem
- Translational Cancer Research Section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Syed S Islam
- Translational Cancer Research Section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Serdar Coskun
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Namik Kaya
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Bedri Karakas
- Translational Cancer Research Section, Department of Molecular Oncology, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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24
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Chen Z, Zhang S, Li C, Xu C, Zhao J, Miao L. Comprehensive Evaluation of the Factors Affecting Plasma Circulating Cell-Free DNA Levels and Their Application in Diagnosing Nonsmall Cell Lung Cancer. Genet Test Mol Biomarkers 2019; 23:270-276. [PMID: 30986099 DOI: 10.1089/gtmb.2018.0106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
AIMS Circulating cell-free DNA (ccfDNA) is a valuable biomarker, but the ccfDNA levels are influenced by variations that occur during sample processing. The feasibility of using ccfDNA as a diagnostic biomarker requires further examination. MATERIALS AND METHODS We established a real-time PCR assay with an external standard to comprehensively evaluate the factors affecting ccfDNA levels, including the extraction kit used, freeze-thaw stability, and stability of delayed extraction. Then we compared the ccfDNA levels between benign controls (64 cases, including 23 sarcoidosis patients, 19 pneumonia patients, and 22 other lung disease patients) and nonsmall cell lung cancer (NSCLC) patients (74 patients). RESULTS The different kits showed different recovery rates. Moreover, the ccfDNA present in plasma or stored in extraction buffer was stable after freeze-thawing, and the ccfDNA concentration remained consistent for 24 h at 4°C and for 12 h at room temperature. The patients with NSCLC-III/IV exhibited significantly higher ccfDNA levels than the patients with NSCLC-I/II (293 copies/μL vs. 190 copies/μL, p = 0.0339). However, no significant differences in the plasma ccfDNA levels were observed between the benign controls and NSCLC patients (241 copies/μL vs. 233 copies/μL, p > 0.05). CONCLUSIONS Variations in sample processing procedures led to variable results. The lack of differences between the NSCLC patients and benign controls indicates that further research is necessary to better characterize ccfDNA as a biomarker for diagnosing NSCLC.
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Affiliation(s)
- Zhiyao Chen
- 1 Department of Clinical Pharmacology Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Shichao Zhang
- 1 Department of Clinical Pharmacology Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China.,2 College of Pharmaceutical Sciences, Soochow University, Suzhou, P.R. China
| | - Chang Li
- 3 Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Chun Xu
- 3 Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Jun Zhao
- 3 Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China
| | - Liyan Miao
- 1 Department of Clinical Pharmacology Research Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, P.R. China.,2 College of Pharmaceutical Sciences, Soochow University, Suzhou, P.R. China
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25
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Çelik F, Tan YZ, Özdemir S, Sılan F. Comparison of SUV max Values Obtained from F-18 FDG PET/CT and Cell-free DNA Levels Measured from Plasma in Oncology Patients. Mol Imaging Radionucl Ther 2019; 28:46-52. [PMID: 31234620 PMCID: PMC6592314 DOI: 10.4274/mirt.galenos.2019.60352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Objectives The aim of this study was to compare the quantitative value of standardized uptake value (SUV) SUVmax obtained from F-18 FDG positron emission tomography/computed tomography (PET/CT) imaging of oncology patients with the cell-free DNA (cfDNA) amounts measured in plasma of patients and thus investigate if cfDNA is a significant marker to identify the presence of malignancy in the early period. Methods A total of 184 patients were included in the study. The clinical, histopathologic, laboratory and treatment parameters were extracted from patient files. SUVmax and cfDNA quantities were assessed Results There was no statistically significant difference in plasma cfDNA values between patient and control groups. The comparison of SUVmax and cfDNA values in the study showed that there was a weak correlation between SUVmaxand cfDNA. There was a significant difference between tumor size and SUVmax values. However, there was no statistically significant difference between tumor size and cfDNA. Conclusion cfDNA measurements in the blood as a screening test have provided hope for early diagnosis and monitoring of cancer patients. Comparison of cfDNA levels obtained from plasma and quantitative parameters from PET/CT images of oncology patients in detailed advanced studies with larger patient series are required.
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Affiliation(s)
- Fatmanur Çelik
- Çanakkale Onsekiz Mart University Faculty of Medicine, Department of Nuclear Medicine, Çanakkale, Turkey
| | - Yusuf Ziya Tan
- Çanakkale Onsekiz Mart University Faculty of Medicine, Department of Nuclear Medicine, Çanakkale, Turkey
| | - Semra Özdemir
- Çanakkale Onsekiz Mart University Faculty of Medicine, Department of Nuclear Medicine, Çanakkale, Turkey
| | - Fatma Sılan
- Çanakkale Onsekiz Mart University Faculty of Medicine, Department of Medical Genetic, Çanakkale, Turkey
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26
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Bedin C, Crotti S, D'Angelo E, D'Aronco S, Pucciarelli S, Agostini M. Circulating Biomarkers for Response Prediction of Rectal Cancer to Neoadjuvant Chemoradiotherapy. Curr Med Chem 2019; 27:4274-4294. [PMID: 31060482 DOI: 10.2174/0929867326666190507084839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 03/05/2019] [Accepted: 04/18/2019] [Indexed: 12/20/2022]
Abstract
Rectal cancer response to neoadjuvant Chemoradiotherapy (pCRT) is highly variable. In fact, it has been estimated that only about 21 % of patients show pathologic Complete Response (pCR) after therapy, while in most of the patients a partial or incomplete tumour regression is observed. Consequently, patients with a priori chemoradioresistant tumour should not receive the treatment, which is associated with substantial adverse effects and does not guarantee any clinical benefit. For Locally Advanced Rectal Cancer Patients (LARC), a standardized neoadjuvant treatment protocol is applied, the identification and the usefulness of prognostic or predictive biomarkers can improve the antitumoural treatment strategy, modifying the sequence, dose, and combination of radiotherapy, chemotherapy and surgical resection. For these reasons, a growing number of studies are actually focussed on the discovery and investigation of new predictive biomarkers of response to pCRT. In this review, we have selected the most recent literature (2012-2017) regarding the employment of blood-based biomarkers potentially predicting pCR in LARC patients and we have critically discussed them to highlight their real clinical benefit and the current limitations of the proposed methodological approaches.
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Affiliation(s)
- Chiara Bedin
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy
| | - Sara Crotti
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy
| | - Edoardo D'Angelo
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy
| | - Sara D'Aronco
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy,First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Science, University of
Padua, Padua, Italy
| | - Salvatore Pucciarelli
- First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Science, University of
Padua, Padua, Italy
| | - Marco Agostini
- Nano-inspired Biomedicine Lab, Paediatric Research Institute-Città della Speranza, Padua, Italy,First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Science, University of
Padua, Padua, Italy
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27
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Iehara T, Yagyu S, Gotoh T, Ouchi K, Yoshida H, Miyachi M, Kikuchi K, Sugimoto T, Hosoi H. A prospective evaluation of liquid biopsy for detecting MYCN amplification in neuroblastoma patients. Jpn J Clin Oncol 2019; 49:743-748. [DOI: 10.1093/jjco/hyz063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Revised: 02/25/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Our previous study reported a method for determining MYCN gene amplification (MNA) status using cell-free DNA in serum. We prospectively analyzed the serum MNA status using sera obtained before the initial diagnosis from patients with neuroblastoma and evaluated the utility of this method.
Methods
Eighty patients were enrolled in the study. The serum MYCN/NAGK ratio was assessed for all cases.
Results
Fifteen cases showed serum MNA, while 65 did not. Of the 80 total patients, tumor samples for a genetic analysis were not obtained from 27 due to the patients’ condition or other reasons. For the 43 of 80 cases that had both serum and tumor samples analyzed, the serum-based MNA status matched to tumor-based MNA status (P < 0.001). The sensitivity and the specificity were 100%, respectively. Seven of 15 cases who diagnosed as MNA by serum-based MNA status were <18 months of age, and tumor samples were not obtained from 4 of these cases. Based on the serum MNA status, these cases were able to start treatment immediately. The 4-year event-free survival rates of cases with and without MNA in sera were 37.5% and 84.8%, respectively (P < 0.001).
Conclusion
The serum-based MNA status was useful for precisely predicting the MNA status in tumor and it has clinical benefits for predicting risk stratification in patients for whom obtaining tumor samples is difficult.
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Affiliation(s)
- Tomoko Iehara
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Shigeki Yagyu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Takahiro Gotoh
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Kazutaka Ouchi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Hideki Yoshida
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Mitsuru Miyachi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Ken Kikuchi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Tohru Sugimoto
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
| | - Hajime Hosoi
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kawaramachi-Hirokoji Kamigyo-ku, Kyoto 602-8566, Japan
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28
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Yang JYC, Verleden SE, Zarinsefat A, Vanaudenaerde BM, Vos R, Verleden GM, Sarwal RD, Sigdel TK, Liberto JM, Damm I, Watson D, Sarwal MM. Cell-Free DNA and CXCL10 Derived from Bronchoalveolar Lavage Predict Lung Transplant Survival. J Clin Med 2019; 8:jcm8020241. [PMID: 30781765 PMCID: PMC6406976 DOI: 10.3390/jcm8020241] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/05/2019] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
Standard methods for detecting chronic lung allograft dysfunction (CLAD) and rejection have poor sensitivity and specificity and have conventionally required bronchoscopies and biopsies. Plasma cell-free DNA (cfDNA) has been shown to be increased in various types of allograft injury in transplant recipients and CXCL10 has been reported to be increased in the lung tissue of patients undergoing CLAD. This study used a novel cfDNA and CXCL10 assay to evaluate the noninvasive assessment of CLAD phenotype and prediction of survival from bronchoalveolar lavage (BAL) fluid. A total of 60 BAL samples (20 with bronchiolitis obliterans (BOS), 20 with restrictive allograft syndrome (RAS), and 20 with stable allografts (STA)) were collected from 60 unique lung transplant patients; cfDNA and CXCL10 were measured by the ELISA-based KIT assay. Median cfDNA was significantly higher in BOS patients (6739 genomic equivalents (GE)/mL) versus STA (2920 GE/mL) and RAS (4174 GE/mL) (p < 0.01 all comparisons). Likelihood ratio tests revealed a significant association of overall survival with cfDNA (p = 0.0083), CXCL10 (p = 0.0146), and the interaction of cfDNA and CXCL10 (p = 0.023) based on multivariate Cox proportional hazards regression. Dichotomizing patients based on the median cfDNA level controlled for the mean level of CXCL10 revealed an over two-fold longer median overall survival time in patients with low levels of cfDNA. The KIT assay could predict allograft survival with superior performance compared with traditional biomarkers. These data support the pursuit of larger prospective studies to evaluate the predictive performance of cfDNA and CXCL10 prior to lung allograft failure.
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Affiliation(s)
- Joshua Y C Yang
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- KIT Bio, 2000 University Avenue, Palo Alto, CA 94303, USA.
| | - Stijn E Verleden
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Arya Zarinsefat
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Bart M Vanaudenaerde
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Robin Vos
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Geert M Verleden
- Leuven Lung Transplant Unit, Department of Chronic Diseases, Metabolism, and Ageing (CHROMETA), KU Leuven, 3000 Leuven, Belgium.
| | - Reuben D Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Tara K Sigdel
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Juliane M Liberto
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Izabella Damm
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
| | - Drew Watson
- KIT Bio, 2000 University Avenue, Palo Alto, CA 94303, USA.
| | - Minnie M Sarwal
- Department of Surgery, University of California San Francisco, San Francisco, CA 94143, USA.
- KIT Bio, 2000 University Avenue, Palo Alto, CA 94303, USA.
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29
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Rushton JG, Ertl R, Klein D, Tichy A, Nell B. Circulating cell-free DNA does not harbour a diagnostic benefit in cats with feline diffuse iris melanomas. J Feline Med Surg 2019; 21:124-132. [PMID: 29529957 PMCID: PMC10814613 DOI: 10.1177/1098612x18762017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
OBJECTIVES Feline diffuse iris melanoma (FDIM) is the most common malignant primary intraocular tumour in cats, with reported metastases rates between 19% and 63%. Currently, the only available diagnostic tool for a tentative diagnosis is histopathological examination of the enucleated eye. Therefore, the veterinary ophthalmologist is often faced with the dilemma of whether to enucleate an oftentimes visual eye or to continue monitoring, with the risk of metastases developing. In the past, cell-free DNA (cfDNA) gained more attention in human medicine, especially in the field of oncology. Prior studies have shown the use of cfDNA as diagnostic or prognostic markers in canine and human cancer patients. Therefore, the aim of this study was to investigate cfDNA concentration and integrity in cats with FDIMs compared with cats with benign iris naevi and without ocular abnormalities. METHODS cfDNA from plasma of cats with iris melanoma (n = 34), iris naevus (n = 30) and without ocular abnormalities (n = 32) were extracted. Primer and probes for feline amyloid beta precursor protein ( APP) and beta actin ( ACTB) were designed for amplicons of various lengths and quantitative PCRs of extracted cfDNA were performed to measure cfDNA concentration and integrity of the plasma samples. Differences of cfDNA concentrations and integrity levels between the three groups (iris melanoma, iris naevi and controls) were analysed using the Mann-Whitney U-test. RESULTS cfDNA concentration and integrity analysis revealed no significant differences between the cats with iris melanoma, iris naevus or the control group ( P >0.01). Cats with metastases showed similar cfDNA concentration and integrity to cats without metastases. CONCLUSIONS AND RELEVANCE cfDNA concentration and integrity seem to be insufficient as a diagnostic or prognostic marker in cats with FDIMs.
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Affiliation(s)
- Jessica G Rushton
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
| | - Reinhard Ertl
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Dieter Klein
- VetCore Facility for Research, Vetmeduni Vienna, Vienna, Austria
| | - Alexander Tichy
- Department of Biomedical Sciences, Vetmeduni Vienna, Vienna, Austria
| | - Barbara Nell
- Department for Companion Animals and Horses, Vetmeduni Vienna, Vienna, Austria
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30
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Buono G, Gerratana L, Bulfoni M, Provinciali N, Basile D, Giuliano M, Corvaja C, Arpino G, Del Mastro L, De Placido S, De Laurentiis M, Cristofanilli M, Puglisi F. Circulating tumor DNA analysis in breast cancer: Is it ready for prime-time? Cancer Treat Rev 2019; 73:73-83. [PMID: 30682661 DOI: 10.1016/j.ctrv.2019.01.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 01/06/2023]
Abstract
Precision Medicine is becoming the new paradigm in healthcare as it enables better resources allocation, treatment optimization with a potential side-effects reduction and consequent impact on quality of life and survival. This revolution is being catalyzed by liquid biopsy technologies, which provide prognostic and predictive information for advanced cancer patients, without the analytical and procedural drawbacks of tissue-biopsy. In particular, circulating tumor DNA (ctDNA) is gaining momentum as a clinically feasible option capable to capture both spatial and temporal tumor heterogeneity. Several techniques are currently available for ctDNA extraction and analysis, each with its preferential case scenarios and preanalytical implications which must be taken into consideration to effectively support clinical decision-making and to better highlight its clinical utility. Aim of this review is to summarize both analytical developments and clinical evidences to offer a comprehensive update on the deployment of ctDNA in breast cancer's (BC) characterization and treatment.
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Affiliation(s)
- Giuseppe Buono
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lorenzo Gerratana
- Department of Medicine (DAME), University of Udine, Italy; Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Michela Bulfoni
- Department of Pathology, ASUIUD University Hospital, Udine, Italy
| | | | - Debora Basile
- Department of Medicine (DAME), University of Udine, Italy
| | - Mario Giuliano
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy; Lester and Sue Smith Breast Center at Baylor College of Medicine, Houston, TX, USA
| | - Carla Corvaja
- Department of Medicine (DAME), University of Udine, Italy
| | - Grazia Arpino
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | - Lucia Del Mastro
- Department of Medical Oncology, IRCCS AOU San Martino-IST, National Cancer Institute, Genova, Italy
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, Oncology Division, University of Naples Federico II, Naples, Italy
| | | | - Massimo Cristofanilli
- Department of Medicine-Hematology and Oncology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Fabio Puglisi
- Department of Medicine (DAME), University of Udine, Italy; Department of Medical Oncology, Centro di Riferimento Oncologico (CRO), IRCCS, Aviano, PN, Italy
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31
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Delmonico L, Costa MASM, Fournier MV, Romano SDO, Nascimento CMD, Barbosa AS, Moreira ADS, Scherrer LR, Ornellas MHF, Alves G. Mutation profiling in the PIK3CA, TP53, and CDKN2A genes in circulating free DNA and impalpable breast lesions. Ann Diagn Pathol 2019; 39:30-35. [PMID: 30634138 DOI: 10.1016/j.anndiagpath.2018.12.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 12/21/2018] [Accepted: 12/30/2018] [Indexed: 01/05/2023]
Abstract
Breast impalpable lesions have become a clinical dilemma because they are small, presenting a heterogeneous cellular phenotype. The aim of this study was to evaluate the mutational profile of the PIK3CA, TP53, and CDKN2A genes, comparing the mammary tissue with the respective circulating free DNA (cfDNA). The PIK3CA, TP53, and CDKN2A genes were sequenced (PCR-Sanger) in 58 women with impalpable lesions (49 malignant and 9 benign) with the respective cfDNA. The chi-square or Fisher's exact test was used to evaluate statistical significance between the clinical variables and mutational profile. A total of 51 out of 58 samples generated successful mutation profiles in both breast lesion and cfDNA. Of the 37 mutations detected, 10 (27%) and 16 (43%) mutations were detected in benign and malignant breast lesions, respectively, while 2 (5%) and 9 (24%) were found in cfDNA of women with benign and malignant lesions, respectively. The lymph node involvement with mutations in the PIK3CA in malignant lesions (P = 0.001), and the relationship between mutations in PIK3CA, comparing ductal tumors with benign lesions (P = 0.05), were statistically significant. This study detected different mutations in PIK3CA, TP53, and CDKN2A genes, which represent, in part, the heterogeneity of impalpable lesions. The results confirm that more studies should be conducted on the functional role of cfDNA in the impalpable lesions.
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Affiliation(s)
- Lucas Delmonico
- Circulating Biomarkers Laboratory, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Graduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.
| | | | | | | | | | | | - Aline Dos Santos Moreira
- Laboratory of Functional Genomics and Bioinformatics, PTDIS/FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | | | - Maria Helena Faria Ornellas
- Circulating Biomarkers Laboratory, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Graduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil
| | - Gilda Alves
- Circulating Biomarkers Laboratory, Faculty of Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil; Graduate Program in Medical Sciences, Rio de Janeiro State University, Rio de Janeiro 20550-170, Brazil.
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Advantage of Next-Generation Sequencing in Dynamic Monitoring of Circulating Tumor DNA over Droplet Digital PCR in Cetuximab Treated Colorectal Cancer Patients. Transl Oncol 2018; 12:426-431. [PMID: 30562681 PMCID: PMC6297189 DOI: 10.1016/j.tranon.2018.11.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 11/27/2018] [Accepted: 11/27/2018] [Indexed: 12/24/2022] Open
Abstract
Epidermal growth factor receptor (EGFR) blockade resistance is common in the treatment of RAS wide type colorectal cancer (CRC). During the treatment of cetuximab, acquired resistant genomic alterations always occurs earlier than disease progression observed by medical images. Identification of genomic alterations dynamically might have certain clinical significance. Because of the limitation of repeated tissue biopsy, liquid biopsy is increasingly recognized. Droplet digital polymerase chain reaction (ddPCR) is the main detection methods for circulating tumor DNA (ctDNA), however, the application of next-generation sequencing (NGS) for ctDNA detection becomes more and more popular. Here we develop a NGS-based ctDNA assay and evaluated its sensitivity and specificity while using ddPCR as control. These two technologies were both used for genomic alteration detection for the peripheral blood samples from cetuximab-treated colorectal cancer patients dynamically. Fifteen patients were enrolled in this study, including eight males and seven females. The sensitivity and specificity of our NGS assay were 87.5% and 100% respectively, and liner regression analysis comparing variant allele frequency (VAF) revealed high concordance between NGS and ddPCR (R2 = 0.98). NGS actually found more mutation information than ddPCR such as the additional dynamic changes of TP53 which were observed in the disease progression patients. Moreover, the variant allele fraction of TP53 was also found by NGS to be changed along with the clinical efficacy evaluation dynamically during the whole treatment process. In conclusion, our newly developed NGS-based ctDNA assay shows similar performance with ddPCR but have more advantages of its high throughput of multigenetic detection for the dynamic monitoring during the treatment of cetuximab in metastasis CRC patients.
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Lin LH, Chang KW, Kao SY, Cheng HW, Liu CJ. Increased Plasma Circulating Cell-Free DNA Could Be a Potential Marker for Oral Cancer. Int J Mol Sci 2018; 19:ijms19113303. [PMID: 30352977 PMCID: PMC6274798 DOI: 10.3390/ijms19113303] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Revised: 10/18/2018] [Accepted: 10/22/2018] [Indexed: 12/28/2022] Open
Abstract
Background: Oral squamous cell carcinoma (OSCC) is a disease that affects patients worldwide. DNA of dead cells is released into the blood stream and may be isolated from plasma or serum samples. This DNA is termed cell-free DNA (cfDNA). cfDNA is increased in several types of malignancies. We investigated if there was a correlation between cfDNA levels and the progression of OSCC. Methods: Using quantitative spectrometry, we measured plasma cfDNA in 121 patients with OSCC and 50 matched controls. Mann Whitney and Wilcoxon tests were used to compare differences among various clinical variants. Receiver operating characteristic (ROC) analysis was used to obtain levels suitable for the separation of the clinical subsets. Kaplan-Meier analysis was used to assess correlation with survival. Results: Plasma cfDNA was significantly elevated in patients with OSCC relative to controls. Plasma cfDNA levels correlated with larger tumor size, cervical lymph node metastasis and late stage. Higher plasma cfDNA levels were associated with a poor prognosis of OSCC, which is a new finding. Conclusion: Plasma cfDNA could serve as a novel and easily accessible biomarker in OSCC, providing diagnostic and prognostic value.
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Affiliation(s)
- Li-Han Lin
- Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan.
| | - Kuo-Wei Chang
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Department of Stomatology, Medical Education and Research, Veterans General Hospital, Taipei 11217, Taiwan.
| | - Shou-Yen Kao
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Department of Stomatology, Medical Education and Research, Veterans General Hospital, Taipei 11217, Taiwan.
| | - Hui-Wen Cheng
- Department of Medical Research, MacKay Memorial Hospital, Taipei 10449, Taiwan.
| | - Chung-Ji Liu
- Institute of Oral Biology, School of Dentistry, National Yang-Ming University, Department of Oral and Maxillofacial Surgery, Taipei MacKay Memorial Hospital, Taipei 10449, Taiwan.
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Garley M, Dziemiańczyk-Pakieła D, Grubczak K, Surażyński A, Dąbrowska D, Ratajczak-Wrona W, Sawicka-Powierza J, Borys J, Moniuszko M, Pałka JA, Jabłońska E. Differences and similarities in the phenomenon of NETs formation in oral inflammation and in oral squamous cell carcinoma. J Cancer 2018; 9:1958-1965. [PMID: 29896280 PMCID: PMC5995950 DOI: 10.7150/jca.24238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 02/17/2018] [Indexed: 12/20/2022] Open
Abstract
Taking into account the previously reported relationship between inflammation and carcinogenesis, and the scant amount of data concerning the role of neutrophil extracellular traps (NETs) in carcinogenesis, we decided to study the process of extracellular trap formation in patients with inflammation as well as in patients with cancer occurring in the same location. For preliminary isolation of neutrophils (PMNs), we used Polymorphprep™, then sorted with Microbeads. The cells were recorded in the incubation chamber with a BD Pathway 855 microscope system. Flow cytometric data (MPO+ neutrophils) were acquired on FACSCalibur flow cytometer. Amounts of cfDNA were determined by Abcam's Circulating DNA Quantification Kit. Neutrophils of patients with inflammation and of subjects with stage I/II oral squamous cell carcinoma (OSCC) produce increased amounts of NETs, while stage III/IV OSCC were comparable with the control group. In all of the studied groups of cells stimulation with LPS and rhIL-17 produced more NETs in relation to unstimulated cells. Neutrophil supernatant of inflammation patients and stage I/II cancer patients demonstrated the increased level of cfDNA, which decreased at stage III/IV. Patients with oral inflammations showed an increased rate of MPO+ neutrophils, which was lower than in stage I/II cancer patients and not significantly different than in Stage III/IV cancer patients and the control group. The direction of changes in NETs formation seems to be a new common element shared by inflammation and early stage cancer. Changes in the formation of NETs observed in patients with advanced cancer, other than an early phase or inflammation, indicate an alternative range of NETs involvement depending on different phases of this disease.
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Affiliation(s)
- Marzena Garley
- Department of Immunology, Medical University of Bialystok, J. Waszyngtona 15A, 15-269 Białystok, Poland
| | - Dorota Dziemiańczyk-Pakieła
- Department of Maxillofacial and Plastic Surgery, Medical University of Bialystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Kamil Grubczak
- Department of Regenerative Medicine and Immunoregulation, Medical University of Bialystok, J. Waszyngtona 13, 15-269 Białystok, Poland
| | - Arkadiusz Surażyński
- Department of Medicinal Chemistry, Medical University of Bialystok, A. Mickiewicza 2D, 15-222 Białystok, Poland
| | - Dorota Dąbrowska
- Department of Immunology, Medical University of Bialystok, J. Waszyngtona 15A, 15-269 Białystok, Poland
| | - Wioletta Ratajczak-Wrona
- Department of Immunology, Medical University of Bialystok, J. Waszyngtona 15A, 15-269 Białystok, Poland
| | - Jolanta Sawicka-Powierza
- Department of Health Sciences, Medical University of Bialystok, Mieszka I 4B, 15-054 Białystok, Poland
| | - Jan Borys
- Department of Maxillofacial and Plastic Surgery, Medical University of Bialystok, M. Skłodowskiej-Curie 24A, 15-276 Białystok, Poland
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immunoregulation, Medical University of Bialystok, J. Waszyngtona 13, 15-269 Białystok, Poland
| | - Jerzy A. Pałka
- Department of Medicinal Chemistry, Medical University of Bialystok, A. Mickiewicza 2D, 15-222 Białystok, Poland
| | - Ewa Jabłońska
- Department of Immunology, Medical University of Bialystok, J. Waszyngtona 15A, 15-269 Białystok, Poland
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Gorgannezhad L, Umer M, Islam MN, Nguyen NT, Shiddiky MJA. Circulating tumor DNA and liquid biopsy: opportunities, challenges, and recent advances in detection technologies. LAB ON A CHIP 2018; 18:1174-1196. [PMID: 29569666 DOI: 10.1039/c8lc00100f] [Citation(s) in RCA: 184] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Cell-free DNA (cfDNA) refers to short fragments of acellular nucleic acids detectable in almost all body fluids, including blood, and is involved in various physiological and pathological phenomena such as immunity, coagulation, aging, and cancer. In cancer patients, a fraction of hematogenous cfDNA originates from tumors, termed circulating tumor DNA (ctDNA), and may carry the same mutations and genetic alterations as those of a primary tumor. Thus, ctDNA potentially provides an opportunity for noninvasive assessment of cancer. Recent advances in ctDNA analysis methods will potentially lead to the development of a liquid biopsy tool for the diagnosis, prognosis, therapy response monitoring, and tracking the rise of new mutant sub-clones in cancer patients. Over the past few decades, cancer-specific mutations in ctDNA have been detected using a variety of untargeted methods such as digital karyotyping, personalized analysis of rearranged ends (PARE), whole-genome sequencing of ctDNA, and targeted approaches such as conventional and digital PCR-based methods and deep sequencing-based technologies. More recently, several chip-based electrochemical sensors have been developed for the analysis of ctDNA in patient samples. This paper aims to comprehensively review the diagnostic, prognostic, and predictive potential of ctDNA as a minimally invasive liquid biopsy for cancer patients. We also present an overview of current advances in the analytical sensitivity and accuracy of ctDNA analysis methods as well as biological and technical challenges, which need to be resolved for the integration of ctDNA analysis into routine clinical practice.
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Affiliation(s)
- Lena Gorgannezhad
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad Umer
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Md Nazmul Islam
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Nam-Trung Nguyen
- Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
| | - Muhammad J A Shiddiky
- School of Environment and Science, Griffith University, Nathan Campus, QLD 4111, Australia. and Queensland Micro- and Nanotechnology Centre, Griffith University, Nathan Campus, QLD 4111, Australia
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Ferrandi PJ, Fico BG, Whitehurst M, Zourdos MC, Bao F, Dodge KM, Rodriguez AL, Pena G, Huang CJ. Acute high-intensity interval exercise induces comparable levels of circulating cell-free DNA and Interleukin-6 in obese and normal-weight individuals. Life Sci 2018; 202:161-166. [PMID: 29653118 DOI: 10.1016/j.lfs.2018.04.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 03/29/2018] [Accepted: 04/07/2018] [Indexed: 12/31/2022]
Abstract
AIMS Obesity is associated with lipid aggregation in adipocytes and macrophage infiltration, leading to increased oxidative stress and inflammation. Increased cell-free DNA (cfDNA) concentrations have been observed in clinical conditions of systemic inflammation. While the beneficial effects of regular physical activity on the release of circulating cfDNA still remain unknown, acute intense exercise has been shown to increase inflammatory cytokines and cfDNA concentrations in normal-weight individuals. Therefore, the primary purpose of this study was to examine the effect of acute high-intensity interval Exercise (HIIE) on plasma cfDNA and interleukin-6 (IL-6) responses in obese and normal-weight subjects. MAIN METHODS Fourteen male subjects (7 obese and 7 normal-weight) participated in an acute HIIE protocol (30 min, 4x4min @ 80% - 90% of VO2max) on a treadmill. Between HIIE intervals, subjects performed 3 min of active recovery at 50-60% VO2max. Blood samples were collected prior to, immediately following exercise, and one hour into recovery for measurements of plasma cfDNA and IL-6. KEY FINDINGS Our results demonstrated a significant elevation in plasma cfDNA immediately following acute HIIE in both obese and normal-weight subjects. A comparable elevation in the concentration of plasma IL-6 was also found between two groups in response to acute HIIE. Furthermore, the level of plasma cfDNA was not correlated with IL-6 either at baseline or in response to acute HIIE. SIGNIFICANCE These findings may support the utilization of HIIE as a time-efficient exercise protocol to understand the obesity-associated cfDNA and inflammatory responses.
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Affiliation(s)
- Peter J Ferrandi
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States; Department of Health and Kinesiology, Purdue University, West Lafayette, IN 47907, United States
| | - Brandon G Fico
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States; Department of Kinesiology and Health Education, University of Texas, Austin, TX 78712, United States
| | - Michael Whitehurst
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Michael C Zourdos
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Fanchen Bao
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Katelyn M Dodge
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Alexandra L Rodriguez
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Gabriel Pena
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States
| | - Chun-Jung Huang
- Exercise Biochemistry Laboratory, Department of Exercise Science and Health Promotion, Florida Atlantic University, Boca Raton, FL 33431, United States.
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Kumar M, Choudhury Y, Ghosh SK, Mondal R. Application and optimization of minimally invasive cell-free DNA techniques in oncogenomics. Tumour Biol 2018; 40:1010428318760342. [PMID: 29484962 DOI: 10.1177/1010428318760342] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The conventional method of measuring biomarkers in malignant tissue samples has already given subversive growth in cancer diagnosis, prognosis, and therapy selection. However, the regression and heterogeneity associated with tumor tissue biopsy have urged for the development of an alternative approach. Considering the limitations, cell-free DNA has emerged as a surrogate alternative, facilitating preoperative chemoradiotherapy (p < 0.0001) treatment response in rectal cancer and detection of biomarker in lung cancer. This potential of cell-free DNA in several other cancers has yet to be explored based on clinical relevance by optimizing the preanalytical factors. This review has highlighted the crucial parameters from blood collection to cell-free DNA analysis that has a significant impact on the accuracy and reliability of clinical data. The quantity of cell-free DNA is also a limiting factor. Therefore, a proper preanalytical factor for blood collection, its stability, centrifugation speed, and plasma storage condition are to be optimized for developing cancer-specific biomarkers useful for clinical purpose. Liquid biopsy-based origin of cell-free DNA has revolutionized the area of cancer research. Lack of preanalytical and analytical procedures may be considered for identification of novel biomarkers through next-generation sequencing of tumor-originated cell-free DNA in contradiction to tissue biopsy for cancer-specific biomarkers.
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Affiliation(s)
- Manish Kumar
- 1 Department of Biotechnology, Assam University, Silchar, India
| | | | - Sankar Kumar Ghosh
- 1 Department of Biotechnology, Assam University, Silchar, India.,2 University of Kalyani, Kalyani, India
| | - Rosy Mondal
- 3 Life Sciences Division, Institute of Advanced Study in Science and Technology, Guwahati, India
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The use of extracellular DNA as a proxy for specific microbial activity. Appl Microbiol Biotechnol 2018; 102:2885-2898. [PMID: 29423636 PMCID: PMC5847193 DOI: 10.1007/s00253-018-8786-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/11/2018] [Accepted: 01/14/2018] [Indexed: 02/07/2023]
Abstract
The ubiquity and relevance of extracellular DNA (exDNA) are well-known and increasingly gaining importance in many fields of application such as medicine and environmental microbiology. Although sources and types of exDNA are manifold, ratios of specific DNA-molecules inside and outside of living cells can give reliable information about the activity of entire systems and of specific microbial groups or species. Here, we introduce a method to discriminate between internal (iDNA), as well as bound and free exDNA, and evaluate various DNA fractions and related ratios (ex:iDNA) regarding their applicability to be used as a fast, convenient, and reliable alternative to more tedious RNA-based activity measurements. In order to deal with microbial consortia that can be regulated regarding their activity, we tested and evaluated the proposed method in comparison to sophisticated dehydrogenase- and RNA-based activity measurements with two anaerobic microbial consortia (anaerobic fungi and syntrophic archaea and a microbial rumen consortium) and three levels of resolution (overall activity, total bacteria, methanogenic archaea). Furthermore, we introduce a 28S rRNA gene-specific primer set and qPCR protocol, targeting anaerobic fungi (Neocallimastigomycota). Our findings show that the amount of actively released free exDNA (fDNA) strongly correlates with different activity measurements and is thus suggested to serve as a proxy for microbial activity.
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39
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Trevisiol C, Di Fabio F, Nascimbeni R, Peloso L, Salbe C, Ferruzzi E, Salerni B, Gion M. Prognostic Value of Circulating KRAS2 Gene Mutations in Colorectal Cancer with Distant Metastases. Int J Biol Markers 2018. [DOI: 10.1177/172460080602100405] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While tissue KRAS2 mutations have been extensively investigated, the role of circulating mutant KRAS2 gene in patients with colorectal carcinoma remains obscure. The aim of the present study was to explore the prognostic significance of circulating KRAS2 gene mutational status in subjects undergoing primary treatment for colorectal cancer. Codon 12 KRAS2 mutations were examined in DNA samples extracted from the serum of 86 patients with colorectal cancer and were compared with the KRAS2 status of their primary tumors. Tissue and serum KRAS2 status was compared with other clinicopathological variables (including CEA and CA 19-9 levels) and with cancer-related survival. KRAS2 mutations were found in tissue samples of 28 patients (33%); serum KRAS2 mutations were detected in 10 of them (36%). Serum KRAS2 status was significantly associated with Dukes' stage D (p=0.001) and with preoperative CA 19-9 levels (p=0.01). At multivariate analysis, cancer-related survival was associated with Dukes' stage (p<0.0001), CEA level (p=0.02), and mutant circulating KRAS2 (p=0.01). All 7 stage D patients with serum KRAS2 mutations died of the disease within 24 months of primary treatment; cancer-related survival was significantly better in 9 stage D patients without serum KRAS2 mutations, with 5 patients (56%) alive after 24 months and 1 patient (13%) alive after 44 months. Residual disease after surgery was evident in all 7 stage D patients with mutant circulating KRAS2, and in 5 out of 9 stage D patients without serum mutations. Serum KRAS2 status may impact substantially on the management of stage D colorectal carcinoma, since it appears to correlate with prognosis in this patient subgroup.
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Affiliation(s)
- C. Trevisiol
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - F. Di Fabio
- Department General Surgery, University of Brescia, Brescia
| | - R. Nascimbeni
- Department General Surgery, University of Brescia, Brescia
| | - L. Peloso
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - C. Salbe
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - E. Ferruzzi
- ABO Association, c/o Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice
| | - B. Salerni
- Department General Surgery, University of Brescia, Brescia
| | - M. Gion
- Center for the Study of Biological Markers of Malignancy, General Regional Hospital ULSS 12, Venice - Italy
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Zanetti-Dällenbach RA, Schmid S, Wight E, Holzgreve W, Ladewing A, Hahn S, Zhong XY. Levels of Circulating Cell-Free Serum DNA in Benign and Malignant Breast Lesions. Int J Biol Markers 2018; 22:95-9. [PMID: 17549664 DOI: 10.1177/172460080702200202] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Purposes of the study: We analyzed circulating cell-free DNA in the serum of patients with benign and malignant breast disease and in healthy individuals to determine its diagnostic value. Basic procedures: Serum samples were obtained from 50 healthy individuals, 33 patients with malignant breast disease and 32 patients with benign breast disease. Circulatory DNA was extracted from serum samples. Cell-free DNA was quantified by real-time quantitative PCR for the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene. Tissue samples from patients with malignant and benign breast lesions were histopathologically examined. Main findings: The mean levels of circulating cell-free DNA in serum samples were 41,149 genome equivalents (GE)/mL in patients with malignant disease, 30,826 GE/mL in patients with benign disease, and 13,267 GE/mL in healthy individuals. Healthy individuals had significantly lower levels of cell-free DNA than patients with malignant or benign breast disease (p=0.001, p=0.031). No significant difference was observed between malignant and benign disease. There was a correlation between cell-free DNA levels and tumor size but not with other tumor characteristics. Principal conclusion: Our results suggest that levels of circulating cell-free DNA in serum could have diagnostic value to discriminate between healthy individuals and patients with breast lesions but not between patients with malignant and benign breast lesions.
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Seefeld M, El Tarhouny S, Fan A, Hahn S, Holzgreve W, Zhong X. Parallel Assessment of Circulatory Cell-Free DNA by PCR and Nucleosomes by ELISA in Breast Tumors. Int J Biol Markers 2018; 23:69-73. [DOI: 10.1177/172460080802300202] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Objectives In order to assess the potential biomolecules for breast cancer, we analyzed in parallel the levels of cell-free glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and cell-free nucleosomes in serum samples from patients with benign and malignant breast tumors. The levels of cell-free DNA obtained by quantitative PCR were compared with those obtained by enzyme-linked immunosorbent assay (ELISA). Methods Twenty-three patients with benign breast tumors, 27 patients with breast cancer, and 32 age-matched healthy women were recruited. The amounts of serum nucleosomes were analyzed by ELISA and the levels of cell-free GAPDH were measured by real-time quantitative PCR. The correlation between nucleosome and cell-free GAPDH levels was examined using the Spearman rank test. Results The levels of cell-free GAPDH were significantly higher in the serum samples of patients with benign and malignant breast tumors than in those of the control group (median 37,966 GE/mL, range 3,802–130,104 versus 11,770 GE/mL, range 2,198–73,522, p=0.035 and median 40,698 GE/mL, range 3,644–192,482 versus 11,770 GE/mL range 2,198–73,522, p=0.001). The concentration of cell-free GAPDH correlated significantly with the quantities of nucleosomes in serum samples (r=0.451, p=0.000). There was, however, no significant difference between healthy individuals and women with benign breast tumors or breast cancer in terms of nucleosomes determined by ELISA. Conclusion Our data suggest that the cell-free serum GAPDH DNA assayed by quantitative PCR is a better biomarker than nucleosomes assayed by ELISA in patients with breast tumors.
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Affiliation(s)
- M. Seefeld
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
- The first two authors contributed
equally to this work
| | - S. El Tarhouny
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
- Department of Medical Biochemistry,
Faculty of Medicine, Zagazig University, Zagazig - Egypt
- The first two authors contributed
equally to this work
| | - A.X.C. Fan
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
| | - S. Hahn
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
| | - W. Holzgreve
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
| | - X.Y. Zhong
- Laboratory for Prenatal Medicine and
Gynecologic Oncology, Women's Hospital / Department of BioMedicine, University of
Basel, Basel - Switzerland
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Qiao CY, Li F, Teng Y, Zhao J, Hu N, Fan YC, Wang K. Aberrant GSTP1 promoter methylation predicts poor prognosis of acute-on-chronic hepatitis B pre-liver failure. Clin Exp Med 2017; 18:51-62. [PMID: 28676943 DOI: 10.1007/s10238-017-0466-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/27/2017] [Indexed: 12/14/2022]
Abstract
It has been demonstrated that glutathione-S-transferase P1 (GSTP1) could protect cells from DNA damage mediated by oxidizing agents or electrophiles in hepatic inflammatory response. Our study evaluated the methylation status and the predictive value for prognosis of GSTP1 promoter region in patients with acute-on-chronic hepatitis B pre-liver failure (pre-ACHBLF). Methylation status of GSTP1 promoter in peripheral blood mononuclear cells (PBMCs) and plasma was measured in 103 patients with pre-ACHBLF, 80 patients with chronic hepatitis B (CHB) and 30 healthy controls (HCs) by methylation-specific polymerase chain reaction. The mRNA level of GSTP1 was detected by quantitative real-time polymerase chain reaction. The methylation frequency of GSTP1 promoter region in patients with pre-ACHBLF (35/103 in PBMCs and 33/103 in plasma) was significantly higher than CHB (2/80) and HCs (0/30), respectively. The mRNA level of GSTP1 in patients with pre-ACHBLF was significantly lower than CHB and HCs. Additionally, pre-ACHBLF patients with methylated GSTP1 presented strikingly higher incidence of ACHBLF than those without. Of note, GSTP1 methylation presented distinctly better performance than model for end-stage liver disease score [area under the receiver operating characteristic curves (AUCs) 0.825 in PBMCs and 0.798 in plasma VS 0.589; AUC 0.804 in PBMCs and 0.779 in plasma VS 0.622; AUC 0.767 in PBMCs and 0.744 in plasma VS 0.602, respectively] when used to predict the 1-, 2- or 3-month incidence of ACHBLF in patients with pre-ACHBLF. Aberrant methylation of GSTP1 has potential to be a prognostic biomarker for pre-ACHBLF.
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Affiliation(s)
- Chen-Yang Qiao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Feng Li
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yue Teng
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Jing Zhao
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Na Hu
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yu-Chen Fan
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, 250012, China.,Institute of Hepatology, Shandong University, Jinan, 250012, China
| | - Kai Wang
- Department of Hepatology, Qilu Hospital of Shandong University, Jinan, 250012, China. .,Institute of Hepatology, Shandong University, Jinan, 250012, China.
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Shafiee G, Heshmat R, Larijani B. Circulating cell-free nucleic acids as potential biomarkers for sarcopenia: a step toward personalized medicine. J Diabetes Metab Disord 2017; 16:19. [PMID: 28439503 PMCID: PMC5399331 DOI: 10.1186/s40200-017-0299-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 04/05/2017] [Indexed: 02/07/2023]
Abstract
Sarcopenia is an age-related loss of muscle mass and function, leading to disability, morbidity and increased mortality in older people. Given the relatively high prevalence and related- outcome of the disease, correct diagnosis, screening, monitoring and treatment of sarcopenia are needed in clinical practice. Recent researches have focused on cell-free nucleic acids, which are released into the circulation following cell death, as a potential biomarker of aging and systematic inflammation. It seems that the diagnosis and treatment of sarcopenia can be possible by the help of the analysis of cell-free nucleic acids as noninvasive method.
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Affiliation(s)
- Gita Shafiee
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Dr shariati hospital, north karegar st, Tehran, 14114 Iran
| | - Ramin Heshmat
- Chronic Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Dr shariati hospital, north karegar st, Tehran, 14114 Iran
| | - Bagher Larijani
- Endocrinology & Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
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Plasma Circulating Tumor DNA Levels for the Monitoring of Melanoma Patients: Landscape of Available Technologies and Clinical Applications. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5986129. [PMID: 28484715 PMCID: PMC5397613 DOI: 10.1155/2017/5986129] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Revised: 03/08/2017] [Accepted: 03/22/2017] [Indexed: 12/18/2022]
Abstract
Melanoma is a cutaneous cancer with an increasing worldwide prevalence and high mortality due to unresectable or metastatic stages. Mutations in BRAF, NRAS, or KIT are present in more than 60% of melanoma cases, but a useful blood-based biomarker for the clinical monitoring of melanoma patients is still lacking. Thus, the analysis of circulating tumor cells (CTCs) and/or cell-free circulating tumor DNA (ctDNA) analysis from blood (liquid biopsies) appears to be a promising noninvasive, repeatable, and systemic sampling tool for detecting and monitoring melanoma. Here, we review the molecular biology-based strategies used for ctDNA quantification in melanoma patients, as well as their main clinical applications. Droplet digital PCR (ddPCR) and next generation sequencing (NGS) technologies appear to be two versatile and complementary strategies to study rare variant mutations for the detection and monitoring of melanoma progression. Among the different clinical uses of ctDNA, we highlight the assessment of molecular heterogeneity and the identification of genetic determinants for targeted therapy as well as the analysis of acquired resistance. Importantly, ctDNA quantification might also be a novel biomarker with a prognostic value for melanoma patients.
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Aucamp J, Bronkhorst AJ, Badenhorst CPS, Pretorius PJ. A historical and evolutionary perspective on the biological significance of circulating DNA and extracellular vesicles. Cell Mol Life Sci 2016; 73:4355-4381. [PMID: 27652382 PMCID: PMC11108302 DOI: 10.1007/s00018-016-2370-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 08/20/2016] [Accepted: 09/15/2016] [Indexed: 01/08/2023]
Abstract
The discovery of quantitative and qualitative differences of the circulating DNA (cirDNA) between healthy and diseased individuals inclined researchers to investigate these molecules as potential biomarkers for non-invasive diagnosis and prognosis of various pathologies. However, except for some prenatal tests, cirDNA analyses have not been readily translated to clinical practice due to a lack of knowledge regarding its composition, function, and biological and evolutionary origins. We believe that, to fully grasp the nature of cirDNA and the extracellular vesicles (EVs) and protein complexes with which it is associated, it is necessary to probe the early and badly neglected work that contributed to the discovery and development of these concepts. Accordingly, this review consists of a schematic summary of the major events that developed and integrated the concepts of heredity, genetic information, cirDNA, EVs, and protein complexes. CirDNA enters target cells and provokes a myriad of gene regulatory effects associated with the messaging functions of various natures, disease progression, somatic genome variation, and transgenerational inheritance. This challenges the traditional views on each of the former topics. All of these discoveries can be traced directly back to the iconic works of Darwin, Lamarck, and their followers. The history of cirDNA that has been revisited here is rich in information that should be considered in clinical practice, when designing new experiments, and should be very useful for generating an empirically up-to-date view of cirDNA and EVs. Furthermore, we hope that it will invite many flights of speculation and stimulate further inquiry into its biological and evolutionary origins.
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Affiliation(s)
- Janine Aucamp
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa.
| | - Abel J Bronkhorst
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
| | - Christoffel P S Badenhorst
- Department of Biotechnology and Enzyme Catalysis, Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487, Greifswald, Germany
| | - Piet J Pretorius
- Centre for Human Metabolomics, Biochemistry Division, North-West University, Potchefstroom, 2520, South Africa
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Pathologists and liquid biopsies: to be or not to be? Virchows Arch 2016; 469:601-609. [PMID: 27553354 DOI: 10.1007/s00428-016-2004-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/25/2016] [Accepted: 08/09/2016] [Indexed: 12/19/2022]
Abstract
Recently, the advent of therapies targeting genomic alterations has improved the care of patients with certain types of cancer. While molecular targets were initially detected in nucleic acid samples extracted from tumor tissue, detection of nucleic acids in circulating blood has allowed the development of what has become known as liquid biopsies, which provide a complementary and alternative sample source allowing identification of genomic alterations that might be addressed by targeted therapy. Consequently, liquid biopsies might rapidly revolutionize oncology practice in allowing administration of more effective treatments. Liquid biopsies also provide an approach towards short-term monitoring of metastatic cancer patients to evaluate efficacy of treatment and/or early detection of secondary mutations responsible for resistance to treatment. In this context, pathologists, who have already been required in recent years to take interest in the domain of molecular pathology of cancer, now face new challenges. The attitude of pathologists to and level of involvement in the practice of liquid biopsies, including mastering the methods employed in molecular analysis of blood samples, need close attention. Regardless of the level of involvement of pathologists in this new field, it is mandatory that oncologists, biologists, geneticists, and pathologists work together to coordinate the pre-analytical, analytical, and post-analytical phases of molecular assessment of tissue and liquid samples of individual cancer patients. The challenges include (1) implementation of effective and efficient procedures for reception and analysis of liquid and tissue samples for histopathological and molecular evaluation and (2) assuring short turn-around times to facilitate rapid optimization of individual patient treatment. In this paper, we will review the following: (1) recent data concerning the concept of liquid biopsies in oncology and its development for patient care, (2) advantages and limitations of molecular analyses performed on blood samples compared to those performed on tissue samples, and (3) short-term challenges facing pathologists in dealing with liquid biopsies of cancer patients and new strategies to early detect metastatic tumor cell clones.
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Hocking J, Mithraprabhu S, Kalff A, Spencer A. Liquid biopsies for liquid tumors: emerging potential of circulating free nucleic acid evaluation for the management of hematologic malignancies. Cancer Biol Med 2016; 13:215-25. [PMID: 27458529 PMCID: PMC4944540 DOI: 10.20892/j.issn.2095-3941.2016.0025] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circulating free nucleic acids; cell free DNA and circulating micro-RNA, are found in the
plasma of patients with hematologic and solid malignancies at levels higher than that of
healthy individuals. In patients with hematologic malignancy cell free DNA reflects the
underlying tumor mutational profile, whilst micro-RNAs reflect genetic interference
mechanisms within a tumor and potentially the surrounding microenvironment and immune
effector cells. These circulating nucleic acids offer a potentially simple, non-invasive,
repeatable analysis that can aid in diagnosis, prognosis and therapeutic decisions in
cancer treatment.
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Affiliation(s)
- Jay Hocking
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne 3004, Australia; Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne 3004, Australia
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne 3004, Australia
| | - Anna Kalff
- Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne 3004, Australia
| | - Andrew Spencer
- Myeloma Research Group, Australian Center for Blood Diseases, Monash University, Melbourne 3004, Australia; Malignant Haematology & Stem Cell Transplantation Service, Alfred Hospital, Melbourne 3004, Australia
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Baoutina A, Bhat S, Zheng M, Partis L, Dobeson M, Alexander IE, Emslie KR. Synthetic certified DNA reference material for analysis of human erythropoietin transgene and transcript in gene doping and gene therapy. Gene Ther 2016; 23:708-717. [DOI: 10.1038/gt.2016.47] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 05/24/2016] [Indexed: 12/27/2022]
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Basnet S, Zhang ZY, Liao WQ, Li SH, Li PS, Ge HY. The Prognostic Value of Circulating Cell-Free DNA in Colorectal Cancer: A Meta-Analysis. J Cancer 2016; 7:1105-13. [PMID: 27326254 PMCID: PMC4911878 DOI: 10.7150/jca.14801] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2015] [Accepted: 03/22/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Circulating cell-free DNA (cfDNA) is a promising candidate biomarker for detection, monitoring and survival prediction of colorectal cancer (CRC). However, its prognostic significance for patients with CRC remains controversial. To derive a precise estimation of the prognostic significance of cfDNA, a meta-analysis was performed. METHODS We made a systematic search in data base of the Science Citation Index Embase and Pubmed for studies reporting prognostic data of cfDNA in CRC patients. The data of cfDNA on recurrences-free survival (RFS) and overall survival (OS) were extracted and measured in hazard rates (HRs) and 95% confident intervals (CIs). Subgroup analyses were carried out as well. Finally, the meta-analysis is accompanied with nine studies including 19 subunits. RESULTS The pooled HRs with 95% CIs revealed strong associations between cfDNA and RFS (HR [95%CI]=2.78[2.08-3.72], I(2)=32.23%, n=7) along with OS (HR [95%CI]=3.03[2.51-3.66], I(2)=29.24%, n=12) in patients with CRC. Entire subgroup analyses indicated strong prognostic value of cfDNA irrespective tumor stage, study size, tumor markers, detection methods and marker origin. CONCLUSIONS All the results exhibits that appearance of cfDNA in blood is an indicator for adverse RFS and OS in CRC patients.
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Affiliation(s)
- Shiva Basnet
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Zhen-yu Zhang
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Wen-qiang Liao
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shu-heng Li
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ping-shu Li
- 2. Department of Research Administration, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Hai-yan Ge
- 1. Department of Gastrointestinal Surgery, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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50
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Rodrigues Filho EM, Ikuta N, Simon D, Regner AP. Prognostic value of circulating DNA levels in critically ill and trauma patients. Rev Bras Ter Intensiva 2016; 26:305-12. [PMID: 25295826 PMCID: PMC4188468 DOI: 10.5935/0103-507x.20140043] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 07/15/2014] [Indexed: 12/21/2022] Open
Abstract
The number of studies investigating circulating nucleic acids as potential biomarkers
has increased in recent years. The detection of such biomarkers is a minimally
invasive alternative for the diagnosis and prognosis of various clinical conditions.
The value of circulating DNA levels as a predictive biomarker has been demonstrated
in patients suffering from numerous acute pathologies that have a high risk of
intensive care needs and in-hospital deaths. The mechanism by which circulating DNA
levels increase in patients with these conditions remains unclear. In this review, we
focused on the potential use of this biomarker for prognosis prediction in critically
ill and trauma patients. The literature review was performed by searching MedLine
using PubMed in the English language.
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Affiliation(s)
| | - Nilo Ikuta
- Laboratório de Biomarcadores do Trauma, Universidade Luterana do Brasil, Canoas, RS, Brasil
| | - Daniel Simon
- Laboratório de Biomarcadores do Trauma, Universidade Luterana do Brasil, Canoas, RS, Brasil
| | - Andrea Pereira Regner
- Laboratório de Biomarcadores do Trauma, Universidade Luterana do Brasil, Canoas, RS, Brasil
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