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Kaur P, Nazeer N, Gurjar V, Tiwari R, Mishra PK. Nanophotonic waveguide-based sensing of circulating cell-free mitochondrial DNA: implications for personalized medicine. Drug Discov Today 2024; 29:104086. [PMID: 38960132 DOI: 10.1016/j.drudis.2024.104086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 06/20/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Circulating cell-free mitochondrial DNA (ccf-mtDNA) has emerged as a promising biomarker, with potential implications for disease diagnosis. Changes in mtDNA, such as deletions, mutations or variations in the number of copies, have been associated with mitochondrial disorders, heart diseases, cancer and age-related non-communicable diseases. Previous methods, such as polymerase chain reaction-based approaches, next-generation sequencing and imaging-based techniques, have shown improved accuracy in identifying rare mtDNA variants or mutations, but they have limitations. This article explains the basic principles and benefits of using planar optical waveguide-based detection devices, which represent an advanced approach in the field of sensing.
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Affiliation(s)
- Prasan Kaur
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Nazim Nazeer
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Vikas Gurjar
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Rajnarayan Tiwari
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India
| | - Pradyumna Kumar Mishra
- Division of Environmental Biotechnology, Genetics & Molecular Biology, ICMR-National Institute for Research in Environmental Health (NIREH), Bhopal, India.
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2
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Zhu S, Li Y, Zhang F, Xiong C, Gao H, Yao Y, Qian W, Ding C, Chen S. Raman spectromics method for fast and label-free genotype screening. BIOMEDICAL OPTICS EXPRESS 2023; 14:3072-3085. [PMID: 37342689 PMCID: PMC10278603 DOI: 10.1364/boe.493524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/22/2023] [Accepted: 05/22/2023] [Indexed: 06/23/2023]
Abstract
It is now understood that genes and their various mutations are associated with the onset and progression of diseases. However, routine genetic testing techniques are limited by their high cost, time consumption, susceptibility to contamination, complex operation, and data analysis difficulties, rendering them unsuitable for genotype screening in many cases. Therefore, there is an urgent need to develop a rapid, sensitive, user-friendly, and cost-effective method for genotype screening and analysis. In this study, we propose and investigate a Raman spectroscopic method for achieving fast and label-free genotype screening. The method was validated using spontaneous Raman measurements of wild-type Cryptococcus neoformans and its six mutants. An accurate identification of different genotypes was achieved by employing a one-dimensional convolutional neural network (1D-CNN), and significant correlations between metabolic changes and genotypic variations were revealed. Genotype-specific regions of interest were also localized and visualized using a gradient-weighted class activation mapping (Grad-CAM)-based spectral interpretable analysis method. Furthermore, the contribution of each metabolite to the final genotypic decision-making was quantified. The proposed Raman spectroscopic method demonstrated huge potential for fast and label-free genotype screening and analysis of conditioned pathogens.
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Affiliation(s)
- Shanshan Zhu
- Research Institute of Medical and Biological Engineering, Ningbo University, Ningbo 315211, China
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
- Health Science Center, Ningbo University, Ningbo 315211, China
- Key Laboratory of OptoElectronic Science and Technology for Medicine of Ministry of Education, Fujian Provincial Key Laboratory of Photonics Technology, Fujian Normal University, Fuzhou 350117, China
| | - Yanjian Li
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China
| | - Fengdi Zhang
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
| | - Changchun Xiong
- College of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, China
| | - Han Gao
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
| | - Yudong Yao
- Research Institute of Medical and Biological Engineering, Ningbo University, Ningbo 315211, China
| | - Wei Qian
- Research Institute of Medical and Biological Engineering, Ningbo University, Ningbo 315211, China
| | - Chen Ding
- College of Life and Health Sciences, Northeastern University, Shenyang 110169, China
| | - Shuo Chen
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110169, China
- Key Laboratory of Intelligent Computing in Medical Image, Ministry of Education, Shenyang 110169, China
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3
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Memon AA, Vats S, Sundquist J, Li Y, Sundquist K. Mitochondrial DNA Copy Number: Linking Diabetes and Cancer. Antioxid Redox Signal 2022; 37:1168-1190. [PMID: 36169625 DOI: 10.1089/ars.2022.0100] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Recent Advances: Various studies have suggested that mitochondrial DNA copy number (mtDNA-CN), a surrogate biomarker of mitochondrial dysfunction, is an easily quantifiable biomarker for chronic diseases, including diabetes and cancer. However, current knowledge is limited, and the results are controversial. This has been attributed mainly to methodology and study design. Critical Issues: The incidence of diabetes and cancer has increased significantly in recent years. Moreover, type 2 diabetes (T2D) has been shown to be a risk factor for cancer. mtDNA-CN has been associated with both T2D and cancer. However, it is not known whether mtDNA-CN plays any role in the association between T2D and cancer. Significance: In this review, we have discussed mtDNA-CN in diabetes and cancer, and reviewed the literature and methodology used in published studies so far. Based on the literature review, we have speculated how mtDNA-CN may act as a link between diabetes and cancer. Furthermore, we have provided some recommendations for reliable translation of mtDNA-CN as a biomarker. Future Directions: Further research is required to elucidate the role of mtDNA-CN in the association between T2D and cancer. If established, early lifestyle interventions, such as physical activity and diet control that improve mitochondrial function, may help preventing cancer in patients with T2D. Antioxid. Redox Signal. 37, 1168-1190.
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Affiliation(s)
- Ashfaque A Memon
- Center for Primary Health Care Research, Lund University/Region Skåne, Malmö, Sweden
| | - Sakshi Vats
- Center for Primary Health Care Research, Lund University/Region Skåne, Malmö, Sweden
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University/Region Skåne, Malmö, Sweden
| | - Yanni Li
- Center for Primary Health Care Research, Lund University/Region Skåne, Malmö, Sweden
| | - Kristina Sundquist
- Center for Primary Health Care Research, Lund University/Region Skåne, Malmö, Sweden
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4
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Tintos-Hernández JA, Santana A, Keller KN, Ortiz-González XR. Lysosomal dysfunction impairs mitochondrial quality control and is associated with neurodegeneration in TBCK encephaloneuronopathy. Brain Commun 2021; 3:fcab215. [PMID: 34816123 PMCID: PMC8603245 DOI: 10.1093/braincomms/fcab215] [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: 08/03/2020] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 11/14/2022] Open
Abstract
Biallelic variants in the TBCK gene cause intellectual disability with remarkable clinical variability, ranging from static encephalopathy to progressive neurodegeneration (TBCK-Encephaloneuronopathy). The biological factors underlying variable disease penetrance remain unknown. Since previous studies had suggested aberrant autophagy, we tested whether mitophagy and mitochondrial function are altered in TBCK−/− fibroblasts derived from patients exhibiting variable clinical severity. Our data show significant accumulation of mitophagosomes, reduced mitochondrial respiratory capacity and mitochondrial DNA content, suggesting impaired mitochondrial quality control. Furthermore, the degree of mitochondrial dysfunction correlates with a neurodegenerative clinical course. Since mitophagy ultimately depends on lysosomal degradation, we also examined lysosomal function. Our data show that lysosomal proteolytic function is significantly reduced in TBCK−/− fibroblasts. Moreover, acidifying lysosomal nanoparticles rescue the mitochondrial respiratory defects in fibroblasts, suggesting impaired mitochondrial quality control secondary to lysosomal dysfunction. Our data provide insight into the disease mechanisms of TBCK Encephaloneuronopathy and the potential relevance of mitochondrial function as a biomarker beyond primary mitochondrial disorders. It also supports the benefit of lysosomal acidification strategies for disorders of impaired lysosomal degradation affecting mitochondrial quality control.
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Affiliation(s)
- Jesus A Tintos-Hernández
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Adrian Santana
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Kierstin N Keller
- Department of Genetics, Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xilma R Ortiz-González
- Division of Neurology and Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Epilepsy Neurogenetics Initiative and Department of Neurology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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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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6
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Oresta B, Pozzi C, Braga D, Hurle R, Lazzeri M, Colombo P, Frego N, Erreni M, Faccani C, Elefante G, Barcella M, Guazzoni G, Rescigno M. Mitochondrial metabolic reprogramming controls the induction of immunogenic cell death and efficacy of chemotherapy in bladder cancer. Sci Transl Med 2021; 13:13/575/eaba6110. [PMID: 33408185 DOI: 10.1126/scitranslmed.aba6110] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 10/15/2020] [Indexed: 12/22/2022]
Abstract
Although chemotherapeutic agents have been used for decades, the mechanisms of action, mechanisms of resistance, and the best treatment schedule remain elusive. Mitomycin C (MMC) is the gold standard treatment for non-muscle-invasive bladder cancer (NMIBC). However, it is effective only in a subset of patients, suggesting that, aside from cytotoxicity, other mechanisms could be involved in mediating the success of the treatment. Here, we showed that MMC promotes immunogenic cell death (ICD) and in vivo tumor protection. MMC-induced ICD relied on metabolic reprogramming of tumor cells toward increased oxidative phosphorylation. This favored increased mitochondrial permeability leading to the cytoplasmic release of mitochondrial DNA, which activated the inflammasome for efficient IL-1β (interleukin-1β) secretion that promoted dendritic cell maturation. Resistance to ICD was associated with mitochondrial dysfunction related to low abundance of complex I of the respiratory chain. Analysis of complex I in patient tumors indicated that low abundance of this mitochondrial complex was associated with recurrence incidence after chemotherapy in patients with NMIBC. The identification of mitochondria-mediated ICD as a mechanism of action of MMC offers opportunities to optimize bladder cancer management and provides potential markers of treatment efficacy that could be used for patient stratification.
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Affiliation(s)
- Bianca Oresta
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Chiara Pozzi
- Department of Experimental Oncology, European Institute of Oncology-IRCCS, via Ripamonti 435, 20141 Milan, Italy
| | - Daniele Braga
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Rodolfo Hurle
- Department of Urology, Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Massimo Lazzeri
- Department of Urology, Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Piergiuseppe Colombo
- Department of Pathology, Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Nicola Frego
- Department of Urology, Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Marco Erreni
- Unit of Advanced Optical Microscopy, Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Cristina Faccani
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Grazia Elefante
- Department of Pathology, Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy
| | - Matteo Barcella
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, 20142 Milan, Italy
| | - Giorgio Guazzoni
- Department of Urology, Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy.,Humanitas University, Department of Biomedical Sciences, via Rita Levi Montalcini 4, 20090 Pieve Emanuele (Milan), Italy
| | - Maria Rescigno
- Humanitas Clinical and Research Center-IRCCS, via Manzoni 56, 20089 Rozzano (Milan), Italy. .,Humanitas University, Department of Biomedical Sciences, via Rita Levi Montalcini 4, 20090 Pieve Emanuele (Milan), Italy
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7
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Jiang M, Xie X, Zhu X, Jiang S, Milenkovic D, Misic J, Shi Y, Tandukar N, Li X, Atanassov I, Jenninger L, Hoberg E, Albarran-Gutierrez S, Szilagyi Z, Macao B, Siira SJ, Carelli V, Griffith JD, Gustafsson CM, Nicholls TJ, Filipovska A, Larsson NG, Falkenberg M. The mitochondrial single-stranded DNA binding protein is essential for initiation of mtDNA replication. SCIENCE ADVANCES 2021; 7:eabf8631. [PMID: 34215584 PMCID: PMC11057760 DOI: 10.1126/sciadv.abf8631] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
We report a role for the mitochondrial single-stranded DNA binding protein (mtSSB) in regulating mitochondrial DNA (mtDNA) replication initiation in mammalian mitochondria. Transcription from the light-strand promoter (LSP) is required both for gene expression and for generating the RNA primers needed for initiation of mtDNA synthesis. In the absence of mtSSB, transcription from LSP is strongly up-regulated, but no replication primers are formed. Using deep sequencing in a mouse knockout model and biochemical reconstitution experiments with pure proteins, we find that mtSSB is necessary to restrict transcription initiation to optimize RNA primer formation at both origins of mtDNA replication. Last, we show that human pathological versions of mtSSB causing severe mitochondrial disease cannot efficiently support primer formation and initiation of mtDNA replication.
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Affiliation(s)
- Min Jiang
- Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Xie Xie
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Xuefeng Zhu
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Shan Jiang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Dusanka Milenkovic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Jelena Misic
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Yonghong Shi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Nirwan Tandukar
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Xinping Li
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Ilian Atanassov
- Proteomics Core Facility, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Louise Jenninger
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Emily Hoberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Sara Albarran-Gutierrez
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Zsolt Szilagyi
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Bertil Macao
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences (DIBINEM), University of Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Biosciences Institute, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research and ARC Centre of Excellence in Synthetic Biology, Nedlands, WA 6009, Australia
- Telethon Kids Institute, Northern Entrance, Perth Children's Hospital, 15 Hospital Avenue, Nedlands, WA, Australia
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden.
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden.
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8
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Filograna R, Mennuni M, Alsina D, Larsson NG. Mitochondrial DNA copy number in human disease: the more the better? FEBS Lett 2020; 595:976-1002. [PMID: 33314045 PMCID: PMC8247411 DOI: 10.1002/1873-3468.14021] [Citation(s) in RCA: 207] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 12/19/2022]
Abstract
Most of the genetic information has been lost or transferred to the nucleus during the evolution of mitochondria. Nevertheless, mitochondria have retained their own genome that is essential for oxidative phosphorylation (OXPHOS). In mammals, a gene‐dense circular mitochondrial DNA (mtDNA) of about 16.5 kb encodes 13 proteins, which constitute only 1% of the mitochondrial proteome. Mammalian mtDNA is present in thousands of copies per cell and mutations often affect only a fraction of them. Most pathogenic human mtDNA mutations are recessive and only cause OXPHOS defects if present above a certain critical threshold. However, emerging evidence strongly suggests that the proportion of mutated mtDNA copies is not the only determinant of disease but that also the absolute copy number matters. In this review, we critically discuss current knowledge of the role of mtDNA copy number regulation in various types of human diseases, including mitochondrial disorders, neurodegenerative disorders and cancer, and during ageing. We also provide an overview of new exciting therapeutic strategies to directly manipulate mtDNA to restore OXPHOS in mitochondrial diseases.
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Affiliation(s)
- Roberta Filograna
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Mara Mennuni
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - David Alsina
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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9
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An in Situ Atlas of Mitochondrial DNA in Mammalian Tissues Reveals High Content in Stem and Proliferative Compartments. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1565-1579. [PMID: 32304697 DOI: 10.1016/j.ajpath.2020.03.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 02/25/2020] [Accepted: 03/19/2020] [Indexed: 02/07/2023]
Abstract
Mitochondria regulate ATP production, metabolism, and cell death. Alterations in mitochondrial DNA (mtDNA) sequence and copy number are implicated in aging and organ dysfunction in diverse inherited and sporadic diseases. Because most measurements of mtDNA use homogenates of complex tissues, little is known about cell-type-specific mtDNA copy number heterogeneity in normal physiology, aging, and disease. Thus, the precise cell types whose loss of mitochondrial activity and altered mtDNA copy number that result in organ dysfunction in aging and disease have often not been clarified. Here, an in situ hybridization approach to generate a single-cell-resolution atlas of mtDNA content in mammalian tissues was validated. In hierarchically organized self-renewing tissues, higher levels of mtDNA were observed in stem/proliferative compartments compared with differentiated compartments. Striking zonal patterns of mtDNA levels in the liver reflected the known oxygen tension gradient. In the kidney, proximal and distal tubules had markedly higher mtDNA levels compared with cells within glomeruli and collecting duct epithelial cells. In mice, decreased mtDNA levels were visualized in renal tubules as a function of aging, which was prevented by calorie restriction. This study provides a novel approach for quantifying species- and cell-type-specific mtDNA copy number and dynamics in any normal or diseased tissue that can be used for monitoring the effects of interventions in animal and human studies.
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10
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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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11
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Successful Treatment of Mitochondrial Toxicity in an HIV-Positive Patient After Liver Transplantation. Transplant Proc 2016; 47:2771-4. [PMID: 26680091 DOI: 10.1016/j.transproceed.2015.10.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 10/01/2015] [Indexed: 11/20/2022]
Abstract
Liver transplantation in patients infected with the human immunodeficiency virus (HIV) has been increasingly performed with reasonable outcomes; however, medical management of both immunosuppression and antiretroviral therapy can be challenging owing to drug toxicities and interactions. Nucleoside reverse transcriptase inhibitors (NRTIs), a common backbone of highly active antiretroviral therapy (HAART), were the first class of effective antiretroviral drugs developed. NRTIs are commonly used for posttransplant HAART therapy and have a rare but fatal complication of mitochondrial toxicity, manifesting as severe lactic acidosis, hepatic steatosis, and lipoatrophy. Herein, we have reported on the first known successful treatment of severe mitochondrial toxicity secondary to NRTIs in an HIV-infected transplant recipient.
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12
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Davis CHO, Kim KY, Bushong EA, Mills EA, Boassa D, Shih T, Kinebuchi M, Phan S, Zhou Y, Bihlmeyer NA, Nguyen JV, Jin Y, Ellisman MH, Marsh-Armstrong N. Transcellular degradation of axonal mitochondria. Proc Natl Acad Sci U S A 2014; 111:9633-8. [PMID: 24979790 PMCID: PMC4084443 DOI: 10.1073/pnas.1404651111] [Citation(s) in RCA: 452] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
It is generally accepted that healthy cells degrade their own mitochondria. Here, we report that retinal ganglion cell axons of WT mice shed mitochondria at the optic nerve head (ONH), and that these mitochondria are internalized and degraded by adjacent astrocytes. EM demonstrates that mitochondria are shed through formation of large protrusions that originate from otherwise healthy axons. A virally introduced tandem fluorophore protein reporter of acidified mitochondria reveals that acidified axonal mitochondria originating from the retinal ganglion cell are associated with lysosomes within columns of astrocytes in the ONH. According to this reporter, a greater proportion of retinal ganglion cell mitochondria are degraded at the ONH than in the ganglion cell soma. Consistently, analyses of degrading DNA reveal extensive mtDNA degradation within the optic nerve astrocytes, some of which comes from retinal ganglion cell axons. Together, these results demonstrate that surprisingly large proportions of retinal ganglion cell axonal mitochondria are normally degraded by the astrocytes of the ONH. This transcellular degradation of mitochondria, or transmitophagy, likely occurs elsewhere in the CNS, because structurally similar accumulations of degrading mitochondria are also found along neurites in superficial layers of the cerebral cortex. Thus, the general assumption that neurons or other cells necessarily degrade their own mitochondria should be reconsidered.
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Affiliation(s)
- Chung-ha O Davis
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Keun-Young Kim
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Eric A Bushong
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Elizabeth A Mills
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Daniela Boassa
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Tiffany Shih
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Mira Kinebuchi
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Sebastien Phan
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Yi Zhou
- Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Nathan A Bihlmeyer
- Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Judy V Nguyen
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
| | - Yunju Jin
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research, Center for Research in Biological Systems, Department of Neurosciences, University of California at San Diego, La Jolla, CA 92093
| | - Nicholas Marsh-Armstrong
- The Solomon H. Snyder Department of Neuroscience, The Johns Hopkins University School of Medicine, Baltimore, MD 21205;Hugo W. Moser Research Institute, Kennedy Krieger Institute, Baltimore, MD 21205; and
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Nieri D, Fioramonti M, Berardinelli F, Leone S, Cherubini R, De Nadal V, Gerardi S, Moreno S, Nardacci R, Tanzarella C, Antoccia A. Radiation response of chemically derived mitochondrial DNA-deficient AG01522 human primary fibroblasts. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 756:86-94. [DOI: 10.1016/j.mrgentox.2013.05.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 05/14/2013] [Indexed: 11/15/2022]
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Hayashi T, Lewis A, Hayashi E, Betenbaugh MJ, Su TP. Antigen retrieval to improve the immunocytochemistry detection of sigma-1 receptors and ER chaperones. Histochem Cell Biol 2011; 135:627-37. [PMID: 21573736 PMCID: PMC3155709 DOI: 10.1007/s00418-011-0811-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2011] [Indexed: 11/27/2022]
Abstract
Molecular chaperones localized at the endoplasmic reticulum (ER) lumen constitutively or cellular stress-dependently associate with a variety of proteins to promote their proper folding or to inhibit protein misfolding. ER chaperones preferentially form large complexes with co-chaperones and/or misfolded proteins in a highly crowded cellular environment that often hampers their detection by immunocytochemistry (ICC). This study establishes an antigen retrieval (AR) protocol to improve the ICC detection of ER chaperones in cultured cells using widely available antibodies against synthetic peptides. Among ten different antigen retrieval/fixation conditions, only the AR with Tris-HCl (pH 9.5) containing 6 M urea (80°C for 10 min) significantly improved the ICC detection of the novel ER chaperone sigma-1 receptor (Sig-1R) in Chinese hamster ovary cells. Extended fixation with 4% paraformaldehyde for 1 h effectively preserved the morphology of the ER under the AR condition. This method greatly enhanced the signal-to-noise ratio in Sig-1R ICC, thus allowing for semi-quantitative detection of protein upregulation under ER stress. The AR similarly improved the ICC detection of a series of other major ER chaperones, including BiP/GRP78, GRP94, calnexin, calreticulin, ERp57, protein disulfide isomerase, and cyclophilin B. The improved ICC methodology using the urea AR at 80°C may improve ICC of ER molecules as well as visualization of ER structure and substructures.
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Affiliation(s)
- Teruo Hayashi
- Cellular Stress Signaling Unit, Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, USA.
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15
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Regulation of axonal trafficking of cytochrome c oxidase IV mRNA. Mol Cell Neurosci 2010; 43:422-30. [PMID: 20144716 DOI: 10.1016/j.mcn.2010.01.009] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Revised: 01/20/2010] [Accepted: 01/26/2010] [Indexed: 01/10/2023] Open
Abstract
Trafficking and local translation of axonal mRNAs play a critical role in the development and function of this neuronal subcellular structural domain. In this report, we studied cytochrome c oxidase subunit IV (COXIV) mRNA trafficking into distal axons of primary superior cervical ganglia (SCG) neurons, and provided evidence that axonal trafficking and mitochondrial association of the mRNA are mediated by an element located in a 38bp-long, hairpin-loop forming region within the 3'UTR of the transcript. Our results also suggest that suppression of local translation of COXIV mRNA results in significant attenuation of axonal elongation. Taken together, the results provide the first evidence for the existence of a cis-acting axonal transport element within a nuclear-encoding mitochondrial gene, and demonstrate the importance of the axonal trafficking and local translation of nuclear-encoded mitochondrial mRNAs in axonal growth.
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Barker PE, Murthy M. Biomarker Validation for Aging: Lessons from mtDNA Heteroplasmy Analyses in Early Cancer Detection. Biomark Insights 2009; 4:165-79. [PMID: 20029650 PMCID: PMC2796862 DOI: 10.4137/bmi.s2253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The anticipated biological and clinical utility of biomarkers has attracted significant interest recently. Aging and early cancer detection represent areas active in the search for predictive and prognostic biomarkers. While applications differ, overlapping biological features, analytical technologies and specific biomarker analytes bear comparison. Mitochondrial DNA (mtDNA) as a biomarker in both biological models has been evaluated. However, it remains unclear whether mtDNA changes in aging and cancer represent biological relationships that are causal, incidental, or a combination of both. This article focuses on evaluation of mtDNA-based biomarkers, emerging strategies for quantitating mtDNA admixtures, and how current understanding of mtDNA in aging and cancer evolves with introduction of new technologies. Whether for cancer or aging, lessons from mtDNA based biomarker evaluations are several. Biological systems are inherently dynamic and heterogeneous. Detection limits for mtDNA sequencing technologies differ among methods for low-level DNA sequence admixtures in healthy and diseased states. Performance metrics of analytical mtDNA technology should be validated prior to application in heterogeneous biologically-based systems. Critical in evaluating biomarker performance is the ability to distinguish measurement system variance from inherent biological variance, because it is within the latter that background healthy variability as well as high-value, disease-specific information reside.
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Affiliation(s)
- Peter E. Barker
- Bioassay Methods Group, Biochemical Sciences Division, Bldg 227/B248, NIST, 100 Bureau Drive, Gaithersburg, Maryland
| | - Mahadev Murthy
- Division of Aging Biology (DAB), National Institute on Aging, 7201 Wisconsin Ave., GW 2C231, Bethesda, MD 20892.
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Lin CH, Sloan DD, Dang CH, Wagner T, Cabrera AJE, Tobin NH, Frenkel LM, Jerome KR. Assessment of mitochondrial toxicity by analysis of mitochondrial protein expression in mononuclear cells. CYTOMETRY PART B-CLINICAL CYTOMETRY 2009; 76:181-90. [PMID: 18823003 DOI: 10.1002/cyto.b.20458] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
BACKGROUND Real-time PCR has quantified decreased mitochondrial DNA levels in association with nucleoside reverse transcriptase inhibitor (NRTI) therapy of HIV-infected populations. However, real-time PCR is best suited to distinguish log differences in an analyte. In an effort to monitor individuals in more detail, we developed a flow cytometric assay to gauge mitochondrial function. METHODS Flow cytometric quantification of a mitochondrial DNA-encoded mitochondrial protein (cytochrome c oxidase subunit I (COX-I)) and a nuclear DNA-encoded mitochondrial protein [ATP synthase subunit D (Sub-D)] was optimized and validated. RESULTS Intra-assay and interassay variability was low using peripheral blood mononuclear cells (PBMCs) (CV of 6.15% for COX-I and 7.11% Sub-D, and 9.38% and 9.83% for COX-I and Sub-D, respectively). Mitochondrial protein depletion was evident with in vitro treatment of cells with ethidium bromide (EtBr) and zalcitabine (ddC). Mitochondrial protein expression in 40 healthy adults clustered tightly. Depletion of mitochondrial protein, however, was neither detected in cryopreserved PBMC from NRTI-treated children (n = 9) nor in adults with a history of symptoms consistent with mitochondrial toxicity or ongoing treatment with didanosine (ddI) or stavudine (d4T) (n = 51). CONCLUSIONS A validated flow cytometric assay allows simultaneous detection of mitochondrial DNA and nuclear DNA encoded proteins at the single cell level, offering a method to monitor for mitochondrial function. Prospective studies are required to evaluate whether mitochondrial protein loss is observed in at-risk patients prior to the onset of symptoms from mitochondrial dysfunction.
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Affiliation(s)
- Chen-Han Lin
- Vaccine and Infectious Disease Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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Shikuma CM, Gerschenson M, Chow D, Libutti DE, Willis JH, Murray J, Capaldi RA, Marusich M. Mitochondrial oxidative phosphorylation protein levels in peripheral blood mononuclear cells correlate with levels in subcutaneous adipose tissue within samples differing by HIV and lipoatrophy status. AIDS Res Hum Retroviruses 2008; 24:1255-62. [PMID: 18844460 DOI: 10.1089/aid.2007.0262] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Depletion of mitochondrial DNA (mtDNA) and mtDNA-encoded respiratory chain proteins in subcutaneous (SC) fat from patients with HIV lipoatrophy have clearly demonstrated the role of mitochondrial dysfunction in this syndrome. Research in HIV lipoatrophy, however, has been severely hampered by the lack of a suitable surrogate marker in blood or other easily obtained clinical specimens as fat biopsies are invasive and mtDNA levels in peripheral blood mononuclear cells (PBMC) do not consistently correlate with the disease process. We used a simple, rapid, quantitative 2-site dipstick immunoassay to measure OXPHOS enzymes Complex I (CI) and Complex IV (CIV), and rtPCR to measure mtDNA in 26 matched SC fat and PBMC specimens previously banked from individuals on potent antiretroviral (ARV) therapy with HIV lipoatrophy, on similar ARV therapy without lipoatrophy, and in HIV seronegative controls. Significant correlations were found between the respective PBMC and fat levels for both CI (r = 0.442, p = 0.024) and for CIV (r = 0.507, p = 0.008). Both CI and CIV protein levels were also significantly reduced in both PBMCs and fat in lipoatrophic subjects compared to HIV seronegative controls (p < or = 0.05), while a comparative reduction in mtDNA levels in lipoatrophic subjects was observed only in fat. We conclude that CI and CIV levels in PBMCs correlate to their respective levels in fat and may have utility as surrogate markers of mitochondrial dysfunction in lipoatrophy.
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Affiliation(s)
- Cecilia M. Shikuma
- Hawaii AIDS Clinical Research Program, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
- Department of Medicine, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
| | - Mariana Gerschenson
- Hawaii AIDS Clinical Research Program, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
- Department of Medicine, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
| | - Dominic Chow
- Hawaii AIDS Clinical Research Program, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
- Department of Medicine, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
- Department of Pediatrics, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
| | - Daniel E. Libutti
- Hawaii AIDS Clinical Research Program, John A. Burns School of Medicine, University of Hawaii–Manoa, Honolulu, Hawaii 96816
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