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Tímermans A, Otero F, Garrido M, Gosálvez J, Johnston S, Fernández JL. The relationship between sperm nuclear DNA fragmentation, mitochondrial DNA fragmentation, and copy number in normal and abnormal human ejaculates. Andrology 2024; 12:870-880. [PMID: 37786274 DOI: 10.1111/andr.13539] [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: 07/17/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/04/2023]
Abstract
BACKGROUND While it is common to clinically evaluate sperm nuclear DNA fragmentation, less attention has been given to sperm mitochondrial DNA. Recently, a digital PCR assay has allowed accurate estimation of the proportion of fragmented mtDNA molecules and relative copy number. OBJECTIVES To determine the correlation of classical sperm parameters, average mtDNA copies per spermatozoon and the level of mtDNA fragmentation (SDF-mtDNA) to that of nuclear DNA fragmentation (SDF-nDNA), measured as the proportion of global, single-strand DNA (SDF-SSBs) and double-strand DNA breaks (SDF-DSBs). To determine whether the level of nuclear and mitochondrial DNA fragmentation and/or copy number can differentiate normozoospermic from non-normozoospermic samples. MATERIALS AND METHODS Ejaculates from 29 normozoospermic and 43 non-normozoospermic were evaluated. SDF was determined using the sperm chromatin dispersion assay. mtDNA copy number and SDF-mtDNA were analyzed using digital PCR assays. RESULTS Relative mtDNA copy increased as sperm concentration or motility decreased, or abnormal morphology increased. Unlike SDF-mtDNA, mtDNA copy number was not correlated with SDF-nDNA. SDF-mtDNA increased as the concentration or proportion of non-vital sperm increased; the higher the mtDNA copy number, the lower the level of fragmentation. Non-normozoospermic samples showed double the level of SDF-nDNA compared to normozoospermic (median 25.00 vs. 13.67). mtDNA copy number per spermatozoon was 3× higher in non-normozoospermic ejaculates (median 16.06 vs. 4.99). Although logistic regression revealed SDF-Global and mtDNA copy number as independent risk factors for non-normozoospermia, when SDF-Global and mtDNA copy number were combined, ROC curve analysis resulted in an even stronger discriminatory ability for predicting the probability of non-normozoospermia (AUC = 0.85, 95% CI 0.76-0.94, p < 0.001). CONCLUSION High-quality ejaculates show lower nuclear SDF and retain less mtDNA copies, with approximately half of them fragmented, so that the absolute number of non-fragmented mtDNA molecules per spermatozoon is extremely low.
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Affiliation(s)
- Ana Tímermans
- INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), Spain
- Laboratory of Molecular Genetics and Radiobiology, Centro Oncológico de Galicia, Doctor Camilo Veiras, Spain
| | - Fátima Otero
- INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), Spain
- Laboratory of Molecular Genetics and Radiobiology, Centro Oncológico de Galicia, Doctor Camilo Veiras, Spain
| | - Manuel Garrido
- Complexo Hospitalario Universitario A Coruña (CHUAC), Clinical Analysis Service, Spain
| | - Jaime Gosálvez
- Genetics Unit, Facultad de Biología, Universidad Autónoma de Madrid, Spain
| | - Stephen Johnston
- School of Environment, The University of Queensland, Gatton, Australia
- School of Veterinary Science, The University of Queensland, Gatton, Gatton, Australia
| | - José Luis Fernández
- INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), Spain
- Laboratory of Molecular Genetics and Radiobiology, Centro Oncológico de Galicia, Doctor Camilo Veiras, Spain
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2
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Omidsalar AA, McCullough CG, Xu L, Boedijono S, Gerke D, Webb MG, Manojlovic Z, Sequeira A, Lew MF, Santorelli M, Serrano GE, Beach TG, Limon A, Vawter MP, Hjelm BE. Common mitochondrial deletions in RNA-Seq: evaluation of bulk, single-cell, and spatial transcriptomic datasets. Commun Biol 2024; 7:200. [PMID: 38368460 PMCID: PMC10874445 DOI: 10.1038/s42003-024-05877-4] [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: 03/15/2023] [Accepted: 01/31/2024] [Indexed: 02/19/2024] Open
Abstract
Common mitochondrial DNA (mtDNA) deletions are large structural variants in the mitochondrial genome that accumulate in metabolically active tissues with age and have been investigated in various diseases. We applied the Splice-Break2 pipeline (designed for high-throughput quantification of mtDNA deletions) to human RNA-Seq datasets and describe the methodological considerations for evaluating common deletions in bulk, single-cell, and spatial transcriptomics datasets. A robust evaluation of 1570 samples from 14 RNA-Seq studies showed: (i) the abundance of some common deletions detected in PCR-amplified mtDNA correlates with levels observed in RNA-Seq data; (ii) RNA-Seq library preparation method has a strong effect on deletion detection; (iii) deletions had a significant, positive correlation with age in brain and muscle; (iv) deletions were enriched in cortical grey matter, specifically in layers 3 and 5; and (v) brain regions with dopaminergic neurons (i.e., substantia nigra, ventral tegmental area, and caudate nucleus) had remarkable enrichment of common mtDNA deletions.
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Affiliation(s)
- Audrey A Omidsalar
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Carmel G McCullough
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Lili Xu
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Stanley Boedijono
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Daniel Gerke
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Zarko Manojlovic
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Mark F Lew
- Department of Neurology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Marco Santorelli
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Geidy E Serrano
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Thomas G Beach
- Banner Sun Health Research Institute (BSHRI), Sun City, AZ, USA
| | - Agenor Limon
- Mitchell Center for Neurodegenerative Diseases, Department of Neurology, School of Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California - Irvine (UCI) School of Medicine, Irvine, CA, USA
| | - Brooke E Hjelm
- Department of Translational Genomics, Keck School of Medicine of USC, Los Angeles, CA, USA.
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3
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Ware SA, Kliment CR, Giordano L, Redding KM, Rumsey WL, Bates S, Zhang Y, Sciurba FC, Nouraie SM, Kaufman BA. Cell-free DNA levels associate with COPD exacerbations and mortality. Respir Res 2024; 25:42. [PMID: 38238743 PMCID: PMC10797855 DOI: 10.1186/s12931-023-02658-1] [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: 11/13/2023] [Accepted: 12/26/2023] [Indexed: 01/22/2024] Open
Abstract
THE QUESTION ADDRESSED BY THE STUDY Good biological indicators capable of predicting chronic obstructive pulmonary disease (COPD) phenotypes and clinical trajectories are lacking. Because nuclear and mitochondrial genomes are damaged and released by cigarette smoke exposure, plasma cell-free mitochondrial and nuclear DNA (cf-mtDNA and cf-nDNA) levels could potentially integrate disease physiology and clinical phenotypes in COPD. This study aimed to determine whether plasma cf-mtDNA and cf-nDNA levels are associated with COPD disease severity, exacerbations, and mortality risk. MATERIALS AND METHODS We quantified mtDNA and nDNA copy numbers in plasma from participants enrolled in the Evaluation of COPD Longitudinally to Identify Predictive Surrogate Endpoints (ECLIPSE, n = 2,702) study and determined associations with relevant clinical parameters. RESULTS Of the 2,128 participants with COPD, 65% were male and the median age was 64 (interquartile range, 59-69) years. During the baseline visit, cf-mtDNA levels positively correlated with future exacerbation rates in subjects with mild/moderate and severe disease (Global Initiative for Obstructive Lung Disease [GOLD] I/II and III, respectively) or with high eosinophil count (≥ 300). cf-nDNA positively associated with an increased mortality risk (hazard ratio, 1.33 [95% confidence interval, 1.01-1.74] per each natural log of cf-nDNA copy number). Additional analysis revealed that individuals with low cf-mtDNA and high cf-nDNA abundance further increased the mortality risk (hazard ratio, 1.62 [95% confidence interval, 1.16-2.25] per each natural log of cf-nDNA copy number). ANSWER TO THE QUESTION Plasma cf-mtDNA and cf-nDNA, when integrated into quantitative clinical measurements, may aid in improving COPD severity and progression assessment.
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Affiliation(s)
- Sarah A Ware
- Department of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh School of Medicine, 200 Lothrop Street BST W1044, Pittsburgh, PA, 15261, USA
| | - Corrine R Kliment
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Luca Giordano
- Department of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh School of Medicine, 200 Lothrop Street BST W1044, Pittsburgh, PA, 15261, USA
| | - Kevin M Redding
- Department of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh School of Medicine, 200 Lothrop Street BST W1044, Pittsburgh, PA, 15261, USA
| | - William L Rumsey
- GlaxoSmithKline Respiratory Therapeutic Area Unit, Collegeville, PA, USA
| | - Stewart Bates
- GlaxoSmithKline Respiratory Therapeutic Area Unit, Stevenage, UK
| | - Yingze Zhang
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Frank C Sciurba
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - S Mehdi Nouraie
- Department of Medicine, Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- UPMC Montefiore Hospital, NW628 3459 Fifth Avenue, Pittsburgh, PA, 15213, USA.
| | - Brett A Kaufman
- Department of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh School of Medicine, 200 Lothrop Street BST W1044, Pittsburgh, PA, 15261, USA.
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Feng J, Cui X, Du B, Zhao H, Feng Y, Cui J, Yan C, Gan L, Fan Z, Fu T, Xu Z, Yu Z, Zhang R, Du S, Tian Z, Zhang Q, Xue G, Yuan J. Detection and Quantification of Klebsiella pneumoniae in Fecal Samples Using Digital Droplet PCR in Comparison with Real-Time PCR. Microbiol Spectr 2023; 11:e0424922. [PMID: 37306605 PMCID: PMC10433836 DOI: 10.1128/spectrum.04249-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/18/2023] [Indexed: 06/13/2023] Open
Abstract
This study aimed to develop a rapid and sensitive droplet digital PCR (ddPCR) assay for the specific detection of Klebsiella pneumoniae in fecal samples, and to evaluate its application in the clinic by comparison with real-time PCR assay and conventional microbial culture. Specific primers and a probe targeting the K. pneumoniae hemolysin (khe) gene were designed. Thirteen other pathogens were used to evaluate the specificity of the primers and probe. A recombinant plasmid containing the khe gene was constructed and used to assess the sensitivity, repeatability, and reproducibility of the ddPCR. Clinical fecal samples (n = 103) were collected and tested by the ddPCR, real-time PCR, and conventional microbial culture methods. The detection limit of ddPCR for K. pneumoniae was 1.1 copies/μL, about a 10-fold increase in sensitivity compared with real-time PCR. The ddPCR was negative for the 13 pathogens other than K. pneumoniae, confirming its high specificity. Clinical fecal samples gave a higher rate of positivity in the K. pneumoniae ddPCR assay than in analysis by real-time PCR or conventional culture. ddPCR also showed less inhibition by the inhibitor in fecal sample than real-time PCR. Thus, we established a sensitive and effective ddPCR-based assay method for K. pneumoniae. It could be a useful tool for K. pneumoniae detection in feces and may serve as a reliable method to identify causal pathogens and help guide treatment decisions. IMPORTANCE Klebsiella pneumoniae can cause a range of illnesses and has a high colonization rate in the human gut, making it crucial to develop an efficient method for detecting K. pneumoniae in fecal samples.
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Affiliation(s)
- Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Bing Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Shuheng Du
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Qun Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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5
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Tomita K, Indo HP, Sato T, Tangpong J, Majima HJ. Development of a sensitive double TaqMan Probe-based qPCR Angle-Degree method to detect mutation frequencies. Mitochondrion 2023; 70:1-7. [PMID: 36841519 DOI: 10.1016/j.mito.2023.02.010] [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: 07/28/2022] [Revised: 02/10/2023] [Accepted: 02/18/2023] [Indexed: 02/26/2023]
Abstract
We designed a method to examine the mutation frequencies of the A3243G mutation of mitochondrial DNA (mtDNA) in patients with mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome. We performed a qPCR assay using the FAM and VIC TaqMan probes, which detect the 3243G (mutated) and 3243A (wild-type) sequences of mtDNA, respectively. The results obtained by "degree" in a series of differential mutation frequencies were used to plot a standard curve of the mutation frequency. The standard curve was then applied for qPCR assays of the desired samples. The standard deviation (%) of the samples calculated using the standard curve for the TaqMan probe was 2.4 ± 1.5%. This method could be used to examine mutation frequencies in the context of diabetes, aging, cancer, and neurodegenerative diseases.
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Affiliation(s)
- Kazuo Tomita
- Department of Maxillofacial Radiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Department of Applied Pharmacology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Hiroko P Indo
- Department of Maxillofacial Radiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Amanogawa Galactic Astronomy Research Center (AGARC), Kagoshima University Graduate School of Sciences and Engineering, 1-21-35 Korimoto, Kagoshima 890-0065, Japan.
| | - Tomoaki Sato
- Department of Applied Pharmacology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan
| | - Jitbanjong Tangpong
- School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand
| | - Hideyuki J Majima
- Department of Maxillofacial Radiology, Kagoshima University Graduate School of Medical and Dental Sciences, 8-35-1 Sakuragaoka, Kagoshima 890-8544, Japan; Amanogawa Galactic Astronomy Research Center (AGARC), Kagoshima University Graduate School of Sciences and Engineering, 1-21-35 Korimoto, Kagoshima 890-0065, Japan; School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat 80160, Thailand; Center of Excellence Research for Melioidosis and Microorganisms, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand.
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6
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Sturm G, Karan KR, Monzel AS, Santhanam B, Taivassalo T, Bris C, Ware SA, Cross M, Towheed A, Higgins-Chen A, McManus MJ, Cardenas A, Lin J, Epel ES, Rahman S, Vissing J, Grassi B, Levine M, Horvath S, Haller RG, Lenaers G, Wallace DC, St-Onge MP, Tavazoie S, Procaccio V, Kaufman BA, Seifert EL, Hirano M, Picard M. OxPhos defects cause hypermetabolism and reduce lifespan in cells and in patients with mitochondrial diseases. Commun Biol 2023; 6:22. [PMID: 36635485 PMCID: PMC9837150 DOI: 10.1038/s42003-022-04303-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/26/2022] [Indexed: 01/13/2023] Open
Abstract
Patients with primary mitochondrial oxidative phosphorylation (OxPhos) defects present with fatigue and multi-system disorders, are often lean, and die prematurely, but the mechanistic basis for this clinical picture remains unclear. By integrating data from 17 cohorts of patients with mitochondrial diseases (n = 690) we find evidence that these disorders increase resting energy expenditure, a state termed hypermetabolism. We examine this phenomenon longitudinally in patient-derived fibroblasts from multiple donors. Genetically or pharmacologically disrupting OxPhos approximately doubles cellular energy expenditure. This cell-autonomous state of hypermetabolism occurs despite near-normal OxPhos coupling efficiency, excluding uncoupling as a general mechanism. Instead, hypermetabolism is associated with mitochondrial DNA instability, activation of the integrated stress response (ISR), and increased extracellular secretion of age-related cytokines and metabokines including GDF15. In parallel, OxPhos defects accelerate telomere erosion and epigenetic aging per cell division, consistent with evidence that excess energy expenditure accelerates biological aging. To explore potential mechanisms for these effects, we generate a longitudinal RNASeq and DNA methylation resource dataset, which reveals conserved, energetically demanding, genome-wide recalibrations. Taken together, these findings highlight the need to understand how OxPhos defects influence the energetic cost of living, and the link between hypermetabolism and aging in cells and patients with mitochondrial diseases.
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Affiliation(s)
- Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Kalpita R Karan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Anna S Monzel
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Balaji Santhanam
- Departments of Biological Sciences, Systems Biology, and Biochemistry and Molecular Biophysics, Institute for Cancer Dynamics, Columbia University, New York, NY, USA
| | - Tanja Taivassalo
- Department of Physiology and Functional Genomics, Clinical and Translational Research Building, University of Florida, Gainesville, FL, USA
| | - Céline Bris
- Department of Genetics and Neurology, Angers Hospital, Angers, France
- UMR CNRS 6015, INSERM U1083, MITOVASC, SFR ICAT, Université d'Angers, Angers, France
| | - Sarah A Ware
- Department of Medicine, Vascular Medicine Institute and Center for Metabolic and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Marissa Cross
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Atif Towheed
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, USA
- Internal Medicine-Pediatrics Residency Program, University of Pittsburgh Medical Centre, Pittsburgh, PA, USA
| | - Albert Higgins-Chen
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Meagan J McManus
- Department of Anesthesiology and Critical Care Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Jue Lin
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
| | - Elissa S Epel
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Shamima Rahman
- Mitochondrial Research Group, UCL Great Ormond Street Institute of Child Health, and Metabolic Unit, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - John Vissing
- Copenhagen Neuromuscular Center, Department of Neurology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bruno Grassi
- Department of Medicine, University of Udine, Udine, Italy
| | | | | | - Ronald G Haller
- Neuromuscular Center, Institute for Exercise and Environmental Medicine of Texas Health Resources and Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guy Lenaers
- Department of Genetics and Neurology, Angers Hospital, Angers, France
- UMR CNRS 6015, INSERM U1083, MITOVASC, SFR ICAT, Université d'Angers, Angers, France
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie-Pierre St-Onge
- Center of Excellence for Sleep & Circadian Research and Division of General Medicine, Department of Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Saeed Tavazoie
- Departments of Biological Sciences, Systems Biology, and Biochemistry and Molecular Biophysics, Institute for Cancer Dynamics, Columbia University, New York, NY, USA
| | - Vincent Procaccio
- Department of Genetics and Neurology, Angers Hospital, Angers, France
- UMR CNRS 6015, INSERM U1083, MITOVASC, SFR ICAT, Université d'Angers, Angers, France
| | - Brett A Kaufman
- Department of Medicine, Vascular Medicine Institute and Center for Metabolic and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Erin L Seifert
- Department of Pathology and Genomic Medicine, and MitoCare Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Michio Hirano
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, 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, NY, 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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7
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Takousis P, Devonshire AS, Redshaw N, von Baumgarten L, Whale AS, Jones GM, Fernandez-Gonzalez A, Martin J, Foy CA, Alexopoulos P, Huggett JF, Perneczky R. A standardised methodology for the extraction and quantification of cell-free DNA in cerebrospinal fluid and application to evaluation of Alzheimer's disease and brain cancers. N Biotechnol 2022; 72:97-106. [PMID: 36202346 DOI: 10.1016/j.nbt.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 09/23/2022] [Accepted: 10/01/2022] [Indexed: 11/27/2022]
Abstract
Cerebrospinal fluid (CSF) is a source of diagnostic biomarkers for a range of neurological conditions. Cell-free DNA (cfDNA) is detected in CSF and differences in the concentration of cell-free mitochondrial DNA have been reported in studies of neurodegenerative disorders including Alzheimer's disease (AD). However, the influence of pre-analytical steps has not been investigated for cfDNA in CSF and there is no standardised approach for quantification of total cfDNA (copies of nuclear genome or mitochondria-derived gene targets). In this study, the suitability of four extraction methods was evaluated: QIAamp Circulating Nucleic Acid (Qiagen), Quick-cfDNA Serum & Plasma (Zymo), NucleoSnap® DNA Plasma (Macherey-Nagel) and Plasma/Serum Circulating DNA Purification Mini (Norgen) kits, for cfDNA extraction from CSF of controls and AD dementia patients, utilising a spike-in control for extraction efficiency and fragment size. One of the optimal extraction methods was applied to a comparison of cfDNA concentrations in CSF from control subjects, AD dementia and primary and secondary brain tumour patients. Extraction efficiency based on spike-in recovery was similar in all three groups whilst both endogenous mitochondrial and nucleus-derived cfDNA was significantly higher in CSF from cancer patients compared to control and AD groups, which typically contained < 100 genome copies/mL. This study shows that it is feasible to measure low concentration nuclear and mitochondrial gene targets in CSF and that normalisation of extraction yield can help control pre-analytical variability influencing biomarker measurements.
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Affiliation(s)
- Petros Takousis
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK
| | - Alison S Devonshire
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK.
| | - Nicholas Redshaw
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Louisa von Baumgarten
- Department of Neurology, University Hospital, LMU Munich, Munich, Germany; Department of Neurosurgery, University Hospital, LMU Munich, Munich, Germany
| | - Alexandra S Whale
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Gerwyn M Jones
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Ana Fernandez-Gonzalez
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Jan Martin
- Department of Anaesthesiology and Intensive Care Medicine, Technical University Munich, Munich, Germany
| | - Carole A Foy
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK
| | - Panagiotis Alexopoulos
- Department of Psychiatry, University of Patras, Rion Patras, Greece; Department of Psychiatry and Psychotherapy, Technical University Munich, Munich, Germany
| | - Jim F Huggett
- Molecular and Cell Biology Team, National Measurement Laboratory, LGC, Teddington, Middlesex, UK; School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Robert Perneczky
- Ageing Epidemiology (AGE) Research Unit, School of Public Health, Imperial College London, London, UK; Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE) Munich, Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany; Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
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8
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A multi-omics longitudinal aging dataset in primary human fibroblasts with mitochondrial perturbations. Sci Data 2022; 9:751. [PMID: 36463290 PMCID: PMC9719499 DOI: 10.1038/s41597-022-01852-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/17/2022] [Indexed: 12/05/2022] Open
Abstract
Aging is a process of progressive change. To develop biological models of aging, longitudinal datasets with high temporal resolution are needed. Here we report a multi-omics longitudinal dataset for cultured primary human fibroblasts measured across their replicative lifespans. Fibroblasts were sourced from both healthy donors (n = 6) and individuals with lifespan-shortening mitochondrial disease (n = 3). The dataset includes cytological, bioenergetic, DNA methylation, gene expression, secreted proteins, mitochondrial DNA copy number and mutations, cell-free DNA, telomere length, and whole-genome sequencing data. This dataset enables the bridging of mechanistic processes of aging as outlined by the "hallmarks of aging", with the descriptive characterization of aging such as epigenetic age clocks. Here we focus on bridging the gap for the hallmark mitochondrial metabolism. Our dataset includes measurement of healthy cells, and cells subjected to over a dozen experimental manipulations targeting oxidative phosphorylation (OxPhos), glycolysis, and glucocorticoid signaling, among others. These experiments provide opportunities to test how cellular energetics affect the biology of cellular aging. All data are publicly available at our webtool: https://columbia-picard.shinyapps.io/shinyapp-Lifespan_Study/.
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9
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Puigròs M, Calderon A, Pérez-Soriano A, de Dios C, Fernández M, Colell A, Martí MJ, Tolosa E, Trullas R. Cell-free mitochondrial DNA deletions in idiopathic, but not LRRK2, Parkinson's disease. Neurobiol Dis 2022; 174:105885. [DOI: 10.1016/j.nbd.2022.105885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/21/2022] [Accepted: 10/03/2022] [Indexed: 11/29/2022] Open
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10
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Smetanina MA, Oscorbin IP, Shadrina AS, Sevost'ianova KS, Korolenya VA, Gavrilov KA, Shevela AI, Shirshova AN, Oskina NA, Zolotukhin IA, Filipenko ML. Quantitative and structural characteristics of mitochondrial DNA in varicose veins. Vascul Pharmacol 2022; 145:107021. [PMID: 35690235 DOI: 10.1016/j.vph.2022.107021] [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: 01/12/2022] [Revised: 05/09/2022] [Accepted: 06/04/2022] [Indexed: 12/13/2022]
Abstract
OBJECTIVE We examined quantitative (in terms of mtDNA/nuclear DNA) and structural (in terms of common deletions in the MT-ND4 gene region) characteristics of mitochondrial DNA (mtDNA) in varicose veins (VVs) and venous wall layers by comparing mitochondrial genome parameters, as well as mitochondrial function (in terms of mitochondrial membrane potential (MtMP)), in varicose vein (VV) vs. non-varicose vein (NV) tissue samples. METHODS We analyzed paired great saphenous vein samples (VV vs. NV segments from each patient left after venous surgery) harvested from patients with VVs. Relative mtDNA level and the proportion of no-deletion mtDNA were determined by a multiplex quantitative PCR (qPCR), confirming the latter with a more sensitive method - droplet digital PCR (ddPCR). Mitochondria's functional state in VVs was assessed using fluorescent (dependent on MtMP) live-staining of mitochondria in venous tissues. RESULTS Total mtDNA level was lower in VV than in NV samples (predominantly in the t. media layer). ddPCR analysis showed lower proportion of no-deletion mtDNA in VVs. Because of the decrease in relative MtMP in VVs, our results suggest a possible reduction of mitochondrial function in VVs. CONCLUSION Quantitative and structural changes (copy number and integrity) of mtDNA are plausibly involved in VV pathogenesis. Future clinical studies implementing the mitochondrial targeting may be eventually fostered after auxiliary mechanistic studies.
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Affiliation(s)
- Mariya A Smetanina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Department of Fundamental Medicine of V. Zelman Institute for the Medicine and Psychology, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Igor P Oscorbin
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexandra S Shadrina
- Laboratory of Glycogenomics, Institute of Cytology and Genetics, Novosibirsk 630090, Russia
| | - Kseniya S Sevost'ianova
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Department of Surgical Diseases of V. Zelman Institute for the Medicine and Psychology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Valeria A Korolenya
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Konstantin A Gavrilov
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Department of Surgical Diseases of V. Zelman Institute for the Medicine and Psychology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Andrey I Shevela
- Center of New Medical Technologies, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Department of Surgical Diseases of V. Zelman Institute for the Medicine and Psychology, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Arina N Shirshova
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Natalya A Oskina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Igor A Zolotukhin
- Department of Faculty Surgery, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Maxim L Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia; Laboratory of Molecular Diagnostics Development, Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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11
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Roy M, Sarkar D, Chatterjee M. Quantitative monitoring of experimental and human leishmaniasis employing amastigote-specific genes. Parasitology 2022; 149:1085-1093. [PMID: 35535469 PMCID: PMC11016204 DOI: 10.1017/s0031182022000610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022]
Abstract
The gold standard for diagnosis of leishmaniasis is the microscopic detection of amastigotes/Leishman Donovan (LD) bodies, but its moderate sensitivity necessitates the development of molecular approaches. This study aimed to quantify in experimental animal models and human leishmaniasis the expression of amastigote-specific virulence genes, A2 and amastin by droplet digital polymerase chain reaction (ddPCR). Total RNA was isolated from L. donovani-infected hamsters or murine peritoneal macrophages and lesional biopsies from patients with post kala-azar dermal leishmaniasis (PKDL). Following cDNA conversion, EvaGreen-based ddPCR was performed using specific primers for A2 or amastin and parasite load expressed in copies per μL. Assay was optimized and the specificity of amastigote-specific A2 and amastin was confirmed. In hepatic and splenic tissues of L. donovani-infected hamsters and peritoneal macrophages, ddPCR demonstrated a greater abundance of A2 than amastin. Treatment of L. donovani-infected peritoneal macrophages with conventional anti-leishmanials, miltefosine and amphotericin B translated into a dose-dependent reduction in copies per μL of A2 and amastin, and the extrapolated IC50 was comparable with results obtained by counting LD bodies in Giemsa-stained macrophages. Similarly, in dermal biopsies of patients with PKDL, A2 and amastin were detected. Overall, monitoring of A2 by ddPCR can be an objective measure of parasite burden and potentially adaptable into a high throughput approach necessary for drug development and monitoring disease progression when the causative species is L. donovani.
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Affiliation(s)
- Madhurima Roy
- Department of Pharmacology, Institute of Postgraduate Medical Education and Research (IPGME&R), 244B, Acharya JC Bose Road, Kolkata 700020, India
| | - Deblina Sarkar
- Department of Pharmacology, Institute of Postgraduate Medical Education and Research (IPGME&R), 244B, Acharya JC Bose Road, Kolkata 700020, India
| | - Mitali Chatterjee
- Department of Pharmacology, Institute of Postgraduate Medical Education and Research (IPGME&R), 244B, Acharya JC Bose Road, Kolkata 700020, India
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12
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Rahman MM, Young CKJ, Goffart S, Pohjoismäki JLO, Young MJ. Heterozygous p.Y955C mutation in DNA polymerase γ leads to alterations in bioenergetics, complex I subunit expression, and mtDNA replication. J Biol Chem 2022; 298:102196. [PMID: 35760101 PMCID: PMC9307957 DOI: 10.1016/j.jbc.2022.102196] [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: 01/23/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 12/03/2022] Open
Abstract
In human cells, ATP is generated using oxidative phosphorylation machinery, which is inoperable without proteins encoded by mitochondrial DNA (mtDNA). The DNA polymerase gamma (Polγ) repairs and replicates the multicopy mtDNA genome in concert with additional factors. The Polγ catalytic subunit is encoded by the POLG gene, and mutations in this gene cause mtDNA genome instability and disease. Barriers to studying the molecular effects of disease mutations include scarcity of patient samples and a lack of available mutant models; therefore, we developed a human SJCRH30 myoblast cell line model with the most common autosomal dominant POLG mutation, c.2864A>G/p.Y955C, as individuals with this mutation can present with progressive skeletal muscle weakness. Using on-target sequencing, we detected a 50% conversion frequency of the mutation, confirming heterozygous Y955C substitution. We found mutated cells grew slowly in a glucose-containing medium and had reduced mitochondrial bioenergetics compared with the parental cell line. Furthermore, growing Y955C cells in a galactose-containing medium to obligate mitochondrial function enhanced these bioenergetic deficits. Also, we show complex I NDUFB8 and ND3 protein levels were decreased in the mutant cell line, and the maintenance of mtDNA was severely impaired (i.e., lower copy number, fewer nucleoids, and an accumulation of Y955C-specific replication intermediates). Finally, we show the mutant cells have increased sensitivity to the mitochondrial toxicant 2′-3′-dideoxycytidine. We expect this POLG Y955C cell line to be a robust system to identify new mitochondrial toxicants and therapeutics to treat mitochondrial dysfunction.
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Affiliation(s)
- Md Mostafijur Rahman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Carolyn K J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, 80101 Joensuu, Finland
| | - Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901.
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13
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Sato T, Goto-Inoue N, Kimishima M, Toyoharu J, Minei R, Ogura A, Nagoya H, Mori T. A novel ND1 mitochondrial DNA mutation is maternally inherited in growth hormone transgenesis in amago salmon (Oncorhynchus masou ishikawae). Sci Rep 2022; 12:6720. [PMID: 35469048 PMCID: PMC9038734 DOI: 10.1038/s41598-022-10521-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 03/22/2022] [Indexed: 11/12/2022] Open
Abstract
Growth hormone (GH) transgenesis can be used to manipulate the growth performance of fish and mammals. In this study, homozygous and hemizygous GH-transgenic amago salmon (Oncorhynchus masou ishikawae) derived from a single female exhibited hypoglycemia. Proteomic and signal network analyses using iTRAQ indicated a decreased NAD+/NADH ratio in transgenic fish, indicative of reduced mitochondrial ND1 function and ROS levels. Mitochondrial DNA sequencing revealed that approximately 28% of the deletion mutations in the GH homozygous- and hemizygous-female-derived mitochondrial DNA occurred in ND1. These fish also displayed decreased ROS levels. Our results indicate that GH transgenesis in amago salmon may induce specific deletion mutations that are maternally inherited over generations and alter energy production.
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Affiliation(s)
- Tomohiko Sato
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan
| | - Naoko Goto-Inoue
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan
| | - Masaya Kimishima
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan
| | - Jike Toyoharu
- Research Institute of Medical Research Support Center Electron Microscope Laboratory, School of Medicine, Nihon University, Tokyo, 173-8610, Japan
| | - Ryuhei Minei
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, 526-0829, Japan
| | - Atsushi Ogura
- Department of Computer Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, 526-0829, Japan
| | - Hiroyuki Nagoya
- National Research Institute of Aquaculture, Fisheries Research and Education Agency, Minamiise, 516-0193, Japan
| | - Tsukasa Mori
- Department of Marine Science and Resources, Nihon University College of Bioresource Sciences, Kameino 1866, Fujisawa, 252-0880, Japan.
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14
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Durand M, Nagot N, Michel L, Le SM, Duong HT, Vallo R, Vizeneux A, Rapoud D, Giang HT, Quillet C, Thanh NTT, Hai Oanh KT, Vinh VH, Feelemyer J, Vande Perre P, Minh KP, Laureillard D, Des Jarlais D, Molès JP. Mental Disorders Are Associated With Leukocytes Telomere Shortening Among People Who Inject Drugs. Front Psychiatry 2022; 13:846844. [PMID: 35782414 PMCID: PMC9247253 DOI: 10.3389/fpsyt.2022.846844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Premature biological aging, assessed by shorter telomere length (TL) and mitochondrial DNA (mtDNA) alterations, has been reported among people with major depressive disorders or psychotic disorders. However, these markers have never been assessed together among people who inject drugs (PWIDs), although mental disorders are highly prevalent in this population, which, in addition, is subject to other aggravating exposures. Diagnosis of mental disorders was performed by a psychiatrist using the Mini International Neuropsychiatric Interview test among active PWIDs in Haiphong, Vietnam. mtDNA copy number (MCN), mtDNA deletion, and TL were assessed by quantitative PCR and compared to those without any mental disorder. We next performed a multivariate analysis to identify risk factors associated with being diagnosed with a major depressive episode (MDE) or a psychotic syndrome (PS). In total, 130 and 136 PWIDs with and without psychiatric conditions were analyzed. Among PWIDs with mental disorders, 110 and 74 were diagnosed with MDE and PS, respectively. TL attrition was significantly associated with hepatitis C virus-infected PWIDs with MDE or PS (adjusted odds ratio [OR]: 0.53 [0.36; 0.80] and 0.59 [0.39; 0.88], respectively). TL attrition was even stronger when PWIDs cumulated at least two episodes of major depressive disorders. On the other hand, no difference was observed in mtDNA alterations between groups. The telomeric age difference with drug users without a diagnosis of psychiatric condition was estimated during 4.2-12.8 years according to the number of MDEs, making this group more prone to age-related diseases.
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Affiliation(s)
- Mélusine Durand
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
| | - Nicolas Nagot
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
| | - Laurent Michel
- Pierre Nicole Center, CESP UMR 1018, Paris-Saclay University, Paris, France
| | - Sao Mai Le
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Huong Thi Duong
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Roselyne Vallo
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
| | - Amélie Vizeneux
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
| | - Delphine Rapoud
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
| | - Hoang Thi Giang
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Catherine Quillet
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
| | | | | | - Vu Hai Vinh
- Infectious and Tropical Diseases Department, Viet Tiep Hospital, Hai Phong, Vietnam
| | - Jonathan Feelemyer
- School of Global Public Health, New York University, New York, NY, United States
| | - Philippe Vande Perre
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
| | - Khue Pham Minh
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Hai Phong, Vietnam
| | - Didier Laureillard
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France.,Infectious and Tropical Diseases Department, Caremeau University Hospital, Nîmes, France
| | - Don Des Jarlais
- School of Global Public Health, New York University, New York, NY, United States
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, Montpellier, France
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15
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Ciesielska EJ, Kim S, Bisimwa HGM, Grier C, Rahman MM, Young CKJ, Young MJ, Oliveira MT, Ciesielski GL. Remdesivir triphosphate blocks DNA synthesis and increases exonucleolysis by the replicative mitochondrial DNA polymerase, Pol γ. Mitochondrion 2021; 61:147-158. [PMID: 34619353 PMCID: PMC8595818 DOI: 10.1016/j.mito.2021.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic prompted the FDA to authorize a new nucleoside analogue, remdesivir, for emergency use in affected individuals. We examined the effects of its active metabolite, remdesivir triphosphate (RTP), on the activity of the replicative mitochondrial DNA polymerase, Pol γ. We found that while RTP is not incorporated by Pol γ into a nascent DNA strand, it remains associated with the enzyme impeding its synthetic activity and stimulating exonucleolysis. In spite of that, we found no evidence for deleterious effects of remdesivir treatment on the integrity of the mitochondrial genome in human cells in culture.
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Affiliation(s)
- Elena J Ciesielska
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States
| | - Shalom Kim
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States
| | | | - Cody Grier
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States
| | - Md Mostafijur Rahman
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, United States
| | - Carolyn K J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, United States
| | - Matthew J Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, United States
| | - Marcos T Oliveira
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista "Júlio de Mesquita Filho", Jaboticabal, SP, Brazil
| | - Grzegorz L Ciesielski
- Department of Chemistry, Auburn University at Montgomery, Montgomery, AL 36117, United States.
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16
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Durand M, Nagot N, Nhu QBT, Vallo R, Thuy LLT, Duong HT, Thanh BN, Rapoud D, Quillet C, Tran HT, Michel L, Tuyet TNT, Hai OKT, Hai VV, Feelemyer J, Perre PV, Jarlais DD, Minh KP, Laureillard D, Molès JP. Mitochondrial Genotoxicity of Hepatitis C Treatment among People Who Inject Drugs. J Clin Med 2021; 10:jcm10214824. [PMID: 34768343 PMCID: PMC8584601 DOI: 10.3390/jcm10214824] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
Antiviral nucleoside analogues (ANA) are newly used therapeutics acting against the hepatitis C virus (HCV). This class of drug is well known to exhibit toxicity on mitochondrial DNA (mtDNA). People who inject drugs (PWID) are particularly affected by HCV infection and cumulated mitotoxic drug exposure from HIV treatments (antiretrovirals, ARV) and other illicit drugs. This study aims to explore the impact of direct-acting antiviral (DAA) treatments on mtDNA among PWID. A total of 470 actively injecting heroin users were included. We used quantitative PCR on whole blood to determine the mitochondrial copy number per cell (MCN) and the proportion of mitochondrial DNA deletion (MDD). These parameters were assessed before and after DAA treatment. MDD was significantly increased after HCV treatment, while MCN did not differ. MDD was even greater when subjects were cotreated with ARV. In multivariate analysis, we identified that poly-exposure to DAA and daily heroin injection or regular consumption of methamphetamines were positively associated with high MCN loss while DAA and ARV treatments or methadone use were identified as risk factors for having mtDNA deletion. These observations deserve attention since they were previously associated with premature cell ageing or cell transformation and therefore call for a long-term follow-up.
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Affiliation(s)
- Mélusine Durand
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
- Correspondence: ; Tel.: +33-43435-9120
| | - Nicolas Nagot
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
| | - Quynh Bach Thi Nhu
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Haiphong 04212, Vietnam; (Q.B.T.N.); (L.L.T.T.); (H.T.D.); (B.N.T.); (H.T.T.); (K.P.M.)
| | - Roselyne Vallo
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
| | - Linh Le Thi Thuy
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Haiphong 04212, Vietnam; (Q.B.T.N.); (L.L.T.T.); (H.T.D.); (B.N.T.); (H.T.T.); (K.P.M.)
| | - Huong Thi Duong
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Haiphong 04212, Vietnam; (Q.B.T.N.); (L.L.T.T.); (H.T.D.); (B.N.T.); (H.T.T.); (K.P.M.)
| | - Binh Nguyen Thanh
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Haiphong 04212, Vietnam; (Q.B.T.N.); (L.L.T.T.); (H.T.D.); (B.N.T.); (H.T.T.); (K.P.M.)
| | - Delphine Rapoud
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
| | - Catherine Quillet
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
| | - Hong Thi Tran
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Haiphong 04212, Vietnam; (Q.B.T.N.); (L.L.T.T.); (H.T.D.); (B.N.T.); (H.T.T.); (K.P.M.)
| | - Laurent Michel
- CESP UMR1018, Paris Saclay, Pierre Nicole Center, French Red Cross, 75005 Paris, France;
| | - Thanh Nham Thi Tuyet
- Supporting Community Development Initiatives, Hanoi 11513, Vietnam; (T.N.T.T.); (O.K.T.H.)
| | - Oanh Khuat Thi Hai
- Supporting Community Development Initiatives, Hanoi 11513, Vietnam; (T.N.T.T.); (O.K.T.H.)
| | - Vinh Vu Hai
- Infectious & Tropical Diseases Department, Viet Tiep Hospital, Haiphong 04708, Vietnam;
| | - Jonathan Feelemyer
- School of Global Public Health, New York University, New York, NY 10003, USA; (J.F.); (D.D.J.)
| | - Philippe Vande Perre
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
| | - Don Des Jarlais
- School of Global Public Health, New York University, New York, NY 10003, USA; (J.F.); (D.D.J.)
| | - Khue Pham Minh
- Faculty of Public Health, Hai Phong University of Medicine and Pharmacy, Haiphong 04212, Vietnam; (Q.B.T.N.); (L.L.T.T.); (H.T.D.); (B.N.T.); (H.T.T.); (K.P.M.)
| | - Didier Laureillard
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
- Infectious & Tropical Diseases Department, Caremeau University Hospital, 30029 Nîmes, France
| | - Jean-Pierre Molès
- Pathogenesis and Control of Chronic and Emerging Infections, University of Montpellier, INSERM, EFS, University of Antilles, 34394 Montpellier, France; (N.N.); (R.V.); (D.R.); (C.Q.); (P.V.P.); (D.L.); (J.-P.M.)
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Zhang C, Xue Y, Wang L, Wu Q, Fang B, Sheng Y, Bai H, Peng B, Yang N, Li L. Progress on the Physiological Function of Mitochondrial DNA and Its Specific Detection and Therapy. Chembiochem 2021; 23:e202100474. [PMID: 34661371 DOI: 10.1002/cbic.202100474] [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: 09/05/2021] [Revised: 10/16/2021] [Indexed: 11/10/2022]
Abstract
Mitochondrial DNA (mtDNA) is the genetic information of mitochondrion, and its structure is circular double-stranded. Despite the diminutive size of the mitochondrial genome, mtDNA mutations are an important cause of mitochondrial diseases which are characterized by defects in oxidative phosphorylation (OXPHOS). Mitochondrial diseases are involved in multiple systems, particularly in the organs that are highly dependent on aerobic metabolism. The diagnosis of mitochondrial disease is more complicated since mtDNA mutations can cause various clinical symptoms. To realize more accurate diagnosis and treatment of mitochondrial diseases, the detection of mtDNA and the design of drugs acting on it are extremely important. Over the past few years, many probes and therapeutic drugs targeting mtDNA have been developed, making significant contributions to fundamental research including elucidation of the mechanisms of mitochondrial diseases at the genetic level. In this review, we summarize the structure, function, and detection approaches for mtDNA. The most current topics in this field, such as mechanistic exploration and treatment of mtDNA mutation-related disorders, are also reviewed. Specific attention is given to discussing the design and development of these probes and drugs for mtDNA. We hope that this review will provide readers with a comprehensive understanding of the importance of mtDNA, and promote the development of effective molecules for theragnosis of mtDNA mutation-related diseases.
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Affiliation(s)
- Congcong Zhang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Yufei Xue
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Lan Wang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Qiong Wu
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Bin Fang
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Yu Sheng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Hua Bai
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Bo Peng
- Frontiers Science Center for Flexible Electronics, Xi'an Institute of Flexible Electronics (IFE) and, Xi'an Institute of Biomedical Materials and Engineering, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, 710072, P. R. China
| | - Naidi Yang
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China
| | - Lin Li
- Key Laboratory of Flexible Electronics (KLOFE) and, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (Nanjing Tech), 30 South Puzhu Road, Nanjing, 211816, P. R. China.,The Institute of Flexible Electronics (IFE, Future Technologies), Xiamen University, Xiamen, 361005, Fujian, P. R. China
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18
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Emerging methods for and novel insights gained by absolute quantification of mitochondrial DNA copy number and its clinical applications. Pharmacol Ther 2021; 232:107995. [PMID: 34592204 DOI: 10.1016/j.pharmthera.2021.107995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 08/26/2021] [Accepted: 09/01/2021] [Indexed: 02/07/2023]
Abstract
The past thirty years have seen a surge in interest in pathophysiological roles of mitochondria, and the accurate quantification of mitochondrial DNA copy number (mCN) in cells and tissue samples is a fundamental aspect of assessing changes in mitochondrial health and biogenesis. Quantification of mCN between studies is surprisingly variable due to a combination of physiological variability and diverse protocols being used to measure this endpoint. The advent of novel methods to quantify nucleic acids like digital polymerase chain reaction (dPCR) and high throughput sequencing offer the ability to measure absolute values of mCN. We conducted an in-depth survey of articles published between 1969 -- 2020 to create an overview of mCN values, to assess consensus values of tissue-specific mCN, and to evaluate consistency between methods of assessing mCN. We identify best practices for methods used to assess mCN, and we address the impact of using specific loci on the mitochondrial genome to determine mCN. Current data suggest that clinical measurement of mCN can provide diagnostic and prognostic value in a range of diseases and health conditions, with emphasis on cancer and cardiovascular disease, and the advent of means to measure absolute mCN should improve future clinical applications of mCN measurements.
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19
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Herbst A, Lee CC, Vandiver AR, Aiken JM, McKenzie D, Hoang A, Allison D, Liu N, Wanagat J. Mitochondrial DNA deletion mutations increase exponentially with age in human skeletal muscle. Aging Clin Exp Res 2021; 33:1811-1820. [PMID: 32965609 PMCID: PMC7985047 DOI: 10.1007/s40520-020-01698-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 08/26/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) deletion mutations lead to electron transport chain-deficient cells and age-induced cell loss in multiple tissues and mammalian species. Accurate quantitation of somatic mtDNA deletion mutations could serve as an index of age-induced cell loss. Quantitation of mtDNA deletion molecules is confounded by their low abundance in tissue homogenates, the diversity of deletion breakpoints, stochastic accumulation in single cells, and mosaic distribution between cells. AIMS Translate a pre-clinical assay to quantitate mtDNA deletions for use in human DNA samples, with technical and biological validation, and test this assay on human subjects of different ages. METHODS We developed and validated a high-throughput droplet digital PCR assay that quantitates human mtDNA deletion frequency. RESULTS Analysis of human quadriceps muscle samples from 14 male subjects demonstrated that mtDNA deletion frequency increases exponentially with age-on average, a 98-fold increase from age 20-80. Sequence analysis of amplification products confirmed the specificity of the assay for human mtDNA deletion breakpoints. Titration of synthetic mutation mixtures found a lower limit of detection of at least 0.6 parts per million. Using muscle DNA from 6-month-old mtDNA mutator mice, we measured a 6.4-fold increase in mtDNA deletion frequency (i.e., compared to wild-type mice), biologically validating the approach. DISCUSSION/CONCLUSIONS The exponential increase in mtDNA deletion frequency is concomitant with the known muscle fiber loss and accelerating mortality that occurs with age. The improved assay permits the accurate and sensitive quantification of deletion mutations from DNA samples and is sufficient to measure changes in mtDNA deletion mutation frequency in healthy individuals across the lifespan and, therefore, patients with suspected mitochondrial diseases.
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Affiliation(s)
- Allen Herbst
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Cathy C Lee
- Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, USA
- Division of Geriatrics, Department of Medicine, UCLA, Los Angeles, CA, USA
| | - Amy R Vandiver
- Division of Dermatology, Department of Medicine, UCLA, 10945 Le Conte Ave, Suite 2339, Los Angeles, CA, 90095, USA
| | - Judd M Aiken
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, AB, Canada
| | - Debbie McKenzie
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Austin Hoang
- Division of Geriatrics, Department of Medicine, UCLA, Los Angeles, CA, USA
| | - David Allison
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN, USA
| | - Nianjun Liu
- Department of Epidemiology and Biostatistics, Indiana University Bloomington, Bloomington, IN, USA
| | - Jonathan Wanagat
- Veterans Administration Greater Los Angeles Healthcare System, Los Angeles, USA.
- Division of Geriatrics, Department of Medicine, UCLA, Los Angeles, CA, USA.
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20
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Mosquera A, Guillén R, Otero F, Rego-Pérez I, Blanco FJ, Fernández JL. Design of a digital-PCR assay to quantify fragmented human mitochondrial DNA. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:364-373. [PMID: 34115400 DOI: 10.1002/em.22449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Digital PCR (dPCR) has been adapted to quantify the proportion of mitochondrial DNA (mtDNA) molecules without and with double-strand DNA breaks (DSBs). This is based on a break-apart approach of two differentially labeled target sequences distantly located in the circular DNA molecule. When the two targets amplify in separated reaction partitions, the original mtDNA molecule should be fragmented by two DSBs at least, each in a different segment between targets. When both targets amplify in the same partition, it must correspond to a circular or linear mtDNA molecule. These two possibilities may be distinguished through a restriction endonuclease (RE) induced unique DSB within a DNA segment between the targets. After RE-digestion, separation of both target signals in different partitions must indicate the presence of a previous linear mtDNA molecule. Otherwise, joint amplification in the same partition would correspond to an initial circular mtDNA that has been linearized by the endonuclease. The procedure was validated by assaying different proportions of mtDNA fragmented by in vitro digestion with REs, evidencing a perfect accordance between the expected theoretical values and dPCR quantification. Samples from peripheral blood cells, cellular and extracellular DNA from the U2OS cell line, as well as cells incubated with ethidium bromide to induce mtDNA depletion, were evaluated. The technique may be of interest to complement the studies of mtDNA in relation to aging and human disease, as well as to assess possible adverse effects of certain drugs that could be related to affectation of mtDNA.
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Affiliation(s)
- Alejandro Mosquera
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Rebeca Guillén
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
- Centro Oncológico de Galicia, Laboratory of Genetics and Radiobiology, A Coruña, Spain
| | - Fátima Otero
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
- Centro Oncológico de Galicia, Laboratory of Genetics and Radiobiology, A Coruña, Spain
| | - Ignacio Rego-Pérez
- Rheumatology Division, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Francisco J Blanco
- Rheumatology Division, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - José Luis Fernández
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
- Centro Oncológico de Galicia, Laboratory of Genetics and Radiobiology, A Coruña, Spain
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21
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Hiraga C, Yamamoto S, Hashimoto S, Kasahara M, Minamisawa T, Matsumura S, Katakura A, Yajima Y, Nomura T, Shiba K. Pentapartite fractionation of particles in oral fluids by differential centrifugation. Sci Rep 2021; 11:3326. [PMID: 33558596 PMCID: PMC7870959 DOI: 10.1038/s41598-021-82451-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/18/2021] [Indexed: 12/30/2022] Open
Abstract
Oral fluids (OFs) contain small extracellular vesicles (sEVs or exosomes) that carry disease-associated diagnostic molecules. However, cells generate extracellular vesicles (EVs) other than sEVs, so the EV population is quite heterogeneous. Furthermore, molecules not packaged in EVs can also serve as diagnostic markers. For these reasons, developing a complete picture of particulate matter in the oral cavity is important before focusing on specific subtypes of EVs. Here, we used differential centrifugation to fractionate human OFs from healthy volunteers and patients with oral squamous cell carcinoma into 5 fractions, and we characterized the particles, nucleic acids, and proteins in each fraction. Canonical exosome markers, including CD63, CD9, CD133, and HSP70, were found in all fractions, whereas CD81 and AQP5 were enriched in the 160K fraction, with non-negligible amounts in the 2K fraction. The 2K fraction also contained its characteristic markers that included short derivatives of EGFR and E-cadherin, as well as an autophagosome marker, LC3, and large multi-layered vesicles were observed by electronic microscopy. Most of the DNA and RNA was recovered from the 0.3K and 2K fractions, with some in the 160K fraction. These results can provide guideline information for development of purpose-designed OF-based diagnostic systems.
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Affiliation(s)
- Chiho Hiraga
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Ariake 3-8-31, Koto-ku, Tokyo, 135-8550, Japan
- Department of Oral Oncology, Oral and Maxillofacial Surgery, Tokyo Dental College, 5-11-13 Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Satoshi Yamamoto
- Department of Pharmacology, Tokyo Dental College, 2-1-14 Misaki-cho, Chiyoda-ku, Tokyo, 101-0061, Japan
| | - Sadamitsu Hashimoto
- Laboratory of Biology, Tokyo Dental College, 2-9-7 Kanda-Surugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
| | - Masataka Kasahara
- Department of Pharmacology, Tokyo Dental College, 2-1-14 Misaki-cho, Chiyoda-ku, Tokyo, 101-0061, Japan
| | - Tamiko Minamisawa
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Ariake 3-8-31, Koto-ku, Tokyo, 135-8550, Japan
| | - Sachiko Matsumura
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Ariake 3-8-31, Koto-ku, Tokyo, 135-8550, Japan
| | - Akira Katakura
- Department of Oral Pathobiological Science and Surgery, Tokyo Dental College, 2-9-18 Misaki-cho, Chiyoda-ku, Tokyo, 101-0061, Japan
| | - Yasutomo Yajima
- Department of Oral Implantology, Tokyo Dental College, 2-9-18 Misaki-cho, Chiyoda-ku, Tokyo, 101-0061, Japan
| | - Takeshi Nomura
- Department of Oral Oncology, Oral and Maxillofacial Surgery, Tokyo Dental College, 5-11-13 Sugano, Ichikawa, Chiba, 272-8513, Japan
| | - Kiyotaka Shiba
- Division of Protein Engineering, Cancer Institute, Japanese Foundation for Cancer Research, Ariake 3-8-31, Koto-ku, Tokyo, 135-8550, Japan.
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22
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Levy MA, Kerkhof J, Belmonte FR, Kaufman BA, Bhai P, Brady L, Bursztyn LLCD, Tarnopolsky M, Rupar T, Sadikovic B. Validation and clinical performance of a combined nuclear-mitochondrial next-generation sequencing and copy number variant analysis panel in a Canadian population. Am J Med Genet A 2020; 185:486-499. [PMID: 33300680 DOI: 10.1002/ajmg.a.61998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/17/2022]
Abstract
Diagnosing mitochondrial disorders is a challenge due to the heterogeneous clinical presentation and large number of associated genes. A custom next generation sequencing (NGS) panel was developed incorporating the full mitochondrial genome (mtDNA) plus 19 nuclear genes involved in structural mitochondrial defects and mtDNA maintenance. This assay is capable of simultaneously detecting small gene sequence variations and larger copy number variants (CNVs) in both the nuclear and mitochondrial components along with heteroplasmy detection down to 5%. We describe technical validations of this panel and its implementation for clinical testing in a Canadian reference laboratory, and report its clinical performance in the initial 950 patients tested. Using this assay, we demonstrate a diagnostic yield of 18.1% of patients with known pathogenic variants. In addition to the common 5 kb mtDNA deletion, we describe significant contribution of pathogenic CNVs in both the mitochondrial genome and nuclear genes in this patient population.
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Affiliation(s)
- Michael A Levy
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Jennifer Kerkhof
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Frances R Belmonte
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Brett A Kaufman
- Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Pratibha Bhai
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Lauren Brady
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Mark Tarnopolsky
- Division of Neuromuscular and Neurometabolic Disease, Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Tony Rupar
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Departments of Biochemistry and Paediatrics, Schulich School of Medicine & Dentistry, Western University, and Biochemical Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada.,Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Ontario, Canada
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23
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Kathrada AI, Wei SC, Xu Y, Cheow, LF, Chen CH. Microfluidic compartmentalization to identify gene biomarkers of infection. BIOMICROFLUIDICS 2020; 14:061502. [PMID: 33312326 PMCID: PMC7717927 DOI: 10.1063/5.0032849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 11/09/2020] [Indexed: 05/20/2023]
Abstract
Infectious diseases caused by pathogens, such as SARS-COV, H7N9, severe fever with thrombocytopenia syndrome virus, and human immunodeficiency virus, have fatal outcomes with common features of severe fever and subsequent bacterial invasion progressing to multiorgan failure. Gene biomarkers are promising to distinguish specific infections from others with similar presenting symptoms for the prescription of correct therapeutics, preventing pandemics. While routine laboratory methods based on polymerase chain reaction (PCR) to measure gene biomarkers have provided highly sensitive and specific viral detection techniques over the years, they are still hampered by their precision and resource intensity precluding their point-of-care use. Recently, there has been growing interest in employing microfluidic technologies to advance current methods for infectious disease determination via gene biomarker measurements. Here, based on the requirement of infection detection, we will review three microfluidic approaches to compartmentalize gene biomarkers: (1) microwell-based PCR platforms; (2) droplet-based PCR; and (3) point-of-care devices including centrifugal chip, SlipChip, and self-powered integrated microfluidic point-of-care low-cost enabling chip. By capturing target genes in microwells with a small sample volume (∼μl), sensitivity can be enhanced. Additionally, with the advance of significant sample volume minimization (∼pl) using droplet technology, gene quantification is possible. These improvements in cost, automation, usability, and portability have thereby allowed point-of-care applications to decentralize testing platforms from laboratory-based settings to field use against infections.
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Affiliation(s)
- Ahmad Ismat Kathrada
- Department of Biomedical Engineering, National University of Singapore, 4 Engineering Drive 3, Block 4, #04-08, Singapore 117583
| | | | - Ying Xu
- Department of Biomedical Engineering, City University of Hong Kong, Room Y6700, 6/F, Yeung Kin Man Academic Building, 83 Tat Chee Avenue, Hong Kong, China
| | | | - Chia-Hung Chen
- Department of Biomedical Engineering, City University of Hong Kong, Room Y6700, 6/F, Yeung Kin Man Academic Building, 83 Tat Chee Avenue, Hong Kong, China
- Author to whom correspondence should be addressed:
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24
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Li B, Li Y, Jiang Y, Manz A, Wu W. A digital PCR system based on the thermal cycled chip with multi helix winding capillary. Sci Rep 2020; 10:17824. [PMID: 33082428 PMCID: PMC7576587 DOI: 10.1038/s41598-020-74711-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/05/2020] [Indexed: 12/19/2022] Open
Abstract
This paper presents a digital PCR system based on a novel thermal cycled chip, which wraps microchannels on a trapezoidal structure made of polydimethylsiloxane (PDMS) in a multi-helix manner for the first time. It is found that compared to the single helix chip commonly used in previous reports, this kind of novel multi-helix chip can make the surface temperature in the renaturation zone more uniform, and even in the case of rapid fluid flow, it can improve the efficiency of the polymerase chain reaction. What’s more, the winding method of multi helix (such as double helix, six helix and eight helix) can obtain better temperature uniformity than the winding of odd helix (such as single helix and three helix). As a proof of concept, the temperature-optimized double-helical chip structure is applied to continuous-flow digital PCR and there is no need to add any surfactant to both the oil phase and reagent. In addition, we successfully analyzed the fluorescence signal of continuous-flow digital PCR by using CMOS camera. Finally, this method is applied for the absolute quantification of the clinical serum sample infected by HBV. The accuracy of the test results has been confirmed by commercial instruments.
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Affiliation(s)
- Bin Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanming Li
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Yangyang Jiang
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China
| | - Andreas Manz
- Systems Engineering Department, Saarland University, 66123, Saarbrücken, Germany.,Bio Sensor & Materials Group, KIST Europe, 66123, Saarbrücken, Germany
| | - Wenming Wu
- State Key Laboratory of Applied Optics, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033, China.
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25
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Ware SA, Desai N, Lopez M, Leach D, Zhang Y, Giordano L, Nouraie M, Picard M, Kaufman BA. An automated, high-throughput methodology optimized for quantitative cell-free mitochondrial and nuclear DNA isolation from plasma. J Biol Chem 2020; 295:15677-15691. [PMID: 32900851 DOI: 10.1074/jbc.ra120.015237] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 09/03/2020] [Indexed: 02/06/2023] Open
Abstract
Progress in the study of circulating, cell-free nuclear DNA (ccf-nDNA) in cancer detection has led to the development of noninvasive clinical diagnostic tests and has accelerated the evaluation of ccf-nDNA abundance as a disease biomarker. Likewise, circulating, cell-free mitochondrial DNA (ccf-mtDNA) is under similar investigation. However, optimal ccf-mtDNA isolation parameters have not been established, and inconsistent protocols for ccf-nDNA collection, storage, and analysis have hindered its clinical utility. Until now, no studies have established a method for high-throughput isolation that considers both ccf-nDNA and ccf-mtDNA. We initially optimized human plasma digestion and extraction conditions for maximal recovery of these DNAs using a magnetic bead-based isolation method. However, when we incorporated this method onto a high-throughput platform, initial experiments found that DNA isolated from identical human plasma samples displayed plate edge effects resulting in low ccf-mtDNA reproducibility, whereas ccf-nDNA was less affected. Therefore, we developed a detailed protocol optimized for both ccf-mtDNA and ccf-nDNA recovery that uses a magnetic bead-based isolation process on an automated 96-well platform. Overall, we calculate an improved efficiency of recovery of ∼95-fold for ccf-mtDNA and 20-fold for ccf-nDNA when compared with the initial procedure. Digestion conditions, liquid-handling characteristics, and magnetic particle processor programming all contributed to increased recovery without detectable positional effects. To our knowledge, this is the first high-throughput approach optimized for ccf-mtDNA and ccf-nDNA recovery and serves as an important starting point for clinical studies.
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Affiliation(s)
- Sarah A Ware
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Nikita Desai
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mabel Lopez
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel Leach
- Optimize Laboratory Consultants, LLC, Lansdale, Pennsylvania, USA
| | - Yingze Zhang
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Luca Giordano
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mehdi Nouraie
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Martin Picard
- Division of Behavioral Medicine, Departments of Psychiatry and Neurology, Columbia University Irving Medical Center, New York, New York, USA
| | - Brett A Kaufman
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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26
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Exclusive use of digital PCR allows an absolute assay of heat-killed Lactobacilli in foods targeting multiple copies of 16S rDNA. Sci Rep 2020; 10:12691. [PMID: 32728064 PMCID: PMC7391674 DOI: 10.1038/s41598-020-69206-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/09/2020] [Indexed: 11/15/2022] Open
Abstract
The real-time PCR (qPCR) and digital PCR (dPCR) to amplify a single-copy of house-keeping genes (i.e., hsp60, pheS or tuf) are used for the assay of limited microbial species. In general, with a single-copy gene, there are obviously varied DNA sequences for even the same microbial species, which could cause difficulties with design of primers and probes for PCR when targeting various single copy genes. In general, for identification by dPCR (as a representative case: Lactobacillus paracasei), accumulated DNA sequence information of 16S rDNA, which is much more frequently used, should be targeted. In contrast, next-generation sequencing revealed that there are five copies of 16S rDNA in a live L. paracasei MCC1849. Therefore, we aimed to reveal, if heat-killed L. paracasei supplemented in nutritional foods that aid the host immune system have the relevant five copies per chromosomal DNA, and if the relevant copies remain unchanged on the same chromosomal DNA or remain to be different chromosomal DNA fragments. So, we revealed the actual distribution of the potential original five copies of 16S rDNA using our innovative dPCR, in which both 16S rDNA and hsp60 genes were simultaneously elongated. The molecular ratios of 16S rDNA/hsp60 dispersed in the dPCR chip were then estimated. The 16S rDNA/hsp60 molecular ratios of the heat-killed L. paracasei in foods, resultantly ranged from 5.0 to 7.2, being the same or higher than that of the five copies determined by next-generation sequencing. The 16S rDNA copy number/ratio indicated the chromosomal DNA molecular number and the associated cell number. As significance, different nutritional foods could potentially cause the loss of chromosomal DNA of supplemented beneficial microbes to a much greater degree. Our absolute dPCR does not require standard correlative samples for the estimation of final products. The estimation principle of the ratio of 16S rDNA/a house-keeping single-copy gene by our absolute dPCR could lead to a useful and accurate assay for various nutritional foods.
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Cappa R, de Campos C, Maxwell AP, McKnight AJ. "Mitochondrial Toolbox" - A Review of Online Resources to Explore Mitochondrial Genomics. Front Genet 2020; 11:439. [PMID: 32457801 PMCID: PMC7225359 DOI: 10.3389/fgene.2020.00439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/09/2020] [Indexed: 12/30/2022] Open
Abstract
Mitochondria play a significant role in many biological systems. There is emerging evidence that differences in the mitochondrial genome may contribute to multiple common diseases, leading to an increasing number of studies exploring mitochondrial genomics. There is often a large amount of complex data generated (for example via next generation sequencing), which requires optimised bioinformatics tools to efficiently and effectively generate robust outcomes from these large datasets. Twenty-four online resources dedicated to mitochondrial genomics were reviewed. This 'mitochondrial toolbox' summary resource will enable researchers to rapidly identify the resource(s) most suitable for their needs. These resources fulfil a variety of functions, with some being highly specialised. No single tool will provide all users with the resources they require; therefore, the most suitable tool will vary between users depending on the nature of the work they aim to carry out. Genetics resources are well established for phylogeny and DNA sequence changes, but further epigenetic and gene expression resources need to be developed for mitochondrial genomics.
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Affiliation(s)
- Ruaidhri Cappa
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Cassio de Campos
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, United Kingdom
| | - Alexander P Maxwell
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
| | - Amy J McKnight
- Centre for Public Health, Institute of Clinical Sciences B, Queen's University Belfast, Royal Victoria Hospital, Belfast, United Kingdom
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Oliveira MT, Pontes CDB, Ciesielski GL. Roles of the mitochondrial replisome in mitochondrial DNA deletion formation. Genet Mol Biol 2020; 43:e20190069. [PMID: 32141473 PMCID: PMC7197994 DOI: 10.1590/1678-4685-gmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are a common cause of human mitochondrial
diseases. Mutations in the genes encoding components of the mitochondrial
replisome, such as DNA polymerase gamma (Pol γ) and the mtDNA helicase Twinkle,
have been associated with the accumulation of such deletions and the development
of pathological conditions in humans. Recently, we demonstrated that changes in
the level of wild-type Twinkle promote mtDNA deletions, which implies that not
only mutations in, but also dysregulation of the stoichiometry between the
replisome components is potentially pathogenic. The mechanism(s) by which
alterations to the replisome function generate mtDNA deletions is(are) currently
under debate. It is commonly accepted that stalling of the replication fork at
sites likely to form secondary structures precedes the deletion formation. The
secondary structural elements can be bypassed by the replication-slippage
mechanism. Otherwise, stalling of the replication fork can generate single- and
double-strand breaks, which can be repaired through recombination leading to the
elimination of segments between the recombination sites. Here, we discuss
aberrances of the replisome in the context of the two debated outcomes, and
suggest new mechanistic explanations based on replication restart and template
switching that could account for all the deletion types reported for
patients.
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Affiliation(s)
- Marcos T Oliveira
- Universidade Estadual Paulista Júlio de Mesquita Filho, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
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Hjelm BE, Rollins B, Morgan L, Sequeira A, Mamdani F, Pereira F, Damas J, Webb MG, Weber MD, Schatzberg AF, Barchas JD, Lee FS, Akil H, Watson SJ, Myers RM, Chao EC, Kimonis V, Thompson PM, Bunney WE, Vawter MP. Splice-Break: exploiting an RNA-seq splice junction algorithm to discover mitochondrial DNA deletion breakpoints and analyses of psychiatric disorders. Nucleic Acids Res 2019; 47:e59. [PMID: 30869147 PMCID: PMC6547454 DOI: 10.1093/nar/gkz164] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/28/2019] [Indexed: 12/20/2022] Open
Abstract
Deletions in the 16.6 kb mitochondrial genome have been implicated in numerous disorders that often display muscular and/or neurological symptoms due to the high-energy demands of these tissues. We describe a catalogue of 4489 putative mitochondrial DNA (mtDNA) deletions, including their frequency and relative read rate, using a combinatorial approach of mitochondria-targeted PCR, next-generation sequencing, bioinformatics, post-hoc filtering, annotation, and validation steps. Our bioinformatics pipeline uses MapSplice, an RNA-seq splice junction detection algorithm, to detect and quantify mtDNA deletion breakpoints rather than mRNA splices. Analyses of 93 samples from postmortem brain and blood found (i) the 4977 bp ‘common deletion’ was neither the most frequent deletion nor the most abundant; (ii) brain contained significantly more deletions than blood; (iii) many high frequency deletions were previously reported in MitoBreak, suggesting they are present at low levels in metabolically active tissues and are not exclusive to individuals with diagnosed mitochondrial pathologies; (iv) many individual deletions (and cumulative metrics) had significant and positive correlations with age and (v) the highest deletion burdens were observed in major depressive disorder brain, at levels greater than Kearns–Sayre Syndrome muscle. Collectively, these data suggest the Splice-Break pipeline can detect and quantify mtDNA deletions at a high level of resolution.
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Affiliation(s)
- Brooke E Hjelm
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA.,Department of Translational Genomics, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Brandi Rollins
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Ling Morgan
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Adolfo Sequeira
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Firoza Mamdani
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Filipe Pereira
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), University of Porto, Matosinhos 4050-123, Portugal
| | - Joana Damas
- The Genome Center, University of California-Davis, Davis, CA 95616, USA
| | - Michelle G Webb
- Department of Translational Genomics, Keck School of Medicine of USC, University of Southern California (USC), Los Angeles, CA 90033, USA
| | - Matthieu D Weber
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Alan F Schatzberg
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Jack D Barchas
- Department of Psychiatry, Weill Cornell Medical College at Cornell University, New York, NY 10065, USA
| | - Francis S Lee
- Department of Psychiatry, Weill Cornell Medical College at Cornell University, New York, NY 10065, USA
| | - Huda Akil
- The Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Stanley J Watson
- The Molecular and Behavioral Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Elizabeth C Chao
- Division of Genetics and Genomic Medicine, Department of Pediatrics, UCI, Irvine, CA, USA
| | - Virginia Kimonis
- Division of Genetics and Genomic Medicine, Department of Pediatrics, UCI, Irvine, CA, USA
| | - Peter M Thompson
- Southwest Brain Bank, Department of Psychiatry, Texas Tech University Health Sciences Center (TTUHSC), El Paso, TX 79905, USA
| | - William E Bunney
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
| | - Marquis P Vawter
- Department of Psychiatry and Human Behavior, University of California-Irvine (UCI), Irvine, CA 92697, USA
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Podlesniy P, Puigròs M, Serra N, Fernández-Santiago R, Ezquerra M, Tolosa E, Trullas R. Accumulation of mitochondrial 7S DNA in idiopathic and LRRK2 associated Parkinson's disease. EBioMedicine 2019; 48:554-567. [PMID: 31631040 PMCID: PMC6838390 DOI: 10.1016/j.ebiom.2019.09.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/03/2019] [Accepted: 09/06/2019] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Both idiopathic and familial Parkinson's disease are associated with mitochondrial dysfunction. Mitochondria have their own mitochondrial DNA (mtDNA) and previous studies have reported that the release of mtDNA is a biomarker of Parkinson's disease. METHODS We have now investigated the relationship between mtDNA replication, transcription and release in fibroblasts from patients with idiopathic (iPD) and Leucine-rich repeat kinase 2G2019S -associated Parkinson's disease (LRRK2-PD), using Selfie-digital PCR, a method that allows absolute quantification of mtDNA genomes and transcripts. FINDINGS In comparison with healthy controls, we found that fibroblasts from patients with iPD or LRRK2-PD had a high amount of mitochondrial 7S DNA along with a low mtDNA replication rate that was associated with a reduction of cf-mtDNA release. Accumulation of 7S DNA in iPD and LRRK2-PD fibroblasts was related with an increase in H-strand mtDNA transcription. INTERPRETATION These results show that 7S DNA accumulation, low mtDNA replication, high H-strand transcription, and low mtDNA release compose a pattern of mtDNA dysfunction shared by both iPD and LRRK2-PD fibroblasts. Moreover, these results suggest that the deregulation of the genetic switch formed by 7SDNA that alternates between mtDNA replication and transcription is a fundamental pathophysiological mechanism in both idiopathic and monogenic Parkinson's disease.
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Affiliation(s)
- Petar Podlesniy
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain.
| | - Margalida Puigròs
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Núria Serra
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Rubén Fernández-Santiago
- Neurology Service, Parkinson's Disease and Movement Disorders Unit, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, University of Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Mario Ezquerra
- Neurology Service, Parkinson's Disease and Movement Disorders Unit, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, University of Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Eduardo Tolosa
- Neurology Service, Parkinson's Disease and Movement Disorders Unit, Institut Clínic de Neurociències, Hospital Clínic de Barcelona, University of Barcelona, Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain
| | - Ramon Trullas
- Neurobiology Unit, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Spain; Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Spain; Centro de Investigación Biomédica en Red Enfermedades Neurodegenerativas (CIBERNED), Barcelona, Spain.
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Heighton JN, Brady LI, Sadikovic B, Bulman DE, Tarnopolsky MA. Genotypes of chronic progressive external ophthalmoplegia in a large adult-onset cohort. Mitochondrion 2019; 49:227-231. [PMID: 31521625 DOI: 10.1016/j.mito.2019.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 03/28/2019] [Accepted: 09/11/2019] [Indexed: 12/11/2022]
Abstract
Chronic progressive external ophthalmoplegia (CPEO) is a common presentation of mitochondrial disease. We performed a retrospective evaluation of the molecular genetic testing and genotype-phenotype correlations in a large cohort of adult-onset CPEO patients (N = 111). One hundred percent of patients tested had at least one mitochondrial DNA (mtDNA) deletion. Genetic testing of nuclear genes encoding mitochondrial proteins identified pathogenic/likely pathogenic variants likely to be associated with CPEO in 7.6% of patients. As expected, the nuclear gene most associated with DNA variation was POLG. A single likely pathogenic mitochondrial DNA variant (m.12278T>C) was identified in two unrelated patients. No significant differences were noted in the clinical phenotypes of patients with pathogenic or likely pathogenic nuclear variants in comparison to those with negative nuclear gene testing. Analysis of deletion size and heteroplasmy in muscle-derived mtDNA showed significant correlations with age of symptom onset but not disease severity (number of canonical CPEO features). Results suggest that smaller mtDNA deletions (p = 0.0127, r2 = 0.1201) and higher heteroplasmy of single mtDNA deletions (p = 0.0112, r2 = 0.2483) are associated with an earlier age of onset in CPEO patients.
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Affiliation(s)
- Julia N Heighton
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Lauren I Brady
- Department of Pediatrics, McMaster University, Hamilton, ON, Canada
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada; Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON, Canada
| | - Dennis E Bulman
- Newborn Screening Ontario and CHEO Research Institute, Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
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Trumpff C, Marsland AL, Sloan RP, Kaufman BA, Picard M. Predictors of ccf-mtDNA reactivity to acute psychological stress identified using machine learning classifiers: A proof-of-concept. Psychoneuroendocrinology 2019; 107:82-92. [PMID: 31112904 PMCID: PMC6637411 DOI: 10.1016/j.psyneuen.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 03/21/2019] [Accepted: 05/01/2019] [Indexed: 12/15/2022]
Abstract
OBJECTIVE We have previously found that acute psychological stress may affect mitochondria and trigger an increase in serum mitochondrial DNA, known as circulating cell-free mtDNA (ccf-mtDNA). Similar to other stress reactivity measures, there are substantial unexplained inter-individual differences in the magnitude of ccf-mtDNA reactivity, as well as within-person differences across different occasions of testing. Here, we sought to identify psychological and physiological predictors of ccf-mtDNA reactivity using machine learning-based multivariate classifiers. METHOD We used data from serum ccf-mtDNA concentration measured pre- and post-stress in 46 healthy midlife adults tested on two separate occasions. To identify variables predicting the magnitude of ccf-mtDNA reactivity, two multivariate classification models, partial least-squares discriminant analysis (PLS-DA) and random forest (RF), were trained to discriminate between high and low ccf-mtDNA responders. Potential predictors used in the models included state variables such as physiological measures and affective states, and trait variables such as sex and personality measures. Variables identified across both models were considered to be predictors of ccf-mtDNA reactivity and selected for downstream analyses. RESULTS Identified predictors were significantly enriched for state over trait measures (X2 = 7.03; p = 0.008) and for physiological over psychological measures (X2 = 4.36; p = 0.04). High responders were more likely to be male (X2 = 26.95; p < 0.001) and differed from low-responders on baseline cardiovascular and autonomic measures, and on stress-induced reduction in fatigue (Cohen's d = 0.38-0.73). These group-level findings also accurately accounted for within-person differences in 90% of cases. CONCLUSION These results suggest that acute cardiovascular and psychological indices, rather than stable individual traits, predict stress-induced ccf-mtDNA reactivity. This work provides a proof-of-concept that machine learning approaches can be used to explore determinants of inter-individual and within-person differences in stress psychophysiology.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Anna L Marsland
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Richard P Sloan
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Brett A Kaufman
- University of Pittsburgh School of Medicine, Division of Cardiology, Center for Metabolism and Mitochondrial Medicine and Vascular Medicine Institute, Pittsburgh, PA, 15261, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA; Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, 10032, USA.
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Xiu L, Zhang C, Li Y, Wang F, Peng J. Simultaneous detection of eleven sexually transmitted agents using multiplexed PCR coupled with MALDI-TOF analysis. Infect Drug Resist 2019; 12:2671-2682. [PMID: 31695443 PMCID: PMC6717854 DOI: 10.2147/idr.s219580] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 08/10/2019] [Indexed: 01/02/2023] Open
Abstract
Purpose Sexually transmitted infections (STIs), representing a major global health problem, are caused by different microbes, including bacteria, viruses, and protozoa. Unfortunately, infections of different sexually transmitted pathogens often present similar clinical symptoms, so it is almost impossible to distinguish them clinically. Therefore, the aim of the current study was to develop a sensitive, multitarget, and high-throughput method that can detect various agents responsible for STIs. Methods We developed and tested a 23-plex PCR coupled with matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry (MS) assay (sexually transmitted infection-mass spectrometry, STI-MS) that simultaneously targets 11 different agents, including 8 most common clinical pathogens related to STIs (HSV-1, HSV-2, Neisseria gonorrhoeae, Chlamydia trachomatis, Treponema pallidum, Trichomonas vaginalis, Mycoplasma genitalium, and Haemophilus ducreyi) and 3 controversial microorganisms as pathogens (Mycoplasma hominis, Ureaplasma urealyticum, and Ureaplasma parvum). Results The results showed that the STI-MS approach can accurately detect the expected agents, without cross-reaction with other organisms. The limit of detection of each STI-MS assay was ranged from 1.739 to 10.009 copies/reaction, using probit analyses. The verification rate for each target organism of the STI-MS ranged from a minimum of 89.3% to a maximum of 100%, using conventional assays and ultrasensitive digital PCR to confirm the STI-MS-positive results. To further evaluate the clinical performance of this assay, 241 clinical specimens (124 urethral/cervical swabs and 117 urine) were tested in parallel using the STI-MS assay and monoplex real-time PCR for each agent. The overall validation parameters of STI-MS were extremely high including sensitivity (from 85.7% to 100%), specificity (from 92.3% to 100%), PPV (from 50% to 100%), and NPV (from 99.1% to 100%) for each target. Conclusion STI-MS is a useful high-throughput screening tool for detecting mixed infections of STIs and has great potential for application in large-scale epidemiological programs for specific microorganisms of STI.
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Affiliation(s)
- Leshan Xiu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Chi Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Yamei Li
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Feng Wang
- Shenzhen Center for Chronic Disease Control, Shenzhen, People's Republic of China
| | - Junping Peng
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
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Trumpff C, Marsland AL, Basualto-Alarcón C, Martin JL, Carroll JE, Sturm G, Vincent AE, Mosharov EV, Gu Z, Kaufman BA, Picard M. Acute psychological stress increases serum circulating cell-free mitochondrial DNA. Psychoneuroendocrinology 2019; 106:268-276. [PMID: 31029929 PMCID: PMC6589121 DOI: 10.1016/j.psyneuen.2019.03.026] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/20/2019] [Accepted: 03/25/2019] [Indexed: 01/09/2023]
Abstract
Intrinsic biological mechanisms transduce psychological stress into physiological adaptation that requires energy, but the role of mitochondria and mitochondrial DNA (mtDNA) in this process has not been defined in humans. Here, we show that similar to physical injury, exposure to psychological stress increases serum circulating cell-free mtDNA (ccf-mtDNA) levels. Healthy midlife adults exposed on two separate occasions to a brief psychological challenge exhibited a 2-3-fold increase in ccf-mtDNA, with no change in ccf-nuclear DNA levels, establishing the magnitude and specificity for ccf-mtDNA reactivity. In cell-based studies, we show that glucocorticoid signaling - a consequence of psychological stress in humans - is sufficient to induce mtDNA extrusion in a time frame consistent with stress-induced ccf-mtDNA increase. Collectively, these findings provide evidence that acute psychological stress induces ccf-mtDNA and implicate neuroendocrine signaling as a potential trigger for ccf-mtDNA release. Further controlled work is needed to confirm that observed increases in ccf-mtDNA result from stress exposure and to determine the functional significance of this effect.
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Affiliation(s)
- Caroline Trumpff
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA; New York State Psychiatric Institute, New York, NY, 10032, USA
| | - Anna L Marsland
- Department of Psychology, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
| | - Carla Basualto-Alarcón
- Universidad de Aysén, Coyhaique, Chile; Anatomy and Legal Medicine Department, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - James L Martin
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, 15261, USA
| | - Judith E Carroll
- Cousins Center for Psychoneuroimmunology, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, CA, 90095, USA
| | - Gabriel Sturm
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Amy E Vincent
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA; Wellcome Trust Centre for Mitochondrial Research, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Eugene V Mosharov
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA; New York State Psychiatric Institute, New York, NY, 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Zhenglong Gu
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, NY, 14850, USA
| | - Brett A Kaufman
- Department of Medicine, Division of Cardiology, Vascular Medicine Institute, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, 15261, USA.
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA; New York State Psychiatric Institute, New York, NY, 10032, USA; Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, 10032, USA; Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, 10032, USA.
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Wheeler JH, Young CKJ, Young MJ. Analysis of Human Mitochondrial DNA Content by Southern Blotting and Nonradioactive Probe Hybridization. CURRENT PROTOCOLS IN TOXICOLOGY 2019; 80:e75. [PMID: 30982231 PMCID: PMC6581606 DOI: 10.1002/cptx.75] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A single cell can contain several thousand copies of the mitochondrial DNA genome or mtDNA. Tools for assessing mtDNA content are necessary for clinical and toxicological research, as mtDNA depletion is linked to genetic disease and drug toxicity. For instance, mtDNA depletion syndromes are typically fatal childhood disorders that are characterized by severe declines in mtDNA content in affected tissues. Mitochondrial toxicity and mtDNA depletion have also been reported in human immunodeficiency virus-infected patients treated with certain nucleoside reverse transcriptase inhibitors. Further, cell culture studies have demonstrated that exposure to oxidative stress stimulates mtDNA degradation. Here we outline a Southern blot and nonradioactive digoxigenin-labeled probe hybridization method to estimate mtDNA content in human genomic DNA samples. © 2019 by John Wiley & Sons, Inc.
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Affiliation(s)
- Joel H. Wheeler
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Carolyn K. J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
| | - Matthew J. Young
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois 62901
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Zhang Z, Zhang Y, Lin X, Chen Z, Wu S. Development of a novel reverse transcription droplet digital PCR assay for the sensitive detection of Senecavirus A. Transbound Emerg Dis 2018; 66:517-525. [PMID: 30375741 DOI: 10.1111/tbed.13056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 12/27/2022]
Abstract
In pigs, Senecavirus A (SVA) causes a vesicular disease that is clinically indistinguishable from foot-and-mouth disease, vesicular stomatitis and swine vesicular disease. Sensitive and specific detection of SVA is critical for controlling this emerging disease. In this study, a novel reverse transcription droplet digital PCR (RT-ddPCR) assay, targeting the conserved viral polymerase 3D gene, was established for the detection of SVA. This assay exhibited good linearity, repeatability and reproducibility, and maintained linearity at extremely low concentrations of SVA nucleic acid templates. The detection limit of RT-ddPCR was 1.53 ± 0.22 copies of SVA RNA per reaction (n = 8), and the assay showed approximately 10-fold greater sensitivity than a reverse transcription real-time PCR (RT-rPCR) assay. Moreover, specificity analysis showed that the RT-ddPCR for SVA had no cross-reactivity with other important swine pathogens. In clinical diagnosis of 134 pig serum and tissue samples, 26 and 21 samples were identified as positive by RT-ddPCR and RT-rPCR, respectively. The overall agreement between the two assays was 96.27% (129/134). Further linear regression analysis showed a significant correlation between the RT-ddPCR and RT-rPCR assays with an R2 value of 0.9761. Our results indicate that the RT-ddPCR assay is a robust diagnostic tool for the sensitive detection of SVA, even in samples with a low viral load.
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Affiliation(s)
- Zhou Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Yongning Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xiangmei Lin
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Jiangsu, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Jiangsu, China
| | - Shaoqiang Wu
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
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37
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Application of droplet digital PCR to detect the pathogens of infectious diseases. Biosci Rep 2018; 38:BSR20181170. [PMID: 30341241 PMCID: PMC6240714 DOI: 10.1042/bsr20181170] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/07/2018] [Accepted: 10/09/2018] [Indexed: 12/20/2022] Open
Abstract
Polymerase chain reaction (PCR) is a molecular biology technique used to multiply certain deoxyribonucleic acid (DNA) fragments. It is a common and indispensable technique that has been applied in many areas, especially in clinical laboratories. The third generation of polymerase chain reaction, droplet digital polymerase chain reaction (ddPCR), is a biotechnological refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify DNA. Droplet digital polymerase chain reaction is now widely used in low-abundance nucleic acid detection and is useful in diagnosis of infectious diseases. Here, we summarized the potential advantages of droplet digital polymerase chain reaction in clinical diagnosis of infectious diseases, including viral diseases, bacterial diseases and parasite infections, concluded that ddPCR provides a more sensitive, accurate, and reproducible detection of low-abundance pathogens and may be a better choice than quantitative polymerase chain reaction for clinical applications in the future.
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38
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Goudenège D, Bris C, Hoffmann V, Desquiret-Dumas V, Jardel C, Rucheton B, Bannwarth S, Paquis-Flucklinger V, Lebre AS, Colin E, Amati-Bonneau P, Bonneau D, Reynier P, Lenaers G, Procaccio V. eKLIPse: a sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genet Med 2018; 21:1407-1416. [PMID: 30393377 DOI: 10.1038/s41436-018-0350-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 10/17/2018] [Indexed: 12/26/2022] Open
Abstract
PURPOSE Accurate detection of mitochondrial DNA (mtDNA) alterations is essential for the diagnosis of mitochondrial diseases. The development of high-throughput sequencing technologies has enhanced the detection sensitivity of mtDNA pathogenic variants, but the detection of mtDNA rearrangements, especially multiple deletions, is still poorly processed. Here, we present eKLIPse, a sensitive and specific tool allowing the detection and quantification of large mtDNA rearrangements from single and paired-end sequencing data. METHODS The methodology was first validated using a set of simulated data to assess the detection sensitivity and specificity, and second with a series of sequencing data from mitochondrial disease patients carrying either single or multiple deletions, related to pathogenic variants in nuclear genes involved in mtDNA maintenance. RESULTS eKLIPse provides the precise breakpoint positions and the cumulated percentage of mtDNA rearrangements at a given gene location with a detection sensitivity lower than 0.5% mutant. eKLIPse software is available either as a script to be integrated in a bioinformatics pipeline, or as user-friendly graphical interface to visualize the results through a Circos representation ( https://github.com/dooguypapua/eKLIPse ). CONCLUSION Thus, eKLIPse represents a useful resource to study the causes and consequences of mtDNA rearrangements, for further genotype/phenotype correlations in mitochondrial disorders.
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Affiliation(s)
- David Goudenège
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Celine Bris
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Virginie Hoffmann
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Valerie Desquiret-Dumas
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Claude Jardel
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Benoit Rucheton
- Biochemistry Department and Genetics Center, APHP, GHU Pitié-Salpêtrière, Paris, France
| | - Sylvie Bannwarth
- Université Côte d'Azur, CHU de Nice, INSERM, CNRS, IRCAN, Nice, France
| | | | - Anne Sophie Lebre
- CHU Reims, Hôpital Maison Blanche, Pole de biologie, Service de génétique, Reims, France
| | - Estelle Colin
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Patrizia Amati-Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Dominique Bonneau
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Pascal Reynier
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France.,Biochemistry and Genetics Department, Angers Hospital, Angers, France
| | - Guy Lenaers
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France
| | - Vincent Procaccio
- MitoLab, UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University, Angers, France. .,Biochemistry and Genetics Department, Angers Hospital, Angers, France.
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39
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Clonal expansion of mtDNA deletions: different disease models assessed by digital droplet PCR in single muscle cells. Sci Rep 2018; 8:11682. [PMID: 30076399 PMCID: PMC6076247 DOI: 10.1038/s41598-018-30143-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 07/18/2018] [Indexed: 01/07/2023] Open
Abstract
Deletions in mitochondrial DNA (mtDNA) are an important cause of human disease and their accumulation has been implicated in the ageing process. As mtDNA is a high copy number genome, the coexistence of deleted and wild-type mtDNA molecules within a single cell defines heteroplasmy. When deleted mtDNA molecules, driven by intracellular clonal expansion, reach a sufficiently high level, a biochemical defect emerges, contributing to the appearance and progression of clinical pathology. Consequently, it is relevant to determine the heteroplasmy levels within individual cells to understand the mechanism of clonal expansion. Heteroplasmy is reflected in a mosaic distribution of cytochrome c oxidase (COX)-deficient muscle fibers. We applied droplet digital PCR (ddPCR) to single muscle fibers collected by laser-capture microdissection (LCM) from muscle biopsies of patients with different paradigms of mitochondrial disease, characterized by the accumulation of single or multiple mtDNA deletions. By combining these two sensitive approaches, ddPCR and LCM, we document different models of clonal expansion in patients with single and multiple mtDNA deletions, implicating different mechanisms and time points for the development of COX deficiency in these molecularly distinct mitochondrial cytopathies.
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40
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Droplet digital PCR shows the D-Loop to be an error prone locus for mitochondrial DNA copy number determination. Sci Rep 2018; 8:11392. [PMID: 30061621 PMCID: PMC6065360 DOI: 10.1038/s41598-018-29621-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/13/2018] [Indexed: 02/07/2023] Open
Abstract
Absolute quantification of mitochondrial DNA copy number (mCN) provides important insights in many fields of research including cancer, cardiovascular and reproductive health. Droplet digital PCR (ddPCR) natively reports absolute copy number, and we have developed a single-dye, multiplex assay to measure rat mCN that is accurate, precise and affordable. We demonstrate simple methods to optimize this assay and to determine nuclear reference pseudogene copy number to extend the range of mCN that can be measured with this assay. We evaluated two commonly used mitochondrial DNA reference loci to determine mCN, the ND1 gene and the D-Loop. Harnessing the absolute measures of ddPCR, we found that the D-Loop amplifies with a copy number of ~1.0–1.5 relative to other sites on the mitochondrial genome. This anomalous copy number varied significantly between rats and tissues (aorta, brain, heart, liver, soleus muscle). We advocate for avoiding the D-Loop as a mitochondrial reference in future studies of mCN. Further, we report a novel approach to quantifying immunolabelled mitochondrial DNA that provides single-cell estimates of mCN that closely agree with the population analyses by ddPCR. The combination of these assays represents a cost-effective and powerful suite of tools to study mCN.
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41
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Bahder BW, Helmick EE, Mou DF, Harrison NA, Davis R. Digital PCR Technology for Detection of Palm-Infecting Phytoplasmas Belonging to Group 16SrIV that Occur in Florida. PLANT DISEASE 2018; 102:1008-1014. [PMID: 30673395 DOI: 10.1094/pdis-06-17-0787-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Phytoplasmas are an economically important group of plant pathogens that negatively impact a wide variety of plants in agricultural and natural ecosystems. In Florida, palm trees are essential elements in the nursery and landscaping industries that suffer from diseases caused by phytoplasmas that are related to each other but are classified in two different subgroups, 16SrIV-A and 16SrIV-D. In this study, a TaqMan assay was developed for digital polymerase chain reaction (dPCR) to detect both palm-infecting phytoplasmas found in Florida. When compared with real-time PCR assays and nested PCR assays, dPCR was capable of detecting the phytoplasmas at much lower concentrations than was possible by using real-time PCR and nested PCR. Additionally, the assay was capable of detecting 16SrIV-B phytoplasma as well as isolates representing the 16SrI and 16SrIII phytoplasma groups. Due to sequence identity of primer annealing regions across diverse phytoplasmas, the assay is likely to be successful for detection of a wide variety of phytoplasmas. The increased sensitivity of this dPCR assay over real-time PCR will allow for earlier detection of phytoplasma infection in palm trees, as well as for screening of salivary glands of candidate insect vector species. These advantages should aid timely management decisions to reduce disease spread and rapid determination of phytoplasma transmission by vectors.
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Affiliation(s)
- Brian W Bahder
- Department of Entomology and Nematology, University of Florida, Fort Lauderdale Research and Education Center (FLREC), Davie 33314-7719
| | - Ericka E Helmick
- Department of Entomology and Nematology, University of Florida, Fort Lauderdale Research and Education Center (FLREC), Davie 33314-7719
| | - De-Fen Mou
- Department of Entomology and Nematology, University of Florida, Fort Lauderdale Research and Education Center (FLREC), Davie 33314-7719
| | | | - Robert Davis
- Molecular Plant Pathology Laboratory, United States Department of Agriculture-Agricultural Research Service, Beltsville, MD 20705
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42
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Howlett EH, Jensen N, Belmonte F, Zafar F, Hu X, Kluss J, Schüle B, Kaufman BA, Greenamyre JT, Sanders LH. LRRK2 G2019S-induced mitochondrial DNA damage is LRRK2 kinase dependent and inhibition restores mtDNA integrity in Parkinson's disease. Hum Mol Genet 2018; 26:4340-4351. [PMID: 28973664 DOI: 10.1093/hmg/ddx320] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are associated with increased risk for developing Parkinson's disease (PD). Previously, we found that LRRK2 G2019S mutation carriers have increased mitochondrial DNA (mtDNA) damage and after zinc finger nuclease-mediated gene mutation correction, mtDNA damage was no longer detectable. While the mtDNA damage phenotype can be unambiguously attributed to the LRRK2 G2019S mutation, the underlying mechanism(s) is unknown. Here, we examine the role of LRRK2 kinase function in LRRK2 G2019S-mediated mtDNA damage, using both genetic and pharmacological approaches in cultured neurons and PD patient-derived cells. Expression of LRRK2 G2019S induced mtDNA damage in primary rat midbrain neurons, but not in cortical neuronal cultures. In contrast, the expression of LRRK2 wild type or LRRK2 D1994A mutant (kinase dead) had no effect on mtDNA damage in either midbrain or cortical neuronal cultures. In addition, human LRRK2 G2019S patient-derived lymphoblastoid cell lines (LCL) demonstrated increased mtDNA damage relative to age-matched controls. Importantly, treatment of LRRK2 G2019S expressing midbrain neurons or patient-derived LRRK2 G2019S LCLs with the LRRK2 kinase inhibitor GNE-7915, either prevented or restored mtDNA damage to control levels. These findings support the hypothesis that LRRK2 G2019S-induced mtDNA damage is LRRK2 kinase activity dependent, uncovering a novel pathological role for this kinase. Blocking or reversing mtDNA damage via LRRK2 kinase inhibition or other therapeutic approaches may be useful to slow PD-associated pathology.
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Affiliation(s)
- Evan H Howlett
- Department of Neurology, Pittsburgh Institute for Neurodegenerative Diseases
| | - Nicholas Jensen
- Department of Neurology, Pittsburgh Institute for Neurodegenerative Diseases
| | - Frances Belmonte
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Faria Zafar
- Parkinson's Institute and Clinical Center, Sunnyvale, CA 94085, USA
| | - Xiaoping Hu
- Department of Neurology, Pittsburgh Institute for Neurodegenerative Diseases
| | - Jillian Kluss
- Department of Neurology, Pittsburgh Institute for Neurodegenerative Diseases
| | - Birgitt Schüle
- Parkinson's Institute and Clinical Center, Sunnyvale, CA 94085, USA
| | - Brett A Kaufman
- Department of Medicine, Center for Metabolism and Mitochondrial Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - J T Greenamyre
- Department of Neurology, Pittsburgh Institute for Neurodegenerative Diseases
| | - Laurie H Sanders
- Department of Neurology, Duke University Medical Center, Durham, NC 27710, USA
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43
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Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations. Molecules 2018; 23:molecules23020323. [PMID: 29401641 PMCID: PMC6017848 DOI: 10.3390/molecules23020323] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
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44
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Guha M, Srinivasan S, Raman P, Jiang Y, Kaufman BA, Taylor D, Dong D, Chakrabarti R, Picard M, Carstens RP, Kijima Y, Feldman M, Avadhani NG. Aggressive triple negative breast cancers have unique molecular signature on the basis of mitochondrial genetic and functional defects. Biochim Biophys Acta Mol Basis Dis 2018; 1864:1060-1071. [PMID: 29309924 DOI: 10.1016/j.bbadis.2018.01.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 12/05/2017] [Accepted: 01/02/2018] [Indexed: 12/15/2022]
Abstract
Metastatic breast cancer is a leading cause of cancer-related deaths in women worldwide. Patients with triple negative breast cancer (TNBCs), a highly aggressive tumor subtype, have a particularly poor prognosis. Multiple reports demonstrate that altered content of the multicopy mitochondrial genome (mtDNA) in primary breast tumors correlates with poor prognosis. We earlier reported that mtDNA copy number reduction in breast cancer cell lines induces an epithelial-mesenchymal transition associated with metastasis. However, it is unknown whether the breast tumor subtypes (TNBC, Luminal and HER2+) differ in the nature and amount of mitochondrial defects and if mitochondrial defects can be used as a marker to identify tumors at risk for metastasis. By analyzing human primary tumors, cell lines and the TCGA dataset, we demonstrate a high degree of variability in mitochondrial defects among the tumor subtypes and TNBCs, in particular, exhibit higher frequency of mitochondrial defects, including reduced mtDNA content, mtDNA sequence imbalance (mtRNR1:ND4), impaired mitochondrial respiration and metabolic switch to glycolysis which is associated with tumorigenicity. We identified that genes involved in maintenance of mitochondrial structural and functional integrity are differentially expressed in TNBCs compared to non-TNBC tumors. Furthermore, we identified a subset of TNBC tumors that contain lower expression of epithelial splicing regulatory protein (ESRP)-1, typical of metastasizing cells. The overall impact of our findings reported here is that mitochondrial heterogeneity among TNBCs can be used to identify TNBC patients at risk of metastasis and the altered metabolism and metabolic genes can be targeted to improve chemotherapeutic response.
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Affiliation(s)
- Manti Guha
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, USA.
| | - Satish Srinivasan
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, USA
| | - Pichai Raman
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, USA; Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, USA
| | - Yuefu Jiang
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Brett A Kaufman
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Deanne Taylor
- Department of Biomedical and Health Informatics, The Children's Hospital of Philadelphia, Philadelphia, USA; Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, USA
| | - Dawei Dong
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, USA
| | - Rumela Chakrabarti
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, USA
| | - Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY, USA
| | - Russ P Carstens
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Yuko Kijima
- Kagoshima University, Department of Digestive, Breast and Thyroid Surgery, 8-35-1 Sakuragaoka, Kagoshima City 890-8544, Japan
| | - Mike Feldman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, USA
| | - Narayan G Avadhani
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, USA
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45
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Ren M, Lin H, Chen S, Yang M, An W, Wang Y, Xue C, Sun Y, Yan Y, Hu J. Detection of pseudorabies virus by duplex droplet digital PCR assay. J Vet Diagn Invest 2017; 30:105-112. [PMID: 29148297 DOI: 10.1177/1040638717743281] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Aujeszky's disease, caused by pseudorabies virus (PRV), has damaged the economy of the Chinese swine industry. A large number of PRV gene-deleted vaccines have been constructed based on deletion of the glycoprotein E ( gE) gene combined with other virulence-related gene deletions, such as thymidine kinase ( TK), whereas PRV wild-type strains contain an intact gE gene. We developed a sensitive duplex droplet digital PCR (ddPCR) assay to rapidly detect PRV wild-type isolates and gE gene-deleted viral vaccines. We compared this assay with a TaqMan real-time PCR (qPCR) using the same primers and probes. Both assays exhibited good linearity and repeatability; however, ddPCR maintained linearity at extremely low concentrations, whereas qPCR did not. Based on positive results for both gE and gB, the detection limit of ddPCR was found to be 4.75 copies/µL in contrast of 76 copies/µL for qPCR, showing that ddPCR provided a 16-fold improvement in sensitivity. In addition, no nonspecific amplification was shown in specificity testing, and the PRV wild-type was distinguished from a gE-deleted strain. The ddPCR was more sensitive when analyzing clinical serum samples. Thus, ddPCR may become an appropriate detection platform for PRV.
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Affiliation(s)
- Meishen Ren
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Hua Lin
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Shijie Chen
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Miao Yang
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Wei An
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Yin Wang
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Changhua Xue
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Yinjie Sun
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Yubao Yan
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
| | - Juan Hu
- College of Veterinary Medicine (Ren), Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province (Wang), Sichuan Agricultural University, Chengdu, China.,Sichuan Entry-Exit Inspection and Quarantine Bureau, Chengdu, China (Lin, Chen, Yang, An, Xue, Sun, Yan, Hu)
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46
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Lee CY, Park HJ, Park J, Park DK, Pyo H, Kim SC, Yun WS. Quantification of antigen by digital domain analysis of integrated nanogap biosensors. Biosens Bioelectron 2017; 97:273-277. [PMID: 28609718 DOI: 10.1016/j.bios.2017.06.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 05/25/2017] [Accepted: 06/07/2017] [Indexed: 11/18/2022]
Abstract
Nanogap biosensor shows a distinct conduction change upon sandwich-type immobilization of gold nanoparticle probes onto the gap region in the presence of target biomolecules. Although this large conductance change could be advantageous in distinguishing signal on or off devices, since the extent of conductance change is quite irregular even at the same analyte concentrations, it fails to extract quantitative information from its level of conductance change. In other words, the conductance change of a single device does not reflect the concentration of the target molecule. In this study, we introduce an alternative approach of interpreting the concentration of target molecules using digital domain analysis of integrated nanogap devices, where the fraction of signal-on-devices, or on-device-percentage (ODP), was translated into the concentration of the target molecule. The ODP was found to be closely related to the number density of the immobilized probes and, therefore, to be an excellent measure of the analyte concentration, which was demonstrated in the immuno-selective detection and quantification of influenza A hemagglutinin and prostate specific antigen.
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Affiliation(s)
- Cho Yeon Lee
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon, Gyeonggi-Do 440-746, Republic of Korea
| | - Hyung Ju Park
- Bio-Medical IT Convergence Research Department, Electronics and Telecommunications Research Institute (ETRI), Daejeon 305-700, Republic of Korea
| | - Jimin Park
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon, Gyeonggi-Do 440-746, Republic of Korea
| | - Dae Keun Park
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon, Gyeonggi-Do 440-746, Republic of Korea
| | - Hannah Pyo
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon, Gyeonggi-Do 440-746, Republic of Korea
| | - Seok Cheol Kim
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon, Gyeonggi-Do 440-746, Republic of Korea
| | - Wan Soo Yun
- Department of Chemistry, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon, Gyeonggi-Do 440-746, Republic of Korea.
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47
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Herbst A, Widjaja K, Nguy B, Lushaj EB, Moore TM, Hevener AL, McKenzie D, Aiken JM, Wanagat J. Digital PCR Quantitation of Muscle Mitochondrial DNA: Age, Fiber Type, and Mutation-Induced Changes. J Gerontol A Biol Sci Med Sci 2017; 72:1327-1333. [PMID: 28460005 DOI: 10.1093/gerona/glx058] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 03/21/2017] [Indexed: 01/07/2023] Open
Abstract
Definitive quantitation of mitochondrial DNA (mtDNA) and mtDNA deletion mutation abundances would help clarify the role of mtDNA instability in aging. To more accurately quantify mtDNA, we applied the emerging technique of digital polymerase chain reaction to individual muscle fibers and muscle homogenates from aged rodents. Individual fiber mtDNA content correlated with fiber type and decreased with age. We adapted a digital polymerase chain reaction deletion assay that was accurate in mixing experiments to a mutation frequency of 0.03% and quantitated an age-induced increase in deletion frequency from rat muscle homogenates. Importantly, the deletion frequency measured in muscle homogenates strongly correlated with electron transport chain-deficient fiber abundance determined by histochemical analyses. These data clarify the temporal accumulation of mtDNA deletions that lead to electron chain-deficient fibers, a process culminating in muscle fiber loss.
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Affiliation(s)
- Allen Herbst
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Canada
| | - Kevin Widjaja
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Beatrice Nguy
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Entela B Lushaj
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison
| | - Timothy M Moore
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Andrea L Hevener
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
| | - Debbie McKenzie
- Department of Biological Sciences, University of Alberta, Edmonton, Canada
| | - Judd M Aiken
- Department of Agricultural, Food and Nutritional Sciences, University of Alberta, Edmonton, Canada
| | - Jonathan Wanagat
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles
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48
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Madic J, Zocevic A, Senlis V, Fradet E, Andre B, Muller S, Dangla R, Droniou ME. Three-color crystal digital PCR. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 10:34-46. [PMID: 27990348 PMCID: PMC5154636 DOI: 10.1016/j.bdq.2016.10.002] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 10/23/2016] [Accepted: 10/24/2016] [Indexed: 01/03/2023]
Abstract
Digital PCR is an exciting new field for molecular analysis, allowing unprecedented precision in the quantification of nucleic acids, as well as the fine discrimination of rare molecular events in complex samples. We here present a novel technology for digital PCR, Crystal Digital PCR™, which relies on the use of a single chip to partition samples into 2D droplet arrays, which are then subjected to thermal cycling and finally read using a three-color fluorescence scanning device. This novel technology thus allows three-color multiplexing, which entails a different approach to data analysis. In the present publication, we present this innovative workflow, which is both fast and user-friendly, and discuss associated data analysis issue, such as fluorescence spillover compensation and data representation. Lastly, we also present proof-of-concept of this three-color detection system, using a quadriplex assay for the detection of EGFR mutations L858R, L861Q and T790M.
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Affiliation(s)
- J Madic
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - A Zocevic
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - V Senlis
- Ecole Polytechnique, Route de Saclay, 91128 Palaiseau, France
| | - E Fradet
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - B Andre
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - S Muller
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - R Dangla
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
| | - M E Droniou
- Stilla Technologies, 1 Mail du Professeur Georges Mathé, 94800 Villejuif, France
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49
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Cao L, Cui X, Hu J, Li Z, Choi JR, Yang Q, Lin M, Ying Hui L, Xu F. Advances in digital polymerase chain reaction (dPCR) and its emerging biomedical applications. Biosens Bioelectron 2016; 90:459-474. [PMID: 27818047 DOI: 10.1016/j.bios.2016.09.082] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/18/2022]
Abstract
Since the invention of polymerase chain reaction (PCR) in 1985, PCR has played a significant role in molecular diagnostics for genetic diseases, pathogens, oncogenes and forensic identification. In the past three decades, PCR has evolved from end-point PCR, through real-time PCR, to its current version, which is the absolute quantitive digital PCR (dPCR). In this review, we first discuss the principles of all key steps of dPCR, i.e., sample dispersion, amplification, and quantification, covering commercialized apparatuses and other devices still under lab development. We highlight the advantages and disadvantages of different technologies based on these steps, and discuss the emerging biomedical applications of dPCR. Finally, we provide a glimpse of the existing challenges and future perspectives for dPCR.
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Affiliation(s)
- Lei Cao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Xingye Cui
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jie Hu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Zedong Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Jane Ru Choi
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Qingzhen Yang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Min Lin
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China
| | - Li Ying Hui
- Foundation of State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing 100094, PR China
| | - Feng Xu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, PR China; Bioinspired Engineering and Biomechanics Center (BEBC), Xi'an Jiaotong University, Xi'an 710049, PR China.
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50
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Abstract
Clonal expansion of mtDNA deletions compromises mitochondrial function in human disease and aging, but how deleterious mtDNA genomes propagate has remained unclear. In this issue (Gitschlag et al., 2016) and in a recent Nature publication, C. elegans studies implicate the mitochondrial unfolded protein response (UPR(mt)) and offer mechanistic insights into this process.
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Affiliation(s)
- Martin Picard
- Department of Psychiatry, Division of Behavioral Medicine, Columbia University Medical Center, New York, NY 10032, USA; Department of Neurology and Columbia Translational Neuroscience Initiative, H. Houston Merritt Center, Columbia University Medical Center, New York, NY 10032, USA; Wellcome Trust Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Amy E Vincent
- Wellcome Trust Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Doug M Turnbull
- Wellcome Trust Centre for Mitochondrial Research and Newcastle Centre for Ageing and Vitality, Institute of Neurosciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK.
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