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Malki Y, Kang G, Lam WKJ, Zhou Q, Cheng SH, Cheung PPH, Bai J, Chan ML, Lee CT, Peng W, Zhang Y, Gai W, Wong WWS, Ma MJL, Li W, Xu X, Gao Z, Tse IOL, Shang H, Choy LYL, Jiang P, Chan KCA, Lo YMD. Analysis of a cell-free DNA-based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations. Genome Res 2025; 35:31-42. [PMID: 39603706 DOI: 10.1101/gr.279667.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Accepted: 11/25/2024] [Indexed: 11/29/2024]
Abstract
The concentration of circulating cell-free DNA (cfDNA) in plasma is an important determinant of the robustness of liquid biopsies. However, biological mechanisms that lead to inter-individual differences in cfDNA concentrations remain unexplored. The concentration of plasma cfDNA is governed by an interplay between its release and clearance. We hypothesized that cfDNA clearance by nucleases might be one mechanism that contributes toward inter-individual variations in cfDNA concentrations. We performed fragmentomic analysis of the plasma cfDNA from 862 healthy individuals, with a cfDNA concentration range of 1.61-41.01 ng/mL. We observed an increase in large DNA fragments (231-600 bp), a decreased frequencies of shorter DNA fragments (20-160 bp), and an increased frequency of G-end motifs with increasing cfDNA concentrations. End motif deconvolution analysis revealed a decreased contribution of DNASE1L3 and DFFB in subjects with higher cfDNA concentration. The five subjects with the highest plasma DNA concentration (top 0.58%) had aberrantly decreased levels of DNASE1L3 protein in plasma. The cfDNA concentration could be inferred from the fragmentomic profile through machine learning and was well correlated to the measured cfDNA concentration. Such an approach could infer the fractional DNA concentration from particular tissue types, such as the fetal and tumor fraction. This work shows that individuals with different cfDNA concentrations are associated with characteristic fragmentomic patterns of the cfDNA pool and that nuclease-mediated clearance of DNA is a key parameter that affects cfDNA concentration. Understanding these mechanisms has facilitated the enhanced measurement of cfDNA species of clinical interest, including circulating fetal and tumor DNA.
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Affiliation(s)
- Yasine Malki
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Guannan Kang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - W K Jacky Lam
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Qing Zhou
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Suk Hang Cheng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Peter P H Cheung
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Jinyue Bai
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Ming Lok Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Chui Ting Lee
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wenlei Peng
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Yiqiong Zhang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wanxia Gai
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Winsome W S Wong
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Mary-Jane L Ma
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Wenshuo Li
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Xinzhou Xu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Zhuoran Gao
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Irene O L Tse
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Huimin Shang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - L Y Lois Choy
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, Hong Kong SAR, China;
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Chemical Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
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Freimane L, Kivrāne A, Ulanova V, Vīksna A, Sevostjanovs E, Grīnberga S, Cīrule A, Krams A, Ranka R. Fluctuations in circulating cell-free mitochondrial and nuclear DNA copy numbers in blood plasma after anti-tuberculosis drug intake in patients with drug-susceptible tuberculosis. Tuberculosis (Edinb) 2025; 151:102611. [PMID: 39862444 DOI: 10.1016/j.tube.2025.102611] [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: 08/01/2024] [Revised: 01/16/2025] [Accepted: 01/20/2025] [Indexed: 01/27/2025]
Abstract
Biomarker research characterising the effect of anti-tuberculosis (TB) chemotherapy on systemic body response is still limited. In this study, we aimed to investigate fluctuations in circulating cell-free mitochondrial DNA (ccf-mtDNA) and circulating cell-free nuclear DNA (ccf-nDNA) copy number (CN) in blood plasma of patients with drug-susceptible TB (DS-TB) and to decipher factors related to these fluctuations. The results showed considerable changes in ccf-mtDNA CN in plasma samples before drug intake and 2 and 6 h afterwards, with high inter patient variability at each time point. Multivariate linear regression revealed that the dynamics of ccf-mtDNA CN was influenced by patients' age, ethambutol pharmacokinetics, and body-mass index (BMI); ethambutol exposure emerged as the most significant factor. Very low ccf-nDNA CN in all three time points with little variation was observed; none factors were strongly associated with ccf-nDNA. In conclusion, our study revealed the effect of anti-TB chemotherapy, age and BMI on acute changes in circulating ccf-mtDNA CN in blood plasma and highlighted the systemic, mitochondria-related effects of ethambutol in patients with TB. Further studies with larger cohorts are needed to understand the biological relevance of ccf-DNA in patients with TB and to validate its application in TB treatment monitoring.
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Affiliation(s)
- Lauma Freimane
- Latvian Biomedical Research and Study Centre, Ratsupites street 1, k-1, Riga, LV-1067, Latvia
| | - Agnija Kivrāne
- Riga Stradiņš University, Pharmacogenetic and Precision Medicine Laboratory, Konsula street 21, Riga, LV-1007, Latvia
| | - Viktorija Ulanova
- Riga Stradiņš University, Pharmacogenetic and Precision Medicine Laboratory, Konsula street 21, Riga, LV-1007, Latvia
| | - Anda Vīksna
- Riga Stradiņš University, Pharmacogenetic and Precision Medicine Laboratory, Konsula street 21, Riga, LV-1007, Latvia; Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Upeslejas, Stopinu district, LV-2118, Latvia
| | - Eduards Sevostjanovs
- Latvian Institute of Organic Synthesis, Aizkraukles street 21, Riga, LV-1006, Latvia
| | - Solveiga Grīnberga
- Latvian Institute of Organic Synthesis, Aizkraukles street 21, Riga, LV-1006, Latvia
| | - Andra Cīrule
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Upeslejas, Stopinu district, LV-2118, Latvia
| | - Alvils Krams
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Upeslejas, Stopinu district, LV-2118, Latvia; University of Latvia, Raiņa bulvāris 19, Rīga, LV-1586, Latvia
| | - Renāte Ranka
- Latvian Biomedical Research and Study Centre, Ratsupites street 1, k-1, Riga, LV-1067, Latvia; Riga Stradiņš University, Pharmacogenetic and Precision Medicine Laboratory, Konsula street 21, Riga, LV-1007, Latvia.
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Lindblad YT, Tóthová Ľ, Celec P, Kublickiene K, Bárány P, Chromek M. Association between extracellular DNA levels, markers of inflammation and left ventricular mass index in children with chronic kidney disease. Sci Rep 2025; 15:2645. [PMID: 39838042 PMCID: PMC11751163 DOI: 10.1038/s41598-025-86857-4] [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: 04/12/2024] [Accepted: 01/14/2025] [Indexed: 01/23/2025] Open
Abstract
Chronic kidney disease (CKD) is associated with chronic low-grade inflammation, but the primary factors triggering this inflammation remain unclear. Extracellular or cell-free DNA (exDNA) originates from virtually all tissues, being released during cell death, and stimulates the innate immune system. Our study was designed as an observational, cross-sectional cohort study of children with CKD (both before and after kidney transplantation) and controls to analyze associations between exDNA, markers of inflammation, and cardiovascular health. Extracellular DNA (total, nuclear, and mitochondrial) was analyzed in plasma using fluorometry and real-time PCR. We found that children with CKD after kidney transplantation had higher concentrations of total and nuclear extracellular DNA (total exDNA and nc_exDNA) in plasma compared to controls. In univariate analysis, levels of interleukin-6 (IL-6), antimicrobial peptide cathelicidin (LL-37), soluble vascular cell adhesion molecule-1 (VCAM-1) and left ventricular mass index (LVMI) were positively correlated with total exDNA and nc_exDNA concentrations. Multivariate analysis revealed LVMI as the only independent variable associated with high levels of both total exDNA and nc_exDNA. We believe that our results contribute new knowledge to the pathogenesis of CKD and its complications and may help identify new treatment targets.
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Affiliation(s)
- Ylva Tranæus Lindblad
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Ľubomíra Tóthová
- Institute of Molecular Biomedicine, Comenius University Medical School, Bratislava, Slovakia
| | - Peter Celec
- Institute of Molecular Biomedicine, Comenius University Medical School, Bratislava, Slovakia
| | - Karolina Kublickiene
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Peter Bárány
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Pediatric Nephrology Unit, K86, Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden
| | - Milan Chromek
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
- Pediatric Nephrology Unit, K86, Karolinska University Hospital Huddinge, 141 86, Stockholm, Sweden.
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4
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Tabrizi S, Martin-Alonso C, Xiong K, Bhatia SN, Adalsteinsson VA, Love JC. Modulating cell-free DNA biology as the next frontier in liquid biopsies. Trends Cell Biol 2024:S0962-8924(24)00249-6. [PMID: 39730275 DOI: 10.1016/j.tcb.2024.11.007] [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: 08/13/2024] [Revised: 11/05/2024] [Accepted: 11/20/2024] [Indexed: 12/29/2024]
Abstract
Technical advances over the past two decades have enabled robust detection of cell-free DNA (cfDNA) in biological samples. Yet, higher clinical sensitivity is required to realize the full potential of liquid biopsies. This opinion article argues that to overcome current limitations, the abundance of informative cfDNA molecules - such as circulating tumor DNA (ctDNA) - collected in a sample needs to increase. To accomplish this, new methods to modulate the biological processes that govern cfDNA production, trafficking, and clearance in the body are needed, informed by a deeper understanding of cfDNA biology. Successful development of such methods could enable a major leap in the performance of liquid biopsies and vastly expand their utility across the spectrum of clinical care.
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Affiliation(s)
- Shervin Tabrizi
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Radiation Oncology, Mass General Brigham, Boston, MA, USA; Harvard Medical School, Boston, MA, USA.
| | - Carmen Martin-Alonso
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kan Xiong
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sangeeta N Bhatia
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard-MIT Division of Health Sciences and Technology, Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA; Wyss Institute at Harvard University, Boston, MA, USA; Howard Hughes Medical Institute, Cambridge, MA, USA
| | | | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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Mansfield L, Ramponi V, Gupta K, Stevenson T, Mathew AB, Barinda AJ, Herbstein F, Morsli S. Emerging insights in senescence: pathways from preclinical models to therapeutic innovations. NPJ AGING 2024; 10:53. [PMID: 39578455 PMCID: PMC11584693 DOI: 10.1038/s41514-024-00181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 10/25/2024] [Indexed: 11/24/2024]
Abstract
Senescence is a crucial hallmark of ageing and a significant contributor to the pathology of age-related disorders. As committee members of the young International Cell Senescence Association (yICSA), we aim to synthesise recent advancements in the identification, characterisation, and therapeutic targeting of senescence for clinical translation. We explore novel molecular techniques that have enhanced our understanding of senescent cell heterogeneity and their roles in tissue regeneration and pathology. Additionally, we delve into in vivo models of senescence, both non-mammalian and mammalian, to highlight tools available for advancing the contextual understanding of in vivo senescence. Furthermore, we discuss innovative diagnostic tools and senotherapeutic approaches, emphasising their potential for clinical application. Future directions of senescence research are explored, underscoring the need for precise, context-specific senescence classification and the integration of advanced technologies such as machine learning, long-read sequencing, and multifunctional senoprobes and senolytics. The dual role of senescence in promoting tissue homoeostasis and contributing to chronic diseases highlights the complexity of targeting these cells for improved clinical outcomes.
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Affiliation(s)
- Luke Mansfield
- The Bateson Centre, School of Medicine and Population Health, The University of Sheffield, Western Bank, Sheffield, UK
| | - Valentina Ramponi
- Cellular Plasticity and Disease Group, Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Kavya Gupta
- Department of Cellular and Molecular Biology and Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Abraham Binoy Mathew
- Department of Developmental Biology and Genetics, Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Agian Jeffilano Barinda
- Department of Pharmacology and Therapeutics, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Metabolic, Cardiovascular, and Aging Cluster, Indonesia Medical Education and Research Institute (IMERI), Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
| | - Florencia Herbstein
- Instituto de Investigación en Biomedicina de Buenos Aires (IBioBA) - CONICET - Partner Institute of the Max Planck Society, Buenos Aires, Argentina.
| | - Samir Morsli
- Karolinska Institutet, Department of Cell and Molecular Biology, Biomedicum Q6A, Stockholm, Sweden.
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Ali M, Kumar KG, Singh K, Rabyang S, Thinlas T, Mishra A. Evaluation of the cell death markers for aberrated cell free DNA release in high altitude pulmonary edema. Clin Sci (Lond) 2024; 138:1467-1480. [PMID: 39509268 DOI: 10.1042/cs20242052] [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: 09/10/2024] [Revised: 11/04/2024] [Accepted: 11/07/2024] [Indexed: 11/15/2024]
Abstract
The effect of high altitude (HA, altitude >2500 m) can trigger a maladaptive response in unacclimatized individuals, leading to various HA illnesses such as high altitude pulmonary edema (HAPE). The present study investigates circulating cell free (cf) DNA, a minimally invasive biomarker that can elicit a pro-inflammatory response. Our earlier study observed altered cfDNA fragment patterns in HAPE patients and the significant correlation of these patterns with peripheral oxygen saturation levels. However, the unclear release mechanisms of cfDNA in circulation limit its characterization and clinical utility. The present study not only observed a significant increase in cfDNA levels in HAPE patients (27.03 ± 1.37 ng/ml; n = 145) compared to healthy HA sojourners (controls, 14.57 ± 0.74 ng/ml; n = 65) and highlanders (HLs, 15.50 ± 0.8 ng/ml; n = 34) but also assayed the known cell death markers involved in cfDNA release at HA. The study found significantly elevated levels of the apoptotic marker, annexin A5, and secondary necrosis or late apoptotic marker, high mobility group box 1, in HAPE patients. In addition, we observed a higher oxidative DNA damage marker, 8-hydroxy-2'-deoxyguanosine, in HAPE compared with controls, suggestive of the role of oxidative DNA status in promoting the inflammatory potential of cfDNA fragments and their plausible role in manifesting HAPE pathophysiology. Extensive in vitro future assays can confirm the immunogenic role of cfDNA fragments that may act as a danger-associated molecular pattern and associate with markers of cellular stresses in HAPE.
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Affiliation(s)
- Manzoor Ali
- Genomics and Genome Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Krishna G Kumar
- Genomics and Genome Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
| | - Kanika Singh
- Genomics and Genome Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Stanzen Rabyang
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh 194101, India
| | - Tashi Thinlas
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh 194101, India
| | - Aastha Mishra
- Genomics and Genome Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Eissa T, Voronina L, Huber M, Fleischmann F, Žigman M. The Perils of Molecular Interpretations from Vibrational Spectra of Complex Samples. Angew Chem Int Ed Engl 2024:e202411596. [PMID: 39508580 DOI: 10.1002/anie.202411596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2024] [Indexed: 11/15/2024]
Abstract
Vibrational spectroscopy is a widely used technique for chemical characterizations across various analytical sciences. Its applications are increasingly extending to the analysis of complex samples such as biofluids, providing high-throughput molecular profiling. While powerful, the technique suffers from an inherent limitation: The overlap of absorption information across different spectral domains hinders the capacity to identify individual molecular substances contributing to measured signals. Despite the awareness of this challenge, the difficulty of analyzing multi-molecular spectra is often underestimated, leading to unsubstantiated molecular interpretations. Here, we examine the prevalent overreliance on spectral band assignment and illuminate the pitfalls of correlating spectral signals to discrete molecular entities or physiological states without rigorous validation. Focusing on blood-based infrared spectroscopy, we provide examples illustrating how peak overlap among different substances, relative substance concentrations, and preprocessing steps can lead to erroneous interpretations. We advocate for a viewpoint shift towards a more careful understanding of complex spectra, which shall lead to either accepting their fingerprinting nature and leveraging machine learning analysis - or involving additional measurement modalities for robust molecular interpretations. Aiming to help translate and improve analytical practices within the field, we highlight the limitations of molecular interpretations and feature their viable applications.
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Affiliation(s)
- Tarek Eissa
- Ludwig-Maximilians-Universität München (LMU), Chair of Exper-imental Physics - Laser Physics, Garching, Germany
- Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
- Technical University of Munich (TUM), School of Computation, Information and Technology, Garching, Germany
| | - Liudmila Voronina
- Ludwig-Maximilians-Universität München (LMU), Chair of Exper-imental Physics - Laser Physics, Garching, Germany
| | - Marinus Huber
- Ludwig-Maximilians-Universität München (LMU), Chair of Exper-imental Physics - Laser Physics, Garching, Germany
- Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Frank Fleischmann
- Ludwig-Maximilians-Universität München (LMU), Chair of Exper-imental Physics - Laser Physics, Garching, Germany
- Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
| | - Mihaela Žigman
- Ludwig-Maximilians-Universität München (LMU), Chair of Exper-imental Physics - Laser Physics, Garching, Germany
- Max Planck Institute of Quantum Optics (MPQ), Laboratory for Attosecond Physics, Garching, Germany
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8
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Anitua E, Zalduendo M, Prado R, Troya M, Tierno R, de la Fuente M, Alkhraisat MH. The Biological Effect of Enriching the Plasma Content in Platelet-Rich Plasma: An In Vitro Study. Biomolecules 2024; 14:1328. [PMID: 39456261 PMCID: PMC11506755 DOI: 10.3390/biom14101328] [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: 09/03/2024] [Revised: 09/27/2024] [Accepted: 10/12/2024] [Indexed: 10/28/2024] Open
Abstract
BACKGROUND Platelet-rich plasma (PRP) formulations have become valuable therapeutic tools in regenerative medicine. In addition, these blood derivates have been successfully included in cell therapy as fetal bovine serum substitutes, due to the real need to avoid the risk of host immunologic reactions and the animal disease transmission associated with reagents from animal origin. However, the protocols for obtaining them should be optimized to improve their biological potential. METHODS PRP-derived preparations with different concentrations of the platelet and plasma components were obtained from the blood of five donors by freeze-drying. Measurements of the pH, protein, and growth factor concentration were performed. Moreover, their biological effects on cell proliferation and migration and their angiogenic potential were assessed. RESULTS An increased plasma component concentration resulted in an augmented quantity of the total protein content, a significative variation in the hepatocyte growth factor concentration, and an experimental but clinically irrelevant alteration of the pH value. No significant changes were induced in their potential to enhance proliferative and migratory responses in epithelial cells, with the latter being reduced for dermal fibroblasts. The endothelial cell capacity for tube formation was significatively reduced. CONCLUSIONS An increased blood plasma content did not improve the biological potential of the formulations. However, they have emerged as a promising approach for regenerative therapies where neovascularization must be avoided.
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Affiliation(s)
- Eduardo Anitua
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain; (M.Z.); (R.P.); (M.T.); (R.T.); (M.d.l.F.); (M.H.A.)
- BTI-Biotechnology Institute, 01005 Vitoria, Spain
| | - Mar Zalduendo
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain; (M.Z.); (R.P.); (M.T.); (R.T.); (M.d.l.F.); (M.H.A.)
- BTI-Biotechnology Institute, 01005 Vitoria, Spain
| | - Roberto Prado
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain; (M.Z.); (R.P.); (M.T.); (R.T.); (M.d.l.F.); (M.H.A.)
- BTI-Biotechnology Institute, 01005 Vitoria, Spain
| | - María Troya
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain; (M.Z.); (R.P.); (M.T.); (R.T.); (M.d.l.F.); (M.H.A.)
- BTI-Biotechnology Institute, 01005 Vitoria, Spain
| | - Roberto Tierno
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain; (M.Z.); (R.P.); (M.T.); (R.T.); (M.d.l.F.); (M.H.A.)
- BTI-Biotechnology Institute, 01005 Vitoria, Spain
| | - María de la Fuente
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain; (M.Z.); (R.P.); (M.T.); (R.T.); (M.d.l.F.); (M.H.A.)
- BTI-Biotechnology Institute, 01005 Vitoria, Spain
| | - Mohammad H. Alkhraisat
- University Institute for Regenerative Medicine and Oral Implantology, UIRMI (UPV/EHU-Fundación Eduardo Anitua), 01007 Vitoria, Spain; (M.Z.); (R.P.); (M.T.); (R.T.); (M.d.l.F.); (M.H.A.)
- BTI-Biotechnology Institute, 01005 Vitoria, Spain
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9
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Varela Martins T, Silva de Melo BM, Toller-Kawahisa JE, da Silva GVL, Aníbal Silva CE, Paiva IM, Públio GA, Rosa MH, da Silva Souza C, Zamboni DS, Cunha FQ, Cunha TM, Ryffel B, Riteau N, Alves-Filho JC. The DNA sensor AIM2 mediates psoriasiform inflammation by inducing type 3 immunity. JCI Insight 2024; 9:e171894. [PMID: 39352743 PMCID: PMC11601563 DOI: 10.1172/jci.insight.171894] [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: 04/28/2023] [Accepted: 09/18/2024] [Indexed: 11/09/2024] Open
Abstract
Psoriasis is a chronic and recurrent inflammatory skin disease characterized by abnormal proliferation and differentiation of keratinocytes and activation of immune cells. However, the molecular driver that triggers this immune response in psoriatic skin remains unclear. The inflammation-related gene absent in melanoma 2 (AIM2) was identified as a susceptibility gene/locus associated with psoriasis. In this study, we investigated the role of AIM2 in the pathophysiology of psoriasis. We found elevated levels of mitochondrial DNA in patients with psoriasis, along with high expression of AIM2 in both the human psoriatic epidermis and a mouse model of psoriasis induced by topical imiquimod (IMQ) application. Genetic ablation of AIM2 reduced the development of IMQ-induced psoriasis by decreasing the production of type 3 cytokines (such as IL-17A and IL-23) and infiltration of immune cells into the inflammatory site. Furthermore, we demonstrate that IL-17A induced AIM2 expression in keratinocytes. Finally, the genetic absence of inflammasome components downstream AIM2, ASC, and caspase-1 alleviated IMQ-induced skin inflammation. Collectively, our data show that AIM2 is involved in developing psoriasis through its canonical activation.
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Affiliation(s)
- Timna Varela Martins
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
- Immune Health Laboratory, Regulation of host responses and immune health, IRL2029, French National Centre for Scientific Research (CNRS) and Ribeirão Preto Medical School (FMRP) of the Sao Paulo University (USP), Sao Paulo, Brazil
- INEM, CNRS, UMR7355 and University, Orleans, France
| | - Bruno Marcel Silva de Melo
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Juliana Escher Toller-Kawahisa
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Gabriel Victor Lucena da Silva
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Conceição Elidianne Aníbal Silva
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Isadora Marques Paiva
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Gabriel Azevedo Públio
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Marcos Henrique Rosa
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | | | - Dario Simões Zamboni
- Department of Cell Biology, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Fernando Q. Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | - Thiago Mattar Cunha
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
| | | | - Nicolas Riteau
- Immune Health Laboratory, Regulation of host responses and immune health, IRL2029, French National Centre for Scientific Research (CNRS) and Ribeirão Preto Medical School (FMRP) of the Sao Paulo University (USP), Sao Paulo, Brazil
- INEM, CNRS, UMR7355 and University, Orleans, France
| | - José C. Alves-Filho
- Department of Pharmacology, Ribeirão Preto Medical School, and
- Center for Research in Inflammatory Diseases, Ribeirão Preto Medical School, University of Sao Paulo, Ribeirão Preto, Sao Paulo, Brazil
- Immune Health Laboratory, Regulation of host responses and immune health, IRL2029, French National Centre for Scientific Research (CNRS) and Ribeirão Preto Medical School (FMRP) of the Sao Paulo University (USP), Sao Paulo, Brazil
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10
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Mirandola A, Kudriavtsev A, Cofre Muñoz CI, Navarro RC, Macagno M, Daoud S, Sanchez C, Pastor B, Pisareva E, Marin MS, Ruiz JG, Piris A, Rodriguez AG, Gonzalez NS, Vivancos A, Quarà V, Mellano A, Borghi F, Corti G, Marchiò C, Sapino A, Bartolini A, Crisafulli G, Bardelli A, Di Maio M, Lossaint G, Frayssinoux F, Crapez E, Ychou M, Soler RS, Fenocchio E, Fernandez Calotti PX, Mazard T, Vivas CS, Elez E, Di Nicolantonio F, Thierry AR. Post-surgery sequelae unrelated to disease progression and chemotherapy revealed in follow-up of patients with stage III colon cancer. EBioMedicine 2024; 108:105352. [PMID: 39303668 PMCID: PMC11437914 DOI: 10.1016/j.ebiom.2024.105352] [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: 12/07/2023] [Revised: 09/02/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
BACKGROUND We studied the poorly-known dynamics of circulating DNA (cir-nDNA), as monitored prospectively over an extended post-surgery period, in patients with cancer. METHODS On patients with stage III colon cancer (N = 120), using personalised molecular tags we carried out the prospective, multicenter, blinded cohort study of the post-surgery serial analysis of cir-nDNA concentration. 74 patients were included and 357 plasma samples tested. FINDINGS During post-operative follow-up, the patients' median cir-nDNA concentration was greater (P < 0.0001 in the [43-364 days range]) than both the median value in healthy individuals and the pre-surgery value. These cir-nDNA levels were highly associated with NETs markers (P-value associating MPO and cir-nDNA, and NE and cir-nDNA are 6.6 x 10-17, and 1.9 x 10-7), in accordance with previous reports which indicate that cir-nDNA are NETs by-products. Unexpectedly, in 34 out of 50 patients we found that NETs continued to be formed for an extended duration post-surgery, even in patients without disease progression. Given that this phenomenon was observed in patients without adjuvant CT, and in patients >18 months post-surgery, the data suggest that the persistence of NETs formation is not due to the adjuvant CT. INTERPRETATION (1), Given the inter-patient heterogeneity, the post-surgery cir-nDNA level cannot be considered a reliable value, and caution must be exercised when determining mutation allele frequency or the mutation status; and (2), specific studies must be undertaken to investigate the possible clinical impact of the persistent, low-grade inflammation resulting from elevated NETs levels, such as observed in these post-surgery patients, given that such levels are known to potentially induce adverse cardiovascular or thrombotic events. FUNDING This work was supported by the H2020 European ERA-NET grant on Translational Cancer Research (TRANSCAN-2).
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Affiliation(s)
- Alexia Mirandola
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France
| | - Andrei Kudriavtsev
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France
| | | | - Raquel Comas Navarro
- VHIO Vall d'Hebron Institute of Oncology, Medical Oncology Department, Barcelona, Spain
| | - Marco Macagno
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy
| | - Saidi Daoud
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France
| | - Cynthia Sanchez
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France
| | - Brice Pastor
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France
| | - Ekaterina Pisareva
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France
| | - Mireia Sanchis Marin
- VHIO Vall d'Hebron Institute of Oncology, Medical Oncology Department, Barcelona, Spain
| | - Javier Gonzalo Ruiz
- VHIO Vall d'Hebron Institute of Oncology, Medical Oncology Department, Barcelona, Spain
| | - Alejandro Piris
- VHIO Vall d'Hebron Institute of Oncology, Medical Oncology Department, Barcelona, Spain
| | | | - Nadia Saoudi Gonzalez
- VHIO Vall d'Hebron Institute of Oncology, Medical Oncology Department, Barcelona, Spain
| | - Ana Vivancos
- VHIO Vall d'Hebron Institute of Oncology, Medical Oncology Department, Barcelona, Spain
| | - Virginia Quarà
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy
| | - Alfredo Mellano
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy
| | - Felice Borghi
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy
| | - Giorgio Corti
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy
| | - Caterina Marchiò
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy; Department of Medical Sciences, University of Torino, Turin, Italy
| | - Anna Sapino
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy; Department of Medical Sciences, University of Torino, Turin, Italy
| | - Alice Bartolini
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy
| | - Giovanni Crisafulli
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology, University of Torino, Turin, Italy
| | - Alberto Bardelli
- IFOM, The AIRC Institute of Molecular Oncology, Milan, Italy; Department of Oncology, University of Torino, Turin, Italy
| | | | - Gerald Lossaint
- ICM, Institut Régional du Cancer de Montpellier, Montpellier, F-34298, France
| | - Florence Frayssinoux
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France
| | - Evelyne Crapez
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France; ICM, Institut Régional du Cancer de Montpellier, Montpellier, F-34298, France
| | - Marc Ychou
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France; ICM, Institut Régional du Cancer de Montpellier, Montpellier, F-34298, France
| | - Ramon Salazar Soler
- Medical Oncology Department, Institut Català d'Oncologia (ICO) - IDIBELL, Barcelona, Spain
| | - Elisabetta Fenocchio
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy
| | | | - Thibault Mazard
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France; ICM, Institut Régional du Cancer de Montpellier, Montpellier, F-34298, France
| | - Cristina Santos Vivas
- Medical Oncology Department, Institut Català d'Oncologia (ICO) - IDIBELL, Barcelona, Spain; Universitat de Barcelona, Barcelona, Spain
| | - Elena Elez
- VHIO Vall d'Hebron Institute of Oncology, Medical Oncology Department, Barcelona, Spain
| | - Federica Di Nicolantonio
- Istituto di Candiolo - Fondazione del Piemonte per l'Oncologia - IRCCS, Candiolo, Torino, Italy; Department of Oncology, University of Torino, Turin, Italy
| | - Alain R Thierry
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier, F-34298, France; ICM, Institut Régional du Cancer de Montpellier, Montpellier, F-34298, France.
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11
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El-Ahmad P, Mendes-Silva AP, Diniz BS. Liquid Biopsy in Neuropsychiatric Disorders: A Step Closer to Precision Medicine. Mol Neurobiol 2024:10.1007/s12035-024-04492-y. [PMID: 39298102 DOI: 10.1007/s12035-024-04492-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 09/11/2024] [Indexed: 09/21/2024]
Abstract
Psychiatric disorders are among the leading causes of disease burden worldwide. Despite their significant impact, their diagnosis remains challenging due to symptom heterogeneity, psychiatric comorbidity, and the lack of objective diagnostic tests and well-defined biomarkers. Leveraging genomic, epigenomic, and fragmentomic technologies, circulating cell-free DNA (ccfDNA)-based liquid biopsies have emerged as a potential non-invasive diagnosis and disease-monitoring tool. ccfDNA is a DNA species released into circulation from all types of cells through passive and active mechanisms and can serve as a biomarker for various diseases, namely, cancer. Despite their potential, the application of ccfDNA in neuropsychiatry remains underdeveloped. In this review, we provide an overview of liquid biopsies and their components, with a particular focus on ccfDNA. With a summary of pre-analytical practices and current ccfDNA technologies, we highlight the current state of research regarding the use of ccfDNA as a biomarker for neuropsychiatric disorders. Finally, we discuss future steps to unlock ccfDNA's potential in clinical practice.
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Affiliation(s)
- Perla El-Ahmad
- UConn Center on Aging, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA.
| | - Ana Paula Mendes-Silva
- Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health (CAMH), Toronto, Canada
- Department of Psychiatry, University of Saskatchewan, Saskatoon, Canada
| | - Breno S Diniz
- UConn Center on Aging, University of Connecticut Health Center, 263 Farmington Ave, Farmington, CT, 06030, USA.
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12
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Kim SH, Weigelt B. Circulating cell-free (cf)DNA analysis: Current technologies and applications in gynecologic cancer. Gynecol Oncol Rep 2024; 54:101431. [PMID: 38947418 PMCID: PMC11211888 DOI: 10.1016/j.gore.2024.101431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/04/2024] [Accepted: 06/09/2024] [Indexed: 07/02/2024] Open
Abstract
Cell-free DNA (cfDNA) analysis has several promising clinical applications in the management of cancer patients, with clinical validity established in different types of solid tumors (e.g., lung, breast, and colon cancer). Cancers harbor unique genetic alterations that can be detected in the plasma and other bodily fluids of cancer patients, constituting an alternate source of tumor-derived DNA. Technologic advances and wide-spread availability of next-generation sequencing (NGS) have made sequencing analysis of circulating tumor DNA (ctDNA) possible, employing both off-the-shelf and personalized tumor-informed panels. Tumor size, disease burden and high-grade histologic types have been shown to correlate with ctDNA levels across multiple solid cancer types. Detection of tumor-derived genetic alterations in plasma-derived cfDNA can facilitate diagnosis, guide treatment selection, and serve as a biomarker for treatment response and prognostication. Molecular residual disease (MRD) is at the forefront of cfDNA analysis, with implications in treatment de-escalation/ escalation in the neoadjuvant and adjuvant settings. The development of cfDNA analysis in early detection of cancers is under active investigation. Proof-of-principles studies in gynecologic cancers have demonstrated feasibility and potential for innovation in cancers lacking specific biomarkers, including the tracking of human papillomavirus (HPV) cfDNA in patients with cervical cancer. In this review, we outline the assays currently available for cfDNA sequencing/ ctDNA detection, the role of cfDNA analysis in clinical decision-making and the current status and potential clinical uses of cfDNA research in gynecologic cancers.
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Affiliation(s)
- Sarah H Kim
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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13
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Cabané P, Correa C, Bode I, Aguilar R, Elorza AA. Biomarkers in Thyroid Cancer: Emerging Opportunities from Non-Coding RNAs and Mitochondrial Space. Int J Mol Sci 2024; 25:6719. [PMID: 38928426 PMCID: PMC11204084 DOI: 10.3390/ijms25126719] [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: 04/20/2024] [Revised: 06/01/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Thyroid cancer diagnosis primarily relies on imaging techniques and cytological analyses. In cases where the diagnosis is uncertain, the quantification of molecular markers has been incorporated after cytological examination. This approach helps physicians to make surgical decisions, estimate cancer aggressiveness, and monitor the response to treatments. Despite the availability of commercial molecular tests, their widespread use has been hindered in our experience due to cost constraints and variability between them. Thus, numerous groups are currently evaluating new molecular markers that ultimately will lead to improved diagnostic certainty, as well as better classification of prognosis and recurrence. In this review, we start reviewing the current preoperative testing methodologies, followed by a comprehensive review of emerging molecular markers. We focus on micro RNAs, long non-coding RNAs, and mitochondrial (mt) signatures, including mtDNA genes and circulating cell-free mtDNA. We envision that a robust set of molecular markers will complement the national and international clinical guides for proper assessment of the disease.
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Affiliation(s)
- Patricio Cabané
- Department of Head and Neck Surgery, Clinica INDISA, Santiago 7520440, Chile; (P.C.); (C.C.)
- Faculty of Medicine, Universidad Andres Bello, Santiago 8370071, Chile
- Department of Basic and Clinical Oncology, Faculty of Medicine, University of Chile, Santiago 8380453, Chile
| | - Claudio Correa
- Department of Head and Neck Surgery, Clinica INDISA, Santiago 7520440, Chile; (P.C.); (C.C.)
- Faculty of Medicine, Universidad Andres Bello, Santiago 8370071, Chile
| | - Ignacio Bode
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Rodrigo Aguilar
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
| | - Alvaro A. Elorza
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago 8370071, Chile;
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14
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Islam MA, Sehar U, Sultana OF, Mukherjee U, Brownell M, Kshirsagar S, Reddy PH. SuperAgers and centenarians, dynamics of healthy ageing with cognitive resilience. Mech Ageing Dev 2024; 219:111936. [PMID: 38657874 DOI: 10.1016/j.mad.2024.111936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/08/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Graceful healthy ageing and extended longevity is the most desired goal for human race. The process of ageing is inevitable and has a profound impact on the gradual deterioration of our physiology and health since it triggers the onset of many chronic conditions like dementia, osteoporosis, diabetes, arthritis, cancer, and cardiovascular disease. However, some people who lived/live more than 100 years called 'Centenarians" and how do they achieve their extended lifespans are not completely understood. Studying these unknown factors of longevity is important not only to establish a longer human lifespan but also to manage and treat people with shortened lifespans suffering from age-related morbidities. Furthermore, older adults who maintain strong cognitive function are referred to as "SuperAgers" and may be resistant to risk factors linked to cognitive decline. Investigating the mechanisms underlying their cognitive resilience may contribute to the development of therapeutic strategies that support the preservation of cognitive function as people age. The key to a long, physically, and cognitively healthy life has been a mystery to scientists for ages. Developments in the medical sciences helps us to a better understanding of human physiological function and greater access to medical care has led us to an increase in life expectancy. Moreover, inheriting favorable genetic traits and adopting a healthy lifestyle play pivotal roles in promoting longer and healthier lives. Engaging in regular physical activity, maintaining a balanced diet, and avoiding harmful habits such as smoking contribute to overall well-being. The synergy between positive lifestyle choices, access to education, socio-economic factors, environmental determinants and genetic supremacy enhances the potential for a longer and healthier life. Our article aims to examine the factors associated with healthy ageing, particularly focusing on cognitive health in centenarians. We will also be discussing different aspects of ageing including genomic instability, metabolic burden, oxidative stress and inflammation, mitochondrial dysfunction, cellular senescence, immunosenescence, and sarcopenia.
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Affiliation(s)
- Md Ariful Islam
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Ujala Sehar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Omme Fatema Sultana
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Upasana Mukherjee
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Malcolm Brownell
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Sudhir Kshirsagar
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - P Hemachandra Reddy
- Department of Internal Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA; Public Health Department of Graduate School of Biomedical Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Speech, Language and Hearing Sciences, School Health Professions, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Neurology, Departments of School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA; Nutritional Sciences Department, College of Human Sciences, Texas Tech University, 1301 Akron Ave, Lubbock, TX 79409, USA.
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15
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Kapoor S, Mihalovičová L, Pisareva E, Pastor B, Mirandola A, Roch B, Bryant J, Princy AP, Chouaib S, Thierry AR. Association of vascular netosis with COVID-19 severity in asymptomatic and symptomatic patients. iScience 2024; 27:109573. [PMID: 38660409 PMCID: PMC11039348 DOI: 10.1016/j.isci.2024.109573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/19/2023] [Accepted: 03/24/2024] [Indexed: 04/26/2024] Open
Abstract
We examined from a large exploratory study cohort of COVID-19 patients (N = 549) a validated panel of neutrophil extracellular traps (NETs) markers in different categories of disease severity. Neutrophil elastase (NE), myeloperoxidase (MPO), and circulating nuclear DNA (cir-nDNA) levels in plasma were seen to gradually and significantly (p < 0.0001) increase with the disease severity: mild (3.7, 48.9, and 15.8 ng/mL, respectively); moderate (9.8, 77.5, and 27.7 ng/mL, respectively); severe (11.7, 99.5, and 29.0 ng/mL, respectively); and critical (13.1, 110.2, and 46.0 ng/mL, respectively); and are also statistically different with healthy individuals (N = 140; p < 0.0001). All observations made in relation to the Delta variant-infected patients are in line with Omicron-infected patients. We unexpectedly observed significantly higher levels of NETs in asymptomatic individuals as compared to healthy subjects (p < 0.0001). Moreover, the balance of cir-nDNA and circulating mitochondrial DNA level was affected in COVID-19 infected patients attesting to mitochondrial dysfunction.
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Affiliation(s)
- Suman Kapoor
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, UAE
| | - Lucia Mihalovičová
- IRCM, Institute of Research in Cancerology of Montpellier, INSERM U1194, Centre Hospitalier Universitaire, University of Montpellier, Montpellier, France
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, Sasinkova, Bratislava, Slovakia
| | - Ekaterina Pisareva
- IRCM, Institute of Research in Cancerology of Montpellier, INSERM U1194, Centre Hospitalier Universitaire, University of Montpellier, Montpellier, France
| | - Brice Pastor
- IRCM, Institute of Research in Cancerology of Montpellier, INSERM U1194, Centre Hospitalier Universitaire, University of Montpellier, Montpellier, France
| | - Alexia Mirandola
- IRCM, Institute of Research in Cancerology of Montpellier, INSERM U1194, Centre Hospitalier Universitaire, University of Montpellier, Montpellier, France
| | - Benoit Roch
- IRCM, Institute of Research in Cancerology of Montpellier, INSERM U1194, Centre Hospitalier Universitaire, University of Montpellier, Montpellier, France
| | - Joe Bryant
- Institute of Human Virology, Baltimore, MD, USA
| | | | - Salem Chouaib
- Thumbay Research Institute for Precision Medicine, Gulf Medical University, Ajman, UAE
- Institut Gustave Roussy, Villejuif, France
| | - Alain Roger Thierry
- IRCM, Institute of Research in Cancerology of Montpellier, INSERM U1194, Centre Hospitalier Universitaire, University of Montpellier, Montpellier, France
- Montpellier Cancer Institute (ICM), Montpellier, France
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Peng H, Pan M, Zhou Z, Chen C, Xing X, Cheng S, Zhang S, Zheng H, Qian K. The impact of preanalytical variables on the analysis of cell-free DNA from blood and urine samples. Front Cell Dev Biol 2024; 12:1385041. [PMID: 38784382 PMCID: PMC11111958 DOI: 10.3389/fcell.2024.1385041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Cell-free DNA (cfDNA), a burgeoning class of molecular biomarkers, has been extensively studied across a variety of biomedical fields. As a key component of liquid biopsy, cfDNA testing is gaining prominence in disease detection and management due to the convenience of sample collection and the abundant wealth of genetic information it provides. However, the broader clinical application of cfDNA is currently impeded by a lack of standardization in the preanalytical procedures for cfDNA analysis. A number of fundamental challenges, including the selection of appropriate preanalytical procedures, prevention of short cfDNA fragment loss, and the validation of various cfDNA measurement methods, remain unaddressed. These existing hurdles lead to difficulties in comparing results and ensuring repeatability, thereby undermining the reliability of cfDNA analysis in clinical settings. This review discusses the crucial preanalytical factors that influence cfDNA analysis outcomes, including sample collection, transportation, temporary storage, processing, extraction, quality control, and long-term storage. The review provides clarification on achievable consensus and offers an analysis of the current issues with the goal of standardizing preanalytical procedures for cfDNA analysis.
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Affiliation(s)
- Hongwei Peng
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ming Pan
- Taihe Skills Training Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zongning Zhou
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Congbo Chen
- Department of Urology, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xing Xing
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shaoping Cheng
- Department of Urology, The First Affiliated Hospital of Yangtze University, Jingzhou, Hubei, China
| | - Shanshan Zhang
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hang Zheng
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Human Genetic Resources Preservation Center of Hubei Province, Hubei Key Laboratory of Urological Diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Urology, Laboratory of Precision Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
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Lehmann J, Giaglis S, Kyburz D, Daoudlarian D, Walker UA. Plasma mtDNA as a possible contributor to and biomarker of inflammation in rheumatoid arthritis. Arthritis Res Ther 2024; 26:97. [PMID: 38715082 PMCID: PMC11075188 DOI: 10.1186/s13075-024-03329-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
OBJECTIVES Neutrophil extracellular trap formation and cell-free DNA (cfDNA) contribute to the inflammation in rheumatoid arthritis (RA), but it is unknown if mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) is more abundant in the circulation. It is unclear if DNA concentration measurements may assist in clinical decision-making. METHODS This single-center prospective observational study collected plasma from consecutive RA patients and healthy blood donors. Platelets were removed, and mtDNA and nDNA copy numbers were quantified by polymerase chain reaction (PCR). RESULTS One hundred six RA patients and 85 healthy controls (HC) were recruited. Circulating median mtDNA copy numbers were increased 19.4-fold in the plasma of patients with RA (median 1.1 x108 copies/mL) compared to HC (median 5.4 x106 copies/mL, p<0.0001). Receiver operating characteristics (ROC) curve analysis of mtDNA copy numbers identified RA patients with high sensitivity (92.5%) and specificity (89.4%) with an area under the curve (AUC) of 0.97, p <0.0001 and a positive likelihood ratio of 8.7. Demographic, serological (rheumatoid factor (RF) positivity, anti-citrullinated protein antibodies (ACPA) positivity) and treatment factors were not associated with DNA concentrations. mtDNA plasma concentrations, however, correlated significantly with disease activity score-28- erythrocyte sedimentation rate (DAS28-ESR) and increased numerically with increasing DAS28-ESR and clinical disease activity index (CDAI) activity. MtDNA copy numbers also discriminated RA in remission (DAS28 <2.6) from HC (p<0.0001). Also, a correlation was observed between mtDNA and the ESR (p = 0.006, R= 0.29). Similar analyses showed no significance for nDNA. CONCLUSION In contrast to nDNA, mtDNA is significantly elevated in the plasma of RA patients compared with HC. Regardless of RA activity, the abundance of circulating mtDNA is a sensitive discriminator between RA patients and HC. Further validation of the diagnostic value of mtDNA testing is required.
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Affiliation(s)
- Julia Lehmann
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Rheumatology, University Hospital Basel, Petersgraben 4, CH 4037, Basel, Switzerland
| | - Stavros Giaglis
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Diego Kyburz
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Department of Rheumatology, University Hospital Basel, Petersgraben 4, CH 4037, Basel, Switzerland
| | - Douglas Daoudlarian
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Ulrich A Walker
- Laboratory for Experimental Rheumatology, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Department of Rheumatology, University Hospital Basel, Petersgraben 4, CH 4037, Basel, Switzerland.
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18
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Lee JS, Cho EH, Kim B, Hong J, Kim YG, Kim Y, Jang JH, Lee ST, Kong SY, Lee W, Shin S, Song EY. Clinical Practice Guideline for Blood-based Circulating Tumor DNA Assays. Ann Lab Med 2024; 44:195-209. [PMID: 38221747 PMCID: PMC10813828 DOI: 10.3343/alm.2023.0389] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/06/2023] [Accepted: 01/06/2024] [Indexed: 01/16/2024] Open
Abstract
Circulating tumor DNA (ctDNA) has emerged as a promising tool for various clinical applications, including early diagnosis, therapeutic target identification, treatment response monitoring, prognosis evaluation, and minimal residual disease detection. Consequently, ctDNA assays have been incorporated into clinical practice. In this review, we offer an in-depth exploration of the clinical implementation of ctDNA assays. Notably, we examined existing evidence related to pre-analytical procedures, analytical components in current technologies, and result interpretation and reporting processes. The primary objective of this guidelines is to provide recommendations for the clinical utilization of ctDNA assays.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
| | - Eun Hye Cho
- Department of Laboratory Medicine, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Boram Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | | | - Young-gon Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seung-Tae Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
- Dxome Co. Ltd., Seongnam, Korea
| | - Sun-Young Kong
- Department of Laboratory Medicine, National Cancer Center, Goyang, Korea
| | - Woochang Lee
- Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Saeam Shin
- Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Eun Young Song
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Korea
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de Miranda FS, Claudio LMAM, de Almeida DSM, Nunes JB, Barauna VG, Luiz WB, Vassallo PF, Campos LCG. Cell-Free Nuclear and Mitochondrial DNA as Potential Biomarkers for Assessing Sepsis Severity. Biomedicines 2024; 12:933. [PMID: 38790895 PMCID: PMC11117867 DOI: 10.3390/biomedicines12050933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/26/2024] [Accepted: 04/19/2024] [Indexed: 05/26/2024] Open
Abstract
Sepsis continues to be a significant public health challenge despite advances in understanding its pathophysiology and management strategies. Therefore, this study evaluated the value of cell-free nuclear DNA (cf-nDNA) and cell-free mitochondrial DNA (cf-mtDNA) for assessing the severity and prognosis of sepsis. Ninety-four patients were divided into three groups: infection (n = 32), sepsis (n = 30), and septic shock (n = 32). Plasma samples were collected at the time of diagnosis, and cfDNA concentrations were determined by qPCR assay. The results showed that plasma cfDNA levels increased with the severity of the disease. To distinguish between patients with infection and those with sepsis, the biomarker L1PA290 achieved the highest AUC of 0.817 (95% CI: 0.725-0.909), demonstrating a sensitivity of 77.0% and a specificity of 79.3%. When cf-nDNA was combined with the SOFA score, there was a significant improvement in the AUC (0.916 (0.853-0.979)), sensitivity (88.1%), and specificity (80.0%). Moreover, patients admitted to the ICU after being diagnosed with sepsis had significantly higher cf-nDNA concentrations. In patients admitted to the ICU, combining cf-nDNA with the SOFA score yielded an AUC of 0.753 (0.622-0.857), with a sensitivity of 95.2% and a specificity of 50.0%. cfDNA can differentiate between patients with infection and those with sepsis. It can also identify patients who are likely to be admitted to the ICU by predicting those with indications for intensive care, suggesting its potential as a biomarker for sepsis.
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Affiliation(s)
- Felipe Silva de Miranda
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Postgraduate Program in Biology and Biotechnology of Microorganisms State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Livia Maria A. M. Claudio
- Post Graduation Program in Physiological Sciences, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil;
| | - Dayanne Silva M. de Almeida
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Juliana Braga Nunes
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Valério Garrone Barauna
- Molecular Physiology Laboratory of Exercise Science, Federal University of Espírito Santo, Vitória 29075-910, Espírito Santo, Brazil;
| | - Wilson Barros Luiz
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Postgraduate Program in Biology and Biotechnology of Microorganisms State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
| | - Paula Frizzera Vassallo
- Clinical Hospital, Federal University of Minas Gerais, Belo Horizonte 30130-100, Minas Gerais, Brazil;
| | - Luciene Cristina Gastalho Campos
- Department of Biological Science State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil; (F.S.d.M.); (D.S.M.d.A.); (J.B.N.); (W.B.L.)
- Postgraduate Program in Biology and Biotechnology of Microorganisms State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
- Laboratory of Applied Pathology and Genetics State, University of Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
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Ali M, Choudhary R, Singh K, Kumari S, Kumar R, Graham BB, Pasha MAQ, Rabyang S, Thinlas T, Mishra A. Hypobaric hypoxia modulated structural characteristics of circulating cell-free DNA in high-altitude pulmonary edema. Am J Physiol Lung Cell Mol Physiol 2024; 326:L496-L507. [PMID: 38349115 DOI: 10.1152/ajplung.00245.2023] [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: 08/01/2023] [Revised: 01/10/2024] [Accepted: 01/25/2024] [Indexed: 04/07/2024] Open
Abstract
The utility of cell-free (cf) DNA has extended as a surrogate or clinical biomarker for various diseases. However, a more profound and expanded understanding of the diverse cfDNA population and its correlation with physiological phenotypes and environmental factors is imperative for using its full potential. The high-altitude (HA; altitude > 2,500 m above sea level) environment characterized by hypobaric hypoxia offers an observational case-control design to study the differential cfDNA profile in patients with high-altitude pulmonary edema (HAPE) (number of subjects, n = 112) and healthy HA sojourners (n = 111). The present study investigated cfDNA characteristics such as concentration, fragment length size, degree of integrity, and subfractions reflecting mitochondrial-cfDNA copies in the two groups. The total cfDNA level was significantly higher in patients with HAPE, and the level increased with increasing HAPE severity (P = 0.0036). A lower degree of cfDNA integrity of 0.346 in patients with HAPE (P = 0.001) indicated the prevalence of shorter cfDNA fragments in circulation in patients compared with the healthy HA sojourners. A significant correlation of cfDNA characteristics with the peripheral oxygen saturation levels in the patient group demonstrated the translational relevance of cfDNA molecules. The correlation was further supported by multivariate logistic regression and receiver operating characteristic curve. To our knowledge, our study is the first to highlight the association of higher cfDNA concentration, a lower degree of cfDNA integrity, and increased mitochondrial-derived cfDNA population with HAPE disease severity. Further deep profiling of cfDNA fragments, which preserves cell-type specific genetic and epigenetic features, can provide dynamic physiological responses to hypoxia.NEW & NOTEWORTHY This study observed altered cell-free (cf) DNA fragment patterns in patients with high-altitude pulmonary edema and the significant correlation of these patterns with peripheral oxygen saturation levels. This suggests deep profiling of cfDNA fragments in the future may identify genetic and epigenetic mechanisms underlying physiological and pathophysiological responses to hypoxia.
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Affiliation(s)
- Manzoor Ali
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Raushni Choudhary
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kanika Singh
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
| | - Swati Kumari
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Rahul Kumar
- Department of Medicine, University of California, San Francisco, California, United States
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States
| | - Brian B Graham
- Department of Medicine, University of California, San Francisco, California, United States
- Lung Biology Center, Zuckerberg San Francisco General Hospital, San Francisco, California, United States
| | | | - Stanzen Rabyang
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, India
| | - Tashi Thinlas
- Department of Medicine, Sonam Norboo Memorial Hospital, Leh, India
| | - Aastha Mishra
- Cardio Respiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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21
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Juškevičiūtė E, Neuberger E, Eimantas N, Venckunas T, Kamandulis S, Simon P, Brazaitis M. Three-week sprint interval training (SIT) reduces cell-free DNA and low-frequency fatigue but does not induce VO2max improvement in older men. Eur J Appl Physiol 2024; 124:1297-1309. [PMID: 38015284 DOI: 10.1007/s00421-023-05366-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 10/29/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE This study aimed to investigate the impact of sprint interval training (SIT) on both the acute and 3-week modulations of cell-free DNA (cfDNA), as well as its association with neuromuscular fatigue and physical performance in healthy young and old men. METHODS Ten young (20-25 year old) and nine elderly (63-72 year old) healthy men performed nine SIT sessions consisting of 4-to-6-all-out cycling repetitions of 30 s interspaced with 4-min rest intervals. We compared the maximal voluntary contractions torque, central activation ratio, low-frequency fatigue (LFF), and cfDNA concentrations between the groups before, immediately after, 1 h after, and 24 h after the first and ninth SIT sessions. RESULTS The plasma cfDNA levels were increased post-exercise (from 1.4 ± 0.258 to 1.91 ± 0.278 ng/ml (P < 0.01) on a log10 scale), without significant differences between the groups. However, older individuals showed a slight decrease in the baseline cfDNA values, from 1.39 ± 0.176 to 1.29 ± 0.085 ng/ml on a log10 scale, after 3 weeks (P = 0.043). Importantly, the elevation of the post-exercise cfDNA values was correlated with an increase in LFF in both groups. Three weeks of SIT induced an improvement in the recovery of LFF (main session effect, P = 0.0029); however, only the young group showed an increase in aerobic capacity (VO2max) (from 40.8 ± 6.74 to 43.0 ± 5.80 ml/kg/min, P = 0.0039). CONCLUSION Three weeks of SIT diminished the baseline cfDNA values in the old group, together with an improvement in the recovery of LFF. However, VO2max was increased only in the young group.
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Affiliation(s)
- Ema Juškevičiūtė
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania.
- Department of Sports Medicine, Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany.
| | - Elmo Neuberger
- Department of Sports Medicine, Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nerijus Eimantas
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
| | - Tomas Venckunas
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
| | - Sigitas Kamandulis
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania
| | - Perikles Simon
- Department of Sports Medicine, Prevention and Rehabilitation, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marius Brazaitis
- Institute of Sport Science and Innovations, Lithuanian Sports University, Kaunas, Lithuania.
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22
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Balasubramanian S, Richert ME, Kong H, Fu S, Jang MK, Andargie TE, Keller MB, Alnababteh M, Park W, Apalara Z, Sun J, Redekar N, Orens J, Aryal S, Bush EL, Cantu E, Diamond J, Shah P, Yu K, Nathan SD, Agbor-Enoh S. Cell-Free DNA Maps Tissue Injury and Correlates with Disease Severity in Lung Transplant Candidates. Am J Respir Crit Care Med 2024; 209:727-737. [PMID: 38117233 PMCID: PMC10945061 DOI: 10.1164/rccm.202306-1064oc] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/28/2023] [Indexed: 12/21/2023] Open
Abstract
Rationale: Plasma cell-free DNA levels correlate with disease severity in many conditions. Pretransplant cell-free DNA may risk stratify lung transplant candidates for post-transplant complications. Objectives: To evaluate if pretransplant cell-free DNA levels and tissue sources identify patients at high risk of primary graft dysfunction and other pre- and post-transplant outcomes. Methods: This multicenter, prospective cohort study recruited 186 lung transplant candidates. Pretransplant plasma samples were collected to measure cell-free DNA. Bisulfite sequencing was performed to identify the tissue sources of cell-free DNA. Multivariable regression models determined the association between cell-free DNA levels and the primary outcome of primary graft dysfunction and other transplant outcomes, including Lung Allocation Score, chronic lung allograft dysfunction, and death. Measurements and Main Results: Transplant candidates had twofold greater cell-free DNA levels than healthy control patients (median [interquartile range], 23.7 ng/ml [15.1-35.6] vs. 12.9 ng/ml [9.9-18.4]; P < 0.0001), primarily originating from inflammatory innate immune cells. Cell-free DNA levels and tissue sources differed by native lung disease category and correlated with the Lung Allocation Score (P < 0.001). High pretransplant cell-free DNA increased the risk of primary graft dysfunction (odds ratio, 1.60; 95% confidence interval [CI], 1.09-2.46; P = 0.0220), and death (hazard ratio, 1.43; 95% CI, 1.07-1.92; P = 0.0171) but not chronic lung allograft dysfunction (hazard ratio, 1.37; 95% CI, 0.97-1.94; P = 0.0767). Conclusions: Lung transplant candidates demonstrate a heightened degree of tissue injury with elevated cell-free DNA, primarily originating from innate immune cells. Pretransplant plasma cell-free DNA levels predict post-transplant complications.
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Affiliation(s)
- Shanti Balasubramanian
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Mary E. Richert
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Hyesik Kong
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Sheng Fu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Moon Kyoo Jang
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Temesgen E. Andargie
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Department of Biology, Howard University, Washington, District of Columbia
| | - Michael B. Keller
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Muhtadi Alnababteh
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Critical Care Medicine Department, National Institutes of Health, Bethesda, Maryland
| | - Woojin Park
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Zainab Apalara
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jian Sun
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Neelam Redekar
- Integrated Data Science Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | - Jonathan Orens
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Shambhu Aryal
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Errol L. Bush
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, The Johns Hopkins School of Medicine, Baltimore, Maryland; and
| | - Edward Cantu
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Joshua Diamond
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Surgery, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Pali Shah
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Steven D. Nathan
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Advanced Lung Disease and Lung Transplant Program, Inova Fairfax Hospital, Fairfax, Virginia
| | - Sean Agbor-Enoh
- Genomic Research Alliance for Transplantation, Bethesda, Maryland
- Division of Intramural Research, Laboratory of Applied Precision Omics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
- Department of Medicine, The Johns Hopkins School of Medicine, Baltimore, Maryland
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Fisher T, Powell E, Yuwono NL, Ford CE, Warton K. Circulating cell-free DNA is elevated in postmenopausal compared with pre- and perimenopausal women. Menopause 2024; 31:171-175. [PMID: 38385729 DOI: 10.1097/gme.0000000000002313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
OBJECTIVE With the rising use of circulating cell-free DNA (cirDNA) liquid biopsies for disease screening, it is important to understand biological differences that may impact the accuracy of cirDNA-based clinical tests. Although a number of biological factors have been researched, the relationship between menopause and cirDNA has not been thoroughly investigated. We aimed to compare plasma cirDNA concentration and DNA fragment integrity in healthy women pre- and postmenopause. METHODS Blood was collected from healthy female volunteers 40 years and older. cirDNA was extracted from plasma (n = 52) and quantified by quantitative polymerase chain reaction (n = 47; 26 premenopause, mean age-46 y; 21 postmenopause, mean age-59 y). cirDNA concentration was quantitated using an ALU repetitive sequence with a 115-base-pair (bp) product (ALU-115), and long cirDNA fragments were quantitated using an ALU repetitive sequence with a 247-bp product (ALU-247). cirDNA integrity was expressed as a ratio of ALU-247 over ALU-115. Mann-Whitney U test was used to compare pre- and postmenopause qPCR results, and a two-tailed, unpaired t test was undertaken to compare the integrity ratio between the two groups. RESULTS Postmenopause plasma samples were found to have a significantly higher cirDNA concentration (P < 0.0001, premenopause: mean, 3.10 ± 1.84 ng/mL; median, 2.90 ng/mL; postmenopause: mean, 5.28 ± 2.76 ng/mL; median, 4.56 ng/mL) and significantly higher concentration of long-stranded cirDNA fragments (P = 0.0033, premenopause: mean, 1.06 ± 0.48 ng/mL; median, 0.96 ng/mL; postmenopause: mean, 1.69 ± 0.89 ng/mL; median, 1.48 ng/mL). There was no significant difference in the integrity ratio between the groups (P = 0.1788). CONCLUSIONS Plasma cirDNA concentrations are higher in postmenopausal women. This has important implications in cirDNA liquid biopsy development and screening, especially for diseases such as cancer where the majority of cases are diagnosed postmenopause.
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Affiliation(s)
- Teagan Fisher
- From the Gynaecological Cancer Research Group, Adult Cancer Program, School of Clinical Medicine University of New South Wales, Sydney, Australia
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24
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Wojtkowska M, Karczewska N, Pacewicz K, Pacak A, Kopeć P, Florczak-Wyspiańska J, Popławska-Domaszewicz K, Małkiewicz T, Sokół B. Quantification of Circulating Cell-Free DNA in Idiopathic Parkinson's Disease Patients. Int J Mol Sci 2024; 25:2818. [PMID: 38474065 DOI: 10.3390/ijms25052818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/21/2024] [Accepted: 02/26/2024] [Indexed: 03/14/2024] Open
Abstract
Parkinson's disease (PD) is one of the most common neurodegenerative disorders globally and leads to an excessive loss of dopaminergic neurons in the substantia nigra of the brain. Circulating cell-free DNA (ccf-DNA) are double-stranded DNA fragments of different sizes and origins that are released into the serum and cerebrospinal fluid (CSF) due to cell death (i.e., necrosis and apoptosis) or are actively released by viable cells via exocytosis and NETosis. Using droplet digital polymerase chain reaction (ddPCR), we comprehensively analyzed and distinguished circulating cell-free mitochondrial DNA (ccf mtDNA) and circulating cell-free nuclear DNA (ccfDNA) in the serum and CSF of PD and control patients. The quantitative analysis of serum ccf-DNA in PD patients demonstrated a significant increase in ccf mtDNA and ccfDNA compared to that in healthy control patients and a significantly higher copy of ccf mtDNA when compared to ccfDNA. Next, the serum ccf mtDNA levels significantly increased in male PD patients compared to those in healthy male controls. Furthermore, CSF ccf mtDNA in PD patients increased significantly compared to ccfDNA, and ccf mtDNA decreased in PD patients more than it did in healthy controls. These decreases were not statistically significant but were in agreement with previous data. Interestingly, ccf mtDNA increased in healthy control patients in both serum and CSF as compared to ccfDNA. The small sample size of serum and CSF were the main limitations of this study. To the best of our knowledge, this is the first comprehensive study on serum and CSF of PD patients using ddPCR to indicate the distribution of the copy number of ccf mtDNA as well as ccfDNA. If validated, we suggest that ccf mtDNA has greater potential than ccfDNA to lead the development of novel treatments for PD patients.
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Affiliation(s)
- Małgorzata Wojtkowska
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Natalia Karczewska
- Centre for Chemical Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704 Poznan, Poland
| | - Klaudia Pacewicz
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Andrzej Pacak
- Department of Gene Expression, Faculty of Biology Poznan, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Piotr Kopeć
- Department of Computational Biology, Faculty of Biology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | | | | | - Tomasz Małkiewicz
- Department of Teaching Anaesthesiology and Intensive Therapy, Poznan University of Medical Sciences, 60-355 Poznan, Poland
| | - Bartosz Sokół
- Department of Neurosurgery, Poznan University of Medical Sciences, 60-355 Poznan, Poland
- Hospital of Joseph Strus in Poznan, 61-285 Poznan, Poland
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León-Paz-de-Rodríguez GE, Rodríguez-León E, Iñiguez-Palomares R. DNA Hyperstructure. ACS OMEGA 2024; 9:9013-9026. [PMID: 38434827 PMCID: PMC10905968 DOI: 10.1021/acsomega.3c07379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/29/2023] [Accepted: 01/24/2024] [Indexed: 03/05/2024]
Abstract
This study presents a new procedure to condense DNA molecules and precipitate them onto a glass slide. The resulting DNA molecules undergo autonomous self-assembly, creating closed superstructures on the micrometer scale, which are called DNA hyperstructures. These structures can be observed using low-magnification (4×) light microscopy. Precisely controlling the alcohol/glacial acetic acid ratio and DNA concentration during precipitation enabled the regulation of structure compaction on the slide. The alcohol/glacial acetic acid ratio is inversely proportional to the DNA concentration to achieve optimal compaction on the slide. Confocal microscopy fluorescence analysis of DNA extracts stained with DAPI shows that nucleic acids self-assemble to form structures during precipitation on the slide. This methodology is relevant since it facilitates the precipitation and visualization of DNA, regardless of its origin or molecular weight. To confirm its versatility, results with DNA extracted from human peripheral blood, the Lambda virus, and plasmid pBR322 are presented. The study examined the morphological features of DNA hyperstructures in both healthy individuals and those diagnosed with different medical conditions or illnesses, revealing distinct patterns specific to each case. This innovative technology has potential for disease detection in peripheral blood samples, ranging from cancer and Alzheimer's disease to determining the gender of the gestational product at an early stage.
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26
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Abstract
Cell-free DNA (cfDNA) tests use small amounts of DNA in the bloodstream as biomarkers. While it is thought that cfDNA is largely released by dying cells, the proportion of dying cells' DNA that reaches the bloodstream is unknown. Here, we integrate estimates of cellular turnover rates to calculate the expected amount of cfDNA. By comparing this to the actual amount of cell type-specific cfDNA, we estimate the proportion of DNA reaching plasma as cfDNA. We demonstrate that <10% of the DNA from dying cells is detectable in plasma, and the ratios of measured to expected cfDNA levels vary a thousand-fold among cell types, often reaching well below 0.1%. The analysis suggests that local clearance, presumably via phagocytosis, takes up most of the dying cells' DNA. Insights into the underlying mechanism may help to understand the physiological significance of cfDNA and improve the sensitivity of liquid biopsies.
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Affiliation(s)
- Ron Sender
- Weizmann Institute of ScienceRehovotIsrael
| | - Elad Noor
- Weizmann Institute of ScienceRehovotIsrael
| | - Ron Milo
- Weizmann Institute of ScienceRehovotIsrael
| | - Yuval Dor
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel Canada, the Hebrew University-Hadassah Medical SchoolJerusalemIsrael
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27
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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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28
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Wang R, Yang Y, Lu T, Cui Y, Li B, Liu X. Circulating cell-free DNA-based methylation pattern in plasma for early diagnosis of esophagus cancer. PeerJ 2024; 12:e16802. [PMID: 38313016 PMCID: PMC10838104 DOI: 10.7717/peerj.16802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024] Open
Abstract
With the increased awareness of early tumor detection, the importance of detecting and diagnosing esophageal cancer in its early stages has been underscored. Studies have consistently demonstrated the crucial role of methylation levels in circulating cell-free DNA (cfDNA) in identifying and diagnosing early-stage cancer. cfDNA methylation pertains to the methylation state within the genomic scope of cfDNA and is strongly associated with cancer development and progression. Several research teams have delved into the potential application of cfDNA methylation in identifying early-stage esophageal cancer and have achieved promising outcomes. Recent research supports the high sensitivity and specificity of cfDNA methylation in early esophageal cancer diagnosis, providing a more accurate and efficient approach for early detection and improved clinical management. Accordingly, this review aims to present an overview of methylation-based cfDNA research with a focus on the latest developments in the early detection of esophageal cancer. Additionally, this review summarizes advanced analytical technologies for cfDNA methylation that have significantly benefited from recent advancements in separation and detection techniques, such as methylated DNA immunoprecipitation sequencing (MeDIP-seq). Recent findings suggest that biomarkers based on cfDNA methylation may soon find successful applications in the early detection of esophageal cancer. However, large-scale prospective clinical trials are required to identify the potential of these biomarkers.
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Affiliation(s)
- Rui Wang
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Yue Yang
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Tianyu Lu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Youbin Cui
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
| | - Bo Li
- School of Public Health, Jilin University, Changchun, Jilin, China
| | - Xin Liu
- Department of Thoracic Surgery, First Hospital of Jilin University, Changchun, Jilin, China
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Janovičová Ľ, Holániová D, Vlková B, Celec P. Pre-Analytical Factors Affecting Extracellular DNA in Saliva. Diagnostics (Basel) 2024; 14:249. [PMID: 38337765 PMCID: PMC10855236 DOI: 10.3390/diagnostics14030249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA (ecDNA) in plasma, could be a promising biomarker for oral or systemic diseases. In contrast to genetics, the quantity of salivary ecDNA is of importance and can be affected by the pre-analytical processing of samples, but the details are not known. The aim of our study was to analyze the effects of centrifugation and freezing of saliva on the concentration of ecDNA in saliva. Fifteen healthy volunteers, free of any known systemic or oral diseases, were asked to collect unstimulated saliva samples. Aliquots were centrifuged at 1600× g and frozen or directly processed. The fresh or thawed cell-free saliva samples underwent subsequent centrifugation at 16,000× g. The supernatants were used for DNA isolation and quantification using fluorometry and real-time PCR. While freezing had minimal effects on the salivary ecDNA concentration, another centrifugation step decreased ecDNA considerably in both fresh and frozen samples (by 97.8% and 98.4%, respectively). This was mirrored in the quantitative PCR targeting a nuclear (decrease by 93.5%) and mitochondrial (decrease by 97.7%) ecDNA sequence. In conclusion, in this first study focusing on the technical aspects of salivary ecDNA quantitation, we show that, regardless of its subcellular origin, the concentration of ecDNA in saliva is mainly affected by additional centrifugation and not by the freezing of centrifuged cell-free saliva samples. This suggests that most salivary ecDNA likely is associated with cell debris and apoptotic bodies. Which fraction is affected by a particular disease should be the focus of further targeted studies.
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Affiliation(s)
- Ľubica Janovičová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Dominika Holániová
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia; (Ľ.J.); (D.H.); (B.V.)
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, 811 08 Bratislava, Slovakia
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30
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Kovalčíková AG, Novák B, Roshko O, Kovaľová E, Pastorek M, Vlková B, Celec P. Extracellular DNA and Markers of Neutrophil Extracellular Traps in Saliva from Patients with Periodontitis-A Case-Control Study. J Clin Med 2024; 13:468. [PMID: 38256602 PMCID: PMC10816443 DOI: 10.3390/jcm13020468] [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: 11/23/2023] [Revised: 12/30/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Periodontitis is a chronic inflammatory disease. We have previously shown that salivary DNA is higher in patients with periodontitis. Neutrophil extracellular traps (NETs) are involved in the pathogenesis of chronic inflammatory diseases. The objective of this case-control study was to compare patients with periodontitis and healthy controls regarding the salivary concentrations of extracellular DNA and NET components. Unstimulated saliva samples were collected from 49 patients with periodontitis and 71 controls before an oral examination. Salivary extracellular DNA was isolated and quantified fluorometrically and using PCR. NET-associated markers were assessed using ELISA. We have found significantly higher concentrations of salivary extracellular DNA in samples from periodontitis patients (five-times higher for supernatant and three times for pellet). Our results show that patients also have three-times-higher salivary nucleosomes and NET-associated enzymes-myeloperoxidase and neutrophil elastase (both two-times higher). Neutrophil elastase and salivary DNA in the pellet correlated positively with the pocket depth/clinical attachment level in periodontitis patients (r = 0.31-weak correlation; p = 0.03 and r = 0.41-moderate correlation, p = 0.004). Correlations between salivary extracellular DNA and NET enzymes were positive and significant. Based on our results, the higher salivary extracellular DNA in periodontitis seems to be related to components of NETs, albeit with weak to moderate correlations indicating that NETs are produced in periodontitis and can play a role in its pathogenesis similarly to other inflammatory diseases. Further studies should prove this assumption with potential diagnostic and therapeutic consequences.
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Affiliation(s)
- Alexandra Gaál Kovalčíková
- Department of Pediatrics, National Institute of Children’s Diseases and Faculty of Medicine, Comenius University in Bratislava, 83340 Bratislava, Slovakia;
| | - Bohuslav Novák
- Department of Stomatology and Maxillofacial Surgery, Faculty of Medicine, Comenius University, 81250 Bratislava, Slovakia;
| | - Oksana Roshko
- Department of Dental Hygiene, Faculty of Health Care, Prešov University, 08001 Prešov, Slovakia; (O.R.); (E.K.)
| | - Eva Kovaľová
- Department of Dental Hygiene, Faculty of Health Care, Prešov University, 08001 Prešov, Slovakia; (O.R.); (E.K.)
| | - Michal Pastorek
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia; (M.P.); (B.V.)
| | - Barbora Vlková
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia; (M.P.); (B.V.)
| | - Peter Celec
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia; (M.P.); (B.V.)
- Institute of Pathophysiology, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
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31
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Roch B, Pisareva E, Mirandola A, Sanchez C, Pastor B, Tanos R, Frayssinoux F, Diab-Assaf M, Anker P, Al Amir Dache Z, Thierry AR. Impact of platelet activation on the release of cell-free mitochondria and circulating mitochondrial DNA. Clin Chim Acta 2024; 553:117711. [PMID: 38101467 DOI: 10.1016/j.cca.2023.117711] [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: 05/09/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Research on circulating mitochondrial DNA (cir-mtDNA) based diagnostic is insufficient, as to its function, origin, structural features, and particularly its standardization of isolation. To date, plasma preparation performed in previous studies do not take into consideration the potential bias resulting from the release of mitochondria by activated platelets. METHODS To tackle this, we compared the mtDNA amount determined by a standard plasma preparation method or a method optimally avoiding platelet activation. MtDNA extracted from the plasma of seven healthy individuals was quantified by Q-PCR in the course of the process of both methods submitted to filtration, freezing or differential centrifugation. RESULTS 98.7 to 99.4% of plasma mtDNA corresponded to extracellular mitochondria, either free or into large extracellular vesicles. Without platelet activation, the proportion of both types of entities remained preponderant (76-80%), but the amount of detected mtDNA decreased 67-fold. CONCLUSION We show the high capacity of platelets to release free mitochondria in "in vitro" conditions. This represents a potent confounding factor when extracting mtDNA for cir-mtDNA investigation. Platelet activation during pre-analytical conditions should therefore be avoided when studying cir-mtDNA. Our findings lead to a profound revision of the assumptions previously made by most works in this field. Overall, our data suggest the need to characterize or isolate mtDNA associated various structural forms, as well as to standardize plasma preparation, to better circumscribe cir-mtDNA's diagnostic capacity.
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Affiliation(s)
- Benoit Roch
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France; Thoracic Oncology Unit, Arnaud de Villeneuve Hospital, University Hospital of Montpellier, Montpellier F-34295, France
| | - Ekaterina Pisareva
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Alexia Mirandola
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Cynthia Sanchez
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Brice Pastor
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Rita Tanos
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Florence Frayssinoux
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Mona Diab-Assaf
- Faculty of Sciences II, Lebanese University Fanar, Beirut, Lebanon
| | - Philippe Anker
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Zahra Al Amir Dache
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France
| | - Alain R Thierry
- IRCM, Montpellier Cancer Research Institute, INSERM U1194, Montpellier University, Montpellier F-34298, France; ICM, Institut Régional du Cancer de Montpellier, Montpellier F-34298, France.
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32
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Blalock ZN, Wu GWY, Lindqvist D, Trumpff C, Flory JD, Lin J, Reus VI, Rampersaud R, Hammamieh R, Gautam A, Doyle FJ, Marmar CR, Jett M, Yehuda R, Wolkowitz OM, Mellon SH. Circulating cell-free mitochondrial DNA levels and glucocorticoid sensitivity in a cohort of male veterans with and without combat-related PTSD. Transl Psychiatry 2024; 14:22. [PMID: 38200001 PMCID: PMC10781666 DOI: 10.1038/s41398-023-02721-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Circulating cell-free mitochondrial DNA (ccf-mtDNA) is a biomarker of cellular injury or cellular stress and is a potential novel biomarker of psychological stress and of various brain, somatic, and psychiatric disorders. No studies have yet analyzed ccf-mtDNA levels in post-traumatic stress disorder (PTSD), despite evidence of mitochondrial dysfunction in this condition. In the current study, we compared plasma ccf-mtDNA levels in combat trauma-exposed male veterans with PTSD (n = 111) with those who did not develop PTSD (n = 121) and also investigated the relationship between ccf mt-DNA levels and glucocorticoid sensitivity. In unadjusted analyses, ccf-mtDNA levels did not differ significantly between the PTSD and non-PTSD groups (t = 1.312, p = 0.191, Cohen's d = 0.172). In a sensitivity analysis excluding participants with diabetes and those using antidepressant medication and controlling for age, the PTSD group had lower ccf-mtDNA levels than did the non-PTSD group (F(1, 179) = 5.971, p = 0.016, partial η2 = 0.033). Across the entire sample, ccf-mtDNA levels were negatively correlated with post-dexamethasone adrenocorticotropic hormone (ACTH) decline (r = -0.171, p = 0.020) and cortisol decline (r = -0.149, p = 0.034) (viz., greater ACTH and cortisol suppression was associated with lower ccf-mtDNA levels) both with and without controlling for age, antidepressant status and diabetes status. Ccf-mtDNA levels were also significantly positively associated with IC50-DEX (the concentration of dexamethasone at which 50% of lysozyme activity is inhibited), a measure of lymphocyte glucocorticoid sensitivity, after controlling for age, antidepressant status, and diabetes status (β = 0.142, p = 0.038), suggesting that increased lymphocyte glucocorticoid sensitivity is associated with lower ccf-mtDNA levels. Although no overall group differences were found in unadjusted analyses, excluding subjects with diabetes and those taking antidepressants, which may affect ccf-mtDNA levels, as well as controlling for age, revealed decreased ccf-mtDNA levels in PTSD. In both adjusted and unadjusted analyses, low ccf-mtDNA levels were associated with relatively increased glucocorticoid sensitivity, often reported in PTSD, suggesting a link between mitochondrial and glucocorticoid-related abnormalities in PTSD.
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Affiliation(s)
- Zachary N Blalock
- Department of Psychiatry and Behavioral Sciences and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Gwyneth W Y Wu
- Department of Psychiatry and Behavioral Sciences and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA.
| | - Daniel Lindqvist
- Unit for Biological and Precision Psychiatry, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
| | - Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, USA
| | - Janine D Flory
- James J. Peters VA Medical Center, Bronx, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Victor I Reus
- Department of Psychiatry and Behavioral Sciences and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Ryan Rampersaud
- Department of Psychiatry and Behavioral Sciences and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Rasha Hammamieh
- Integrative Systems Biology, US Army Medical Research and Materiel Command, USACEHR, Fort Detrick, Frederick, MD, USA
| | - Aarti Gautam
- Integrative Systems Biology, US Army Medical Research and Materiel Command, USACEHR, Fort Detrick, Frederick, MD, USA
| | - Francis J Doyle
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Charles R Marmar
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Marti Jett
- Integrative Systems Biology, US Army Medical Research and Materiel Command, USACEHR, Fort Detrick, Frederick, MD, USA
| | - Rachel Yehuda
- James J. Peters VA Medical Center, Bronx, NY, USA
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Owen M Wolkowitz
- Department of Psychiatry and Behavioral Sciences and Weill Institute for Neurosciences, University of California, San Francisco, CA, USA
| | - Synthia H Mellon
- Department of Obstetrics, Gynecology, & Reproductive Sciences, University of California, San Francisco, CA, USA
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33
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D'Agata R, Bellassai N, Spoto G. Exploiting the design of surface plasmon resonance interfaces for better diagnostics: A perspective review. Talanta 2024; 266:125033. [PMID: 37562226 DOI: 10.1016/j.talanta.2023.125033] [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: 04/13/2023] [Revised: 08/01/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Surface Plasmon Resonance based-sensors are promising tools for precision diagnostics as they can provide tests useful for early and, whenever possible, non-invasive disease detection and monitoring. The design of novel, robust and effective interfaces enabling the sensing of a variety of molecular interactions in a highly selective and sensitive manner is a necessary step to obtain both accurate and reliable detection by SPR. This review covers the recent research efforts in this area, specifically emphasizing well-designed interfaces and applications in real-life samples. In particular, after a short introduction which identifies some of the critical challenges, the emerging strategies for the integration of the linker, the metal substrate and the recognition element on the sensing interface will be explored and discussed in three sections, as well as the opportunities for building SPR biosensors, easy to use, and with excellent sensitivities. Finally, a summary of some of the more promising and latest diagnostic applications will be provided, presenting a new window into the near-future perspectives.
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Affiliation(s)
- Roberta D'Agata
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy; INBB, Istituto Nazionale di Biostrutture e Biosistemi, Viale Delle Medaglie D'Oro, 305, 00136, Roma, Italy.
| | - Noemi Bellassai
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy; INBB, Istituto Nazionale di Biostrutture e Biosistemi, Viale Delle Medaglie D'Oro, 305, 00136, Roma, Italy
| | - Giuseppe Spoto
- Department of Chemical Sciences, University of Catania, Viale Andrea Doria, 6, 95125, Catania, Italy; INBB, Istituto Nazionale di Biostrutture e Biosistemi, Viale Delle Medaglie D'Oro, 305, 00136, Roma, Italy
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Aalami AH, Aalami F, Aliabadi EK, Amirabadi A, Sahebkar A. Detection of Circulating Cell-free DNA to Diagnose Hepatocellular Carcinoma in Chinese Population: A Systematic Review and Meta-analysis. Curr Med Chem 2024; 31:3345-3359. [PMID: 37349993 DOI: 10.2174/0929867330666230622114235] [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: 04/12/2023] [Accepted: 05/12/2023] [Indexed: 06/24/2023]
Abstract
BACKGROUND Cell-free circulating DNA has been known for many years, but this knowledge has not been beneficial for diagnosis. In this meta-analysis, we examine the diagnostic role of circulating cell-free DNA in HCC patients to find a reliable biomarker for the early detection of HCC. MATERIALS AND METHODS We performed a systematic literature search using Science Direct, Web of Science, PubMed/Medline, Scopus, Google Scholar, and Embase, up to April 1st, 2022. Meta-Disc V.1.4 and Comprehensive Meta-Analysis V.3.3 software calculated the pooled specificity, sensitivity, area under the curve (AUC), diagnostic odds ratio (DOR), positive likelihood ratio (PLR), negative likelihood ratio (NLR) Q*index, and summary receiver-- operating characteristic (SROC) for the role of cfDNA as a biomarker for HCC patients. Moreover, the subgroup analyses have been performed based on sample types (serum/plasma) and detection methods (MS-PCR/methylation). RESULTS A total of 7 articles (9 studies) included 697 participants (485 cases and 212 controls). The overall pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), and area under the curve (AUC) were 0.706 (95% CI: 0.671 - 0.739), 0.905 (95% CI: 0.865 - 0.937), 6.66 (95% CI: 4.36 - 10.18), 0.287 (95% CI: 0.185 - 0.445), 28.40 (95% CI: 13.01 - 62.0), and 0.93, respectively. We conducted a subgroup analysis of diagnostic value, which showed that the plasma sample had a better diagnostic value compared to the serum. CONCLUSION This meta-analysis showed that cfDNA could be a fair biomarker for diagnosing HCC patients.
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Affiliation(s)
- Amir Hossein Aalami
- Department of Nutrition and Integrative Physiology, College of Health, University of Utah, Salt Lake City, UT, USA
- Division of Nephrology and Hypertension, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Farnoosh Aalami
- Student Research Committee, Faculty of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Ehsan Kargar Aliabadi
- Department of Chemistry, Faculty of Science, Biochemical Research Center, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Amir Amirabadi
- Department of Internal Medicine, Faculty of Medicine, Mashhad Medical Sciences, Islamic Azad University, Mashhad, Iran
| | - Amirhossein Sahebkar
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
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Pradère P, Zajacova A, Bos S, Le Pavec J, Fisher A. Molecular monitoring of lung allograft health: is it ready for routine clinical use? Eur Respir Rev 2023; 32:230125. [PMID: 37993125 PMCID: PMC10663940 DOI: 10.1183/16000617.0125-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/16/2023] [Indexed: 11/24/2023] Open
Abstract
Maintenance of long-term lung allograft health in lung transplant recipients (LTRs) requires a fine balancing act between providing sufficient immunosuppression to reduce the risk of rejection whilst at the same time not over-immunosuppressing individuals and exposing them to the myriad of immunosuppressant drug side-effects that can cause morbidity and mortality. At present, lung transplant physicians only have limited and rather blunt tools available to assist them with this task. Although therapeutic drug monitoring provides clinically useful information about single time point and longitudinal exposure of LTRs to immunosuppressants, it lacks precision in determining the functional level of immunosuppression that an individual is experiencing. There is a significant gap in our ability to monitor lung allograft health and therefore tailor optimal personalised immunosuppression regimens. Molecular diagnostics performed on blood, bronchoalveolar lavage or lung tissue that can detect early signs of subclinical allograft injury, differentiate rejection from infection or distinguish cellular from humoral rejection could offer clinicians powerful tools in protecting lung allograft health. In this review, we look at the current evidence behind molecular monitoring in lung transplantation and ask if it is ready for routine clinical use. Although donor-derived cell-free DNA and tissue transcriptomics appear to be the techniques with the most immediate clinical potential, more robust data are required on their performance and additional clinical value beyond standard of care.
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Affiliation(s)
- Pauline Pradère
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Department of Respiratory Diseases, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph and Paris Saclay University, Paris, France
| | - Andrea Zajacova
- Prague Lung Transplant Program, Department of Pneumology, Motol University Hospital and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Saskia Bos
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Institute of Transplantation, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
| | - Jérôme Le Pavec
- Department of Respiratory Diseases, Hôpital Marie Lannelongue, Groupe Hospitalier Paris Saint Joseph and Paris Saclay University, Paris, France
| | - Andrew Fisher
- Newcastle University Translational and Clinical Research Institute, Newcastle upon Tyne, UK
- Institute of Transplantation, Newcastle Upon Tyne Hospitals NHS Trust, Newcastle Upon Tyne, UK
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Poulet G, Hulot JS, Blanchard A, Bergerot D, Xiao W, Ginot F, Boutonnet-Rodat A, Justine A, Beinse G, Geromel V, Pellegrina L, Azizi M, Laurent-Puig P, Benhaim L, Taly V. Circadian rhythm and circulating cell-free DNA release on healthy subjects. Sci Rep 2023; 13:21675. [PMID: 38065990 PMCID: PMC10709451 DOI: 10.1038/s41598-023-47851-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
In the last decade, clinical studies have investigated the clinical relevance of circulating cell-free-DNA (ccfDNA) as a diagnostic and prognosis tool in various diseases including cancers. However, limited knowledge on ccfDNA biology restrains its full development in the clinical practice. To improve our understanding, we evaluated the impact of the circadian rhythm on ccfDNA release in healthy subjects over a 24-h period. 10 healthy female subjects underwent blood sampling at 8am and 20 healthy male subjects underwent serial blood sampling (8:00 AM, 9:00 AM, 12:00 PM, 4:00 PM, 8:00 PM, 12:00 AM, 4 AM (+ 1 Day) and 8 AM (+ 1 Day)). We performed digital droplet-based PCR (ddPCR) assays to target 2 DNA fragments (69 & 243 bp) located in the KRAS gene to determine the ccfDNA concentration and fragmentation profile. As control, half of the samples were re-analyzed by capillary miniaturized electrophoresis (BIAbooster system). Overall, we did not detect any influence of the circadian rhythm on ccfDNA release. Instead, we observed a decrease in the ccfDNA concentration after meal ingestion, suggesting either a post-prandial effect or a technical detection bias due to a higher plasma load in lipids and triglycerides. We also noticed a potential effect of gender, weight and creatinine levels on ccfDNA concentration.
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Affiliation(s)
- Geoffroy Poulet
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Eurofins-Biomnis, Gerland, Lyon, France
| | - Jean-Sébastien Hulot
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Anne Blanchard
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Damien Bergerot
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Wenjin Xiao
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | | | | | - Abdelli Justine
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | - Guillaume Beinse
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
| | | | | | - Michel Azizi
- CIC1418 and DMU CARTE, AP-HP, Hôpital Européen Georges-Pompidou, 75015, Paris, France
| | - Pierre Laurent-Puig
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France
- Biochemistry Department - Unit of Pharmacogenetic and Molecular Oncology, Hôpital Européen Georges Pompidou (HEGP), Assistance Publique Hôpitaux de Paris (AP-HP), Paris, France
| | - Leonor Benhaim
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.
- Department of Visceral and Surgical Oncology, Gustave Roussy, Villejuif, France.
| | - Valerie Taly
- Université de Paris, UMR-S1138, CNRS SNC5096, Équipe Labélisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France.
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Leotta C, Hernandez L, Tothova L, Arefin S, Ciceri P, Cozzolino MG, Barany P, Chromek M, Stenvinkel P, Kublickiene K. Levels of Cell-Free DNA in Kidney Failure Patients before and after Renal Transplantation. Cells 2023; 12:2774. [PMID: 38132094 PMCID: PMC10741614 DOI: 10.3390/cells12242774] [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: 10/30/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has diverse applications in oncological, prenatal, toxicological, cardiovascular, and autoimmune diseases, diagnostics, and organ transplantation. In particular, mitochondrial cfDNA (mt-cfDNA) is associated with inflammation and linked to early vascular ageing (EVA) in end-stage kidney failure (ESKF), which could be a noninvasive marker for graft rejection and organ damage. Plasma samples from 44 ESKF patients, of whom half (n = 22) underwent either conservative therapy (non-HD) or hemodialysis (HD) before kidney transplantation (KT). These samples were analyzed at baseline and two years after KT. cfDNA was extracted from plasma and quantified using the fluorometric method. qPCR was used to quantify and differentiate the fractions of mt-cfDNA and nuclear cfDNA (nc-cfDNA). mt-cfDNA levels in KT patients decreased significantly from baseline to two years post-KT (p < 0.0268), while levels of total cfDNA and nc-cfDNA did not differ. Depending on therapy modality (HD vs. non-HD) before KT, total cfDNA levels were higher in HD patients at both baseline (p = 0.0133) and two years post-KT (p = 0.0421), while nc-cfDNA levels were higher in HD only at baseline (p = 0.0079). Males showed a nonsignificant trend of higher cfDNA levels. Patients with assessed vascular fibrosis (p = 0.0068), either alone or in combination with calcification plus fibrosis, showed reduced mt-cfDNA post-KT (p = 0.0195). Changes in mt-cfDNA levels suggests the impact of KT on the inflammatory state of ESKF, as evidenced via its correlation with high sensitivity C-reactive protein after KT. Further studies are warranted to assess if cfDNA could serve as a noninvasive method for monitoring the response to organ transplantation and even for amelioration of EVA status per se.
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Affiliation(s)
- Chiara Leotta
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
- Renal Division, Department of Health Sciences, ASST Santi Paolo e Carlo Hospital Milan, University of Milan, 20142 Milan, Italy (M.G.C.)
| | - Leah Hernandez
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Lubomira Tothova
- Institute of Molecular Biomedicine, Faculty of Medicine, Comenius University, 81108 Bratislava, Slovakia
| | - Samsul Arefin
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Paola Ciceri
- Renal Division, Department of Health Sciences, ASST Santi Paolo e Carlo Hospital Milan, University of Milan, 20142 Milan, Italy (M.G.C.)
| | - Mario Gennaro Cozzolino
- Renal Division, Department of Health Sciences, ASST Santi Paolo e Carlo Hospital Milan, University of Milan, 20142 Milan, Italy (M.G.C.)
| | - Peter Barany
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Milan Chromek
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
- Division of Pediatrics, Clinical Science, Intervention and Technology (CLINTEC), Karolinska University Hospital, 17177 Stockholm, Sweden
| | - Peter Stenvinkel
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
| | - Karolina Kublickiene
- Division of Renal Medicine, Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, 17177 Stockholm, Sweden; (C.L.); (L.H.); (P.B.); (M.C.)
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Singh K, Kumari S, Ali M, Das MK, Mishra A, Singh AK. Association of transient mitochondrial functional impairment with acute heat exposure in children from Muzaffarpur region of Bihar, India. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023; 67:1975-1989. [PMID: 37796289 DOI: 10.1007/s00484-023-02555-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/05/2023] [Accepted: 09/14/2023] [Indexed: 10/06/2023]
Abstract
Over the past several years, the Muzaffarpur district of Bihar (India) has witnessed recurrent outbreaks of acute encephalitis illness of unknown etiology, called acute encephalitis syndrome (AES) among young children, especially during the peak-summer season. Pesticide exposure, viral encephalitis, and litchi toxin intake have all been postulated as potential sources of the ailment. However, no conclusive etiology for AES has been identified in the affected children. During recent rounds of the outbreak, metabolic abnormalities have been documented in these children, and a direct correlation was observed between higher environmental temperature during the peak-summer month and AES caseload. The clinical and metabolic profiles of these children suggested the possible involvement of mitochondrial dysfunction during heat stress as one of the several contributory factors leading to multisystem metabolic derangement. The present study observed that mitochondrial function parameters such as cell death, mitochondrial membrane potential, oxidative stress, and mitochondrial pathway-related gene expression in peripheral blood mononuclear cells (PBMCs) isolated from children were affected in peak-summer when compared to post-summer months. Similar observations of mitochondrial function parameters along with impaired bioenergetic parameters were demonstrated in the heat-exposed model of PBMCs isolated from healthy adult individuals. In conclusion, the results suggested that there is an association of transient mitochondrial dysfunction when exposed to sustained heat during the summer months. One may consider mitochondrial dysfunction as one of the important factors leading to an outbreak of AES among the children from affected regions though this needs to be substantiated with further studies.
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Affiliation(s)
- Kanika Singh
- Cardiorespiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India
| | - Swati Kumari
- Cardiorespiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manzoor Ali
- Cardiorespiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manoja K Das
- Public Health, The INCLEN Trust International, New Delhi, 110020, India
| | - Aastha Mishra
- Cardiorespiratory Disease Unit, CSIR-Institute of Genomics and Integrative Biology, Delhi, 110007, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Arun K Singh
- Department of Neonatology, All India Institute of Medical Sciences, Jodhpur, 342001, India.
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Tessier NP, Hardy LM, Deleuze JF, How-Kit A. Circulating cell-free nucleic acids of plasma in human aging, healthy aging and longevity: current state of knowledge. Front Genet 2023; 14:1321280. [PMID: 38090154 PMCID: PMC10715054 DOI: 10.3389/fgene.2023.1321280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/20/2023] [Indexed: 01/16/2024] Open
Abstract
Circulating cell-free nucleic acids (ccfNAs) of plasma are a remarkable source of genetic, epigenetic and transcriptomic materials originating from different cells, tissues and organs of an individual. They have been increasingly studied over the past decade as they can carry several important pieces of information about the health status of an individual, which makes them biomarkers of choice for non-invasive diagnosis of numerous diseases and health conditions. However, few studies have investigated variations of plasma ccfNAs in healthy subjects, particularly in relation to aging, healthy aging and longevity, despite the great variability of these biological processes among individuals. Here, we reviewed several studies that focused on the analysis of circulating cell-free DNA (ccfDNA) and microRNAs (ccfmiRNAs) during aging and in the elderly, including some on exceptionally long-lived individuals, i.e., centenarians. After a brief overview of the types, origins and functions of plasma ccfNAs, we described the variations of both ccfDNA and ccfmiRNAs during aging as well as the identification of several potential ccfDNA-based and ccfmiRNA-based biomarkers of aging, healthy aging and/or longevity. We finally highlighted some prospects offered by ccfNAs for the understanding and improvement of healthy aging and longevity.
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Affiliation(s)
| | - Lise M. Hardy
- Laboratory for Genomics, Foundation Jean Dausset—CEPH, Paris, France
| | - Jean-François Deleuze
- Laboratory for Genomics, Foundation Jean Dausset—CEPH, Paris, France
- Centre National de Recherche en Génomique Humaine, CEA, Institut François Jacob, Evry, France
| | - Alexandre How-Kit
- Laboratory for Genomics, Foundation Jean Dausset—CEPH, Paris, France
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Evrard C, Ingrand P, Rochelle T, Martel M, Tachon G, Flores N, Randrian V, Ferru A, Haineaux PA, Goujon JM, Karayan-Tapon L, Tougeron D. Circulating tumor DNA in unresectable pancreatic cancer is a strong predictor of first-line treatment efficacy: The KRASCIPANC prospective study. Dig Liver Dis 2023; 55:1562-1572. [PMID: 37308396 DOI: 10.1016/j.dld.2023.03.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/08/2023] [Accepted: 03/27/2023] [Indexed: 06/14/2023]
Abstract
BACKGROUND There is no robust predictor of response to chemotherapy (CT) in unresectable pancreatic adenocarcinomas (UPA). The objective of the KRASCIPANC study was to analyze the kinetics of cell-free DNA (cfDNA)/circulating tumor DNA (ctDNA) as a predictor of response to CT in UPA. METHODS Blood samples were collected just before first CT and at day 28. The primary endpoint was the kinetics of KRAS-mutated ctDNA by digital droplet PCR between D0 and D28 as a predictor of progression-free survival (PFS). RESULTS We analyzed 65 patients with a KRAS-mutated tumor. A high level of cfDNA and KRAS-mutated ctDNA at D0, as well as the presence of KRAS-mutated ctDNA at D28, were strongly associated with lower centralized disease control rate (cDCR), shorter cPFS and OS in multivariate analysis. A score combining cfDNA level at diagnosis ≥ or <30 ng/mL and presence or not of KRAS-mutated ctDNA at D28 was an optimal predictor of cDCR (OR=30.7, IC95% 4.31-218 P=.001), PFS (HR=6.79, IC95% 2.76-16.7, P<.001) and OS (HR=9.98, IC95% 4.14-24.1, P<.001). CONCLUSION A combined score using cfDNA level at diagnosis and KRAS-mutated ctDNA at D28 is strongly associated with patient survival/response to chemotherapy in UPA. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT04560270.
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Affiliation(s)
- Camille Evrard
- Medical Oncology Department, Poitiers University Hospital, Poitiers 86000, France; ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France.
| | - Pierre Ingrand
- Department of Statistics, Faculty of Medicine, University of Poitiers, Poitiers 86000, France
| | - Tristan Rochelle
- Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France
| | - Marine Martel
- Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France
| | - Gaëlle Tachon
- Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France; Cancer Biology Department, Centre Léon Bérard, Lyon 69000, France
| | - Nicolas Flores
- Department of Imaging, University Hospital of Poitiers, Poitiers 86000, France
| | - Violaine Randrian
- ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France; Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers, France
| | - Aurélie Ferru
- Medical Oncology Department, Poitiers University Hospital, Poitiers 86000, France
| | - Paul-Arthur Haineaux
- Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers, France; Hepato-Gastroenterology Department, Poitiers University Hospital, Châtellerault Hospital, Poitiers 86106, France
| | - Jean-Michel Goujon
- Department of Pathology, Poitiers University Hospital, Poitiers 86000, France
| | - Lucie Karayan-Tapon
- ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France; Cancer Biology Department, Poitiers University Hospital, Poitiers 86000, France
| | - David Tougeron
- ProDicET, UR 24144, University of Poitiers, Poitiers 86000, France; Hepato-Gastroenterology Department, Poitiers University Hospital, Poitiers, France.
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Mattox AK, Douville C, Wang Y, Popoli M, Ptak J, Silliman N, Dobbyn L, Schaefer J, Lu S, Pearlman AH, Cohen JD, Tie J, Gibbs P, Lahouel K, Bettegowda C, Hruban RH, Tomasetti C, Jiang P, Chan KA, Lo YMD, Papadopoulos N, Kinzler KW, Vogelstein B. The Origin of Highly Elevated Cell-Free DNA in Healthy Individuals and Patients with Pancreatic, Colorectal, Lung, or Ovarian Cancer. Cancer Discov 2023; 13:2166-2179. [PMID: 37565753 PMCID: PMC10592331 DOI: 10.1158/2159-8290.cd-21-1252] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 12/16/2022] [Accepted: 08/09/2023] [Indexed: 08/12/2023]
Abstract
Cell-free DNA (cfDNA) concentrations from patients with cancer are often elevated compared with those of healthy controls, but the sources of this extra cfDNA have never been determined. To address this issue, we assessed cfDNA methylation patterns in 178 patients with cancers of the colon, pancreas, lung, or ovary and 64 patients without cancer. Eighty-three of these individuals had cfDNA concentrations much greater than those generally observed in healthy subjects. The major contributor of cfDNA in all samples was leukocytes, accounting for ∼76% of cfDNA, with neutrophils predominating. This was true regardless of whether the samples were derived from patients with cancer or the total plasma cfDNA concentration. High levels of cfDNA observed in patients with cancer did not come from either neoplastic cells or surrounding normal epithelial cells from the tumor's tissue of origin. These data suggest that cancers may have a systemic effect on cell turnover or DNA clearance. SIGNIFICANCE The origin of excess cfDNA in patients with cancer is unknown. Using cfDNA methylation patterns, we determined that neither the tumor nor the surrounding normal tissue contributes this excess cfDNA-rather it comes from leukocytes. This finding suggests that cancers have a systemic impact on cell turnover or DNA clearance. See related commentary by Thierry and Pisareva, p. 2122. This article is featured in Selected Articles from This Issue, p. 2109.
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Affiliation(s)
- Austin K. Mattox
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Christopher Douville
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Yuxuan Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Maria Popoli
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Janine Ptak
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Natalie Silliman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Lisa Dobbyn
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joy Schaefer
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Steve Lu
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Alexander H. Pearlman
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Joshua D. Cohen
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Jeanne Tie
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Peter Gibbs
- Division of Systems Biology and Personalized Medicine, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Oncology, Western Health, St Albans, Victoria 3021, Australia
- Department of Medical Oncology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kamel Lahouel
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Chetan Bettegowda
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, 21287
| | - Ralph H. Hruban
- Department of Pathology, Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins Medical Institutions, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Cristian Tomasetti
- Division of Mathematics for Cancer Evolution and Early Detection, Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA 91010
| | - Peiyong Jiang
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - K.C. Allen Chan
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Yuk Ming Dennis Lo
- State Key Laboratory of Translational Oncology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- Centre for Novostics, Hong Kong Science Park, Pak Shek Kok, New Territories, Hong Kong SAR, China
| | - Nickolas Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Sol Goldman Pancreatic Cancer Research Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287
- Howard Hughes Medical Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287
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Kao SH, Shofer FS, Greenwood JC, Alomaja O, Ranganathan A, Piel S, Mesaros C, Shin SS, Ehinger JK, Kilbaugh TJ, Jang DH. Cell-Free DNA as a Biomarker in a Rodent Model of Chlorpyrifos Poisoning Causing Mitochondrial Dysfunction. J Med Toxicol 2023; 19:352-361. [PMID: 37523031 PMCID: PMC10522542 DOI: 10.1007/s13181-023-00956-0] [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: 04/15/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 08/01/2023] Open
Abstract
INTRODUCTION Organophosphates (OPs) are a major public health problem worldwide due to ease of access and high toxicity lacking effective biomarkers and treatment. Cholinergic agents such as OPs and carbamates are responsible for many pesticide-related deaths. While the inhibition of AChE is thought to be the main mechanism of injury, there are other important pathways that contribute to the overall toxicity of OPs such as mitochondrial dysfunction. An existing gap in OP poisoning are biomarkers to gauge severity and prognosis. Cell-free DNA (cfDNA) are novel biomarkers that have gained increased attention as a sensitive biomarker of disease with novel use in acute poisoning. This study investigates alterations in cerebral mitochondrial function in a rodent model of chlorpyrifos poisoning with the use of cfDNA as a potential biomarker. METHODS Twenty rodents were divided into two groups: Control (n = 10) and Chlorpyrifos (n = 10). Chlorpyrifos was administered through the venous femoral line with a Harvard Apparatus 11 Elite Syringe pump (Holliston, MA, USA) at 2 mg/kg. Animals were randomized to receive chlorpyrifos versus the vehicle (10% DMSO) for 60 min which would realistically present an acute exposure with continued absorption. At the end of the exposure (60 min), isolated mitochondria were measured for mitochondrial respiration along with measures of acetylcholinesterase activity, cfDNA, cytokines and western blot. RESULTS The Chlorpyrifos group showed a significant decrease in heart rate but no change in the blood pressure. There was a significant increase in bulk cfDNA concentrations and overall decrease in mitochondrial respiration from brain tissue obtained from animals in the Chlorpyrifos group when compared to the Control group with no difference in acetylcholinesterase activity. In addition, there was a significant increase in both IL-2 and IL-12 in the Chlorpyrifos group. CONCLUSIONS In our study, we found that the total cfDNA concentration may serve as a more accurate biomarker of OP exposure compared to acetylcholinesterase activity. In addition, there was an overall decrease in cerebral mitochondrial function in the Chlorpyrifos group when compared to the Control group.
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Affiliation(s)
- Shih-Han Kao
- The Children's Hospital of Philadelphia, The Resuscitation Science Center, Philadelphia, PA, 19104, USA
| | - Frances S Shofer
- Department of Emergency Medicine, Perelman School of Medicine, The Resuscitation Science Center (RSC), Lab 814F, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - John C Greenwood
- Department of Emergency Medicine, Perelman School of Medicine, The Resuscitation Science Center (RSC), Lab 814F, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Oladunni Alomaja
- Department of Emergency Medicine, Perelman School of Medicine, The Resuscitation Science Center (RSC), Lab 814F, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Abhay Ranganathan
- The Children's Hospital of Philadelphia, The Resuscitation Science Center, Philadelphia, PA, 19104, USA
| | - Sarah Piel
- The Children's Hospital of Philadelphia, The Resuscitation Science Center, Philadelphia, PA, 19104, USA
| | - Clementina Mesaros
- Department of Pharmacology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel S Shin
- Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Johannes K Ehinger
- Mitochondrial Medicine, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Otorhinolaryngology, Head and Neck Surgery, Department of Clinical Sciences Lund, Lund University, Lund, Sweden
- Otorhinolaryngology, Head and Neck Surgery, Skåne University Hospital, Lund, Sweden
| | - Todd J Kilbaugh
- The Children's Hospital of Philadelphia, The Resuscitation Science Center, Philadelphia, PA, 19104, USA
| | - David H Jang
- Department of Emergency Medicine, Perelman School of Medicine, The Resuscitation Science Center (RSC), Lab 814F, University of Pennsylvania, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA.
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Berezina TA, Berezin AE. Cell-free DNA as a plausible biomarker of chronic kidney disease. Epigenomics 2023; 15:879-890. [PMID: 37791402 DOI: 10.2217/epi-2023-0255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023] Open
Abstract
Circulating cell-free DNA (cf-DNA) is released from dead and/or apoptotic leukocytes and due to neutrophil extracellular traps contributing to an inflammatory response. Previous clinical studies have reported that the peak concentrations and dynamic changes of cf-DNA may be used as a noninvasive biomarker of worsening kidney function as well as a guide to the management of kidney allograft rejection. We hypothesized that the pattern and dynamic changes of cf-DNA might be a plausible predictive biomarker for patients at risk of chronic kidney disease (CKD), including individuals with type 2 diabetes mellitus, heart failure, cardiovascular disease and established CKD. Along with it, pre- and posthemodialysis levels of serum cf-DNA appear to be a independent predictor for all-cause mortality in patients with end-stage kidney disease.
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Affiliation(s)
- Tetiana A Berezina
- VitaCenter, Department of Internal Medicine and Nephrology, Zaporozhye, 69000, Ukraine
| | - Alexander E Berezin
- Paracelsus Medical University, Department of Internal Medicine II, Division of Cardiology, Salzburg, 5020, Austria
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Graver AS, Lee D, Power DA, Whitlam JB. Understanding Donor-derived Cell-free DNA in Kidney Transplantation: An Overview and Case-based Guide for Clinicians. Transplantation 2023; 107:1675-1686. [PMID: 36579675 DOI: 10.1097/tp.0000000000004482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Kidney transplant recipients undergo lifelong monitoring of allograft function and evaluation for transplant complications. The current monitoring paradigm utilizes blood, urine, and tissue markers that are insensitive, nonspecific, or invasive to obtain. As a result, problems are detected late, after significant damage has accrued, and often beyond the time at which complete resolution is possible. Indeed, most kidney transplants eventually fail, usually because of chronic rejection and other undetected injury. There is a clear need for a transplant-specific biomarker that enables a proactive approach to monitoring via early detection of reversible pathology. A biomarker that supports timely and personalized treatment would assist in achieving the ultimate goal of improving allograft survival and limiting therapeutic toxicity to the recipient. Donor-derived cell-free DNA (ddcfDNA) has been proposed as one such transplant biomarker. Although the test is presently utilized most in the United States, it is conceivable that its use will become more widespread. This review covers aspects of ddcfDNA that support informed use of the test by general nephrologists, including the basic biology of ddcfDNA, methodological nuances of testing, and general recommendations for use in the kidney transplant population. Clinical contexts are used to illustrate evidence-supported interpretation of ddcfDNA results and subsequent management. Finally, knowledge gaps and areas for further study are discussed.
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Affiliation(s)
- Alison S Graver
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Darren Lee
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Department of Renal Medicine, Eastern Health Clinical School, Monash University, Box Hill, VIC, Australia
| | - David A Power
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - John B Whitlam
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
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Tsirka G, Zikopoulos A, Papageorgiou K, Kostoulas C, Tsigkas I, Moustakli E, Kaltsas A, Sarafi E, Michaelidis TM, Georgiou I. The Ratio of cf-mtDNA vs. cf-nDNA in the Follicular Fluid of Women Undergoing IVF Is Positively Correlated with Age. Genes (Basel) 2023; 14:1504. [PMID: 37510407 PMCID: PMC10379089 DOI: 10.3390/genes14071504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Age-related mitochondrial markers may facilitate the prognosis of artificial reproductive technology outcomes. In this report, we present our study concerning the ratio of cf-mtDNA/cf-nDNA, namely the amount of cell-free mitochondrial DNA relative to cell-free nuclear DNA, in the follicular fluid (FF) of women undergoing IVF, aiming to generate a molecular fingerprint of oocyte quality. The values of this ratio were measured and compared among three groups of women (101 in total): (A) 31 women with polycystic ovary syndrome (PCOS), (B) 34 women younger than 36 years, and (C) 36 women older than 35 years of age. Real-time quantitative PCR (qPCR) was performed to quantify the ratio by using nuclear- and mitochondrial-specific primers and analyzed for potential correlation with age and pregnancy rate. Our analysis showed that the level of FF-cf-mtDNA was lower in the group of advanced-age women than in the groups of PCOS and non-PCOS women. Moreover, a significant positive correlation between FF-cf-mtDNA and the number of mature (MII) oocytes was observed. Collectively, the data show that the relative ratio of cf- mtDNA to cf-nDNA content in human FF can be an effective predictor for assessing the corresponding oocyte's age-related performance in IVF.
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Affiliation(s)
- Georgia Tsirka
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | | | - Kyriaki Papageorgiou
- Department of Biological Applications & Technology, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45115 Ioannina, Greece
| | - Charilaos Kostoulas
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Ioannis Tsigkas
- Department of Biological Applications & Technology, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45115 Ioannina, Greece
| | - Efthalia Moustakli
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Aris Kaltsas
- Laboratory of Spermatology, Department of Urology, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
| | - Eleftheria Sarafi
- Department of Biological Applications & Technology, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45115 Ioannina, Greece
| | - Theologos M Michaelidis
- Department of Biological Applications & Technology, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
- Biomedical Research Institute, Foundation for Research and Technology-Hellas, 45115 Ioannina, Greece
| | - Ioannis Georgiou
- Laboratory of Medical Genetics in Clinical Practice, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
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Michelson J, Rausser S, Peng A, Yu T, Sturm G, Trumpff C, Kaufman BA, Rai AJ, Picard M. MitoQuicLy: A high-throughput method for quantifying cell-free DNA from human plasma, serum, and saliva. Mitochondrion 2023; 71:26-39. [PMID: 37172669 PMCID: PMC10524316 DOI: 10.1016/j.mito.2023.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/12/2023] [Accepted: 05/07/2023] [Indexed: 05/15/2023]
Abstract
Circulating cell-free mitochondrial DNA (cf-mtDNA) is an emerging biomarker of psychobiological stress and disease which predicts mortality and is associated with various disease states. To evaluate the contribution of cf-mtDNA to health and disease states, standardized high-throughput procedures are needed to quantify cf-mtDNA in relevant biofluids. Here, we describe MitoQuicLy: Mitochondrial DNA Quantification in cell-free samples by Lysis. We demonstrate high agreement between MitoQuicLy and the commonly used column-based method, although MitoQuicLy is faster, cheaper, and requires a smaller input sample volume. Using 10 µL of input volume with MitoQuicLy, we quantify cf-mtDNA levels from three commonly used plasma tube types, two serum tube types, and saliva. We detect, as expected, significant inter-individual differences in cf-mtDNA across different biofluids. However, cf-mtDNA levels between concurrently collected plasma, serum, and saliva from the same individual differ on average by up to two orders of magnitude and are poorly correlated with one another, pointing to different cf-mtDNA biology or regulation between commonly used biofluids in clinical and research settings. Moreover, in a small sample of healthy women and men (n = 34), we show that blood and saliva cf-mtDNAs correlate with clinical biomarkers differently depending on the sample used. The biological divergences revealed between biofluids, together with the lysis-based, cost-effective, and scalable MitoQuicLy protocol for biofluid cf-mtDNA quantification, provide a foundation to examine the biological origin and significance of cf-mtDNA to human health.
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Affiliation(s)
- Jeremy Michelson
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Shannon Rausser
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Amanda Peng
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Temmie Yu
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Gabriel Sturm
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, USA
| | - Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA
| | - Brett A Kaufman
- Center for Metabolism and Mitochondrial Medicine and the Vascular Medicine Institute, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, USA
| | - Alex J Rai
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA; New York State Psychiatric Institute, New York, NY, USA.
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Linke C, Hunger R, Reinwald M, Deckert M, Mantke R. Quantification of mitochondrial cfDNA reveals new perspectives for early diagnosis of colorectal cancer. BMC Cancer 2023; 23:291. [PMID: 36997875 PMCID: PMC10064655 DOI: 10.1186/s12885-023-10748-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 03/16/2023] [Indexed: 04/01/2023] Open
Abstract
BACKGROUND To unravel how the integrity of nuclear and mitochondrial circulating cell-free DNA (cfDNA) contributes to its plasma quantity in colorectal cancer (CRC) patients. METHODS CfDNA from plasma samples of 80 CRC patients stratified by tumour stage and 50 healthy individuals were extracted. Total cfDNA concentration was determined and equal template concentrations (ETC) were analyzed by quantitative real-time PCR (qPCR) resulting in small and long fragments of KRAS, Alu and MTCO3. The obtained data was also examined relative to the total cfDNA concentration (NTC) and diagnostic accuracy was estimated using receiver operating characteristics. RESULTS Total cfDNA levels were significantly higher in CRC group compared to healthy control and increased with tumour stage. Long nuclear fragment levels were significantly lower in CRC patients in ETC but not NTC condition. The integrity indices of nuclear cfDNA decreased from controls to patients with highly malignant tumor. Mitochondrial cfDNA fragment quantities were strongly reduced in early and late stages of tumor patients and prognostic value was higher in ETC. Predictive models based on either ETC or NTC predictor set showed comparable classification performance. CONCLUSION Increased blood cfDNA concentration in late UICC stages inversely correlate with nuclear cfDNA integrity index and suggest that necrotic degradation is not a major cause for higher total cfDNA quantity. The diagnostic and prognostic value of MTCO3 is highly significant in early stages of CRC and can be evaluated more comprehensively, using ETC for qPCR analysis. TRIAL REGISTRATION The study was registered retrospectively on DRKS, the german register for clinical trials (DRKS00030257, 29/09/2022).
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Affiliation(s)
- Christian Linke
- Department of General and Gastrointestinal Surgery, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany.
- Department of Hematology, Oncology and Palliative Medicine, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany.
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany.
| | - Richard Hunger
- Department of General and Gastrointestinal Surgery, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
| | - Mark Reinwald
- Department of Hematology, Oncology and Palliative Medicine, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - Markus Deckert
- Department of Hematology, Oncology and Palliative Medicine, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
| | - René Mantke
- Department of General and Gastrointestinal Surgery, University Hospital Brandenburg, Brandenburg Medical School Theodor Fontane, Brandenburg, Germany
- Faculty of Health Sciences, Joint Faculty of the Brandenburg University of Technology Cottbus - Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Potsdam, Germany
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Tichà V, Patelli G, Basso G, Prino A, Repetti E, Grugni M, Damascelli B. Case Report: Potential role of selective venous sampling for liquid biopsy in complex clinical settings: Three case presentations. Front Genet 2023; 14:1065537. [PMID: 37056288 PMCID: PMC10086121 DOI: 10.3389/fgene.2023.1065537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 03/06/2023] [Indexed: 03/30/2023] Open
Abstract
Tumor mutation profiling from a blood sample, known as liquid biopsy, is a reality that has already been approved for some cancers. This molecular diagnostic method complements tissue biopsy but is less invasive and therefore more easily applied, especially during tumor evolution. Its use should allow detection of residual disease, evaluation of treatment response or resistance, and selection of targeted treatments. However, implementation of liquid biopsy in routine clinical practice is hindered by unsolved issues, one of which is the scarcity of circulating tumor DNA in blood samples drawn from peripheral veins. To address this problem, we propose minimally invasive selective venous sampling from the region of interest, as used for some hormonal studies and for mapping of endocrine tumors. Intuitively, selective sampling should improve the sensitivity of liquid biopsy by avoiding the dilution of tumor biomarkers that occurs in the peripheral circulation. We report three cases that illustrate the potential utility of selective liquid biopsy in complex clinical settings, providing implications for diagnosis and treatment as well as for monitoring over time, disease localization, identification of drug resistance, and differential diagnosis.
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Affiliation(s)
- Vladimira Tichà
- Department of Interventional Oncology, EMO GVM Centrocuore Columbus, Milan, Italy
| | - Gianluigi Patelli
- Department of Radiology, ASST Bergamo Est-Bolognini Hospital, Seriate, Italy
| | - Gianpaolo Basso
- School of Medicine and Surgery, San Gerardo Hospital, University of Milano-Bicocca, Monza, Italy
| | - Aurelio Prino
- Palliative Care Department and Hospice, University Hospital Maggiore Della Carità, Novara, Italy
| | - Elena Repetti
- TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Varese, Italy
| | - Maria Grugni
- TOMA Advanced Biomedical Assays S.p.A, Busto Arsizio, Varese, Italy
| | - Bruno Damascelli
- Department of Interventional Oncology, EMO GVM Centrocuore Columbus, Milan, Italy
- *Correspondence: Bruno Damascelli,
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49
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Shin J, Jung C. Improving the Accuracy of Single-Nucleotide Variant Diagnosis Using On-Off Discriminating Primers. BIOSENSORS 2023; 13:380. [PMID: 36979592 PMCID: PMC10046569 DOI: 10.3390/bios13030380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/05/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Early detection of rare mutations through liquid biopsy can provide real-time information related to cancer diagnosis, prognosis, and treatment outcomes. Cell-free DNA samples used in liquid biopsies contain single-nucleotide variants (SNVs) with a variant allele frequency (VAF) of approximately ≤1%. Droplet digital polymerase chain reaction (ddPCR) is considered the gold standard of sequencing using liquid samples, generating amplicons from samples containing mutations with 0.001-0.005% VAF; however, it requires expensive equipment and time-consuming protocols. Therefore, various PCR methods for discriminating SNVs have been developed; nonetheless, non-specific amplification cannot be avoided even in the absence of mutations, which hampers the accurate diagnosis of SNVs. In this study, we introduce single-nucleotide variant on-off discrimination-PCR (Soo-PCR), a highly accurate and practical method that uses a 3'-end tailing primer for the on-off discrimination of low-abundance mutant-type targets, including SNVs. Soo-PCR minimizes the chance of incorrect judgments owing to its high discriminating power. Cancer markers, such as KRAS G12D, EGFR L858R, and EGFR T790M mutations, containing 0.1% VAF, were clearly detected in under 2 h with a high reliability comparable with that of ddPCR. This new method serves as a practical approach to accurately detect and evaluate low-abundance mutations in a user-friendly manner.
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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: 13.5] [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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