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Cheng Q, Liu QQ, Lu CA. A state-of-the-science review of using mitochondrial DNA copy number as a biomarker for environmental exposure. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123642. [PMID: 38402934 DOI: 10.1016/j.envpol.2024.123642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/06/2024] [Accepted: 02/22/2024] [Indexed: 02/27/2024]
Abstract
Mitochondria are bioenergetic, biosynthetic, and signaling organelles in eukaryotes, and contain their own genomes, mitochondrial DNA (mtDNA), to supply energy to cells by generating ATP via oxidative phosphorylation. Therefore, the threat to mitochondria' integrity and health resulting from environmental exposure could induce adverse health effects in organisms. In this review, we summarized the association between mtDNA copy number (mtDNAcn), and environmental exposures as reported in the literature. We conducted a literature search in the Web of Science using [Mitochondrial DNA copy number] and [Exposure] as two keywords and employed three selection criteria for the final inclusion of 97 papers for review. The consensus of data was that mtDNAcn could be used as a plausible biomarker for cumulative exposures to environmental chemical and physical agents. In order to furtherly expand the application of mtDNAcn in ecological and environmental health research, we suggested a series of algorithms aiming to standardize the calculation of mtDNAcn based on the PCR results in this review. We also discussed the pitfalls of using whole blood/plasma samples for mtDNAcn measurements and regard buccal cells a plausible and practical alternative. Finally, we recognized the importance of better understanding the mechanistic analysis and regulatory mechanism of mtDNAcn, in particular the signals release and regulation pathways. We believe that the development of using mtDNAcn as an exposure biomarker will revolutionize the evaluation of chronic sub-lethal toxicity of chemicals to organisms in ecological and environmental health research that has not yet been implemented.
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Affiliation(s)
- Qing Cheng
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Qing Qing Liu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China
| | - Chensheng Alex Lu
- College of Resources and Environment, Southwest University, Chongqing, 400715, People's Republic of China; School of Public Health, University of Washington, Seattle, WA, 98195, USA.
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Daneshkhah A, Prabhala S, Viswanathan P, Subramanian H, Lin J, Chang AS, Bharat A, Roy HK, Backman V. Early detection of lung cancer using artificial intelligence-enhanced optical nanosensing of chromatin alterations in field carcinogenesis. Sci Rep 2023; 13:13702. [PMID: 37608214 PMCID: PMC10444865 DOI: 10.1038/s41598-023-40550-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 08/12/2023] [Indexed: 08/24/2023] Open
Abstract
Supranucleosomal chromatin structure, including chromatin domain conformation, is involved in the regulation of gene expression and its dysregulation has been associated with carcinogenesis. Prior studies have shown that cells in the buccal mucosa carry a molecular signature of lung cancer among the cigarette-smoking population, the phenomenon known as field carcinogenesis or field of injury. Thus, we hypothesized that chromatin structural changes in buccal mucosa can be predictive of lung cancer. However, the small size of the chromatin chain (approximately 20 nm) folded into chromatin packing domains, themselves typically below 300 nm in diameter, preclude the detection of alterations in intradomain chromatin conformation using diffraction-limited optical microscopy. In this study, we developed an optical spectroscopic statistical nanosensing technique to detect chromatin packing domain changes in buccal mucosa as a lung cancer biomarker: chromatin-sensitive partial wave spectroscopic microscopy (csPWS). Artificial intelligence (AI) was applied to csPWS measurements of chromatin alterations to enhance diagnostic performance. Our AI-enhanced buccal csPWS nanocytology of 179 patients at two clinical sites distinguished Stage-I lung cancer versus cancer-free controls with an area under the ROC curve (AUC) of 0.92 ± 0.06 for Site 1 (in-state location) and 0.82 ± 0.11 for Site 2 (out-of-state location).
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Affiliation(s)
- Ali Daneshkhah
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Sravya Prabhala
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | | | - Hariharan Subramanian
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
- NanoCytomics, Evanston, IL, USA
| | | | - Andrew S Chang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Ankit Bharat
- Department of Surgery, Feinberg School of Medicine, Canning Thoracic Institute, Northwestern University, 420 East Superior Street, Chicago, IL, 60611, USA
| | | | - Vadim Backman
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA.
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Mihailova I, Gerbreders V, Krasovska M, Sledevskis E, Mizers V, Bulanovs A, Ogurcovs A. A non-enzymatic electrochemical hydrogen peroxide sensor based on copper oxide nanostructures. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2022; 13:424-436. [PMID: 35601536 PMCID: PMC9086496 DOI: 10.3762/bjnano.13.35] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 04/26/2022] [Indexed: 06/02/2023]
Abstract
This article describes the synthesis of nanostructured copper oxide on copper wires and its application for the detection of hydrogen peroxide. Copper oxide petal nanostructures were obtained by a one-step hydrothermal oxidation method. The resulting coating is uniform and dense and shows good adhesion to the wire surface. Structure, surface, and composition of the obtained samples were studied using field-emission scanning electron microscopy along with energy-dispersive spectroscopy and X-ray diffractometry. The resulting nanostructured samples were used for electrochemical determination of the H2O2 content in a 0.1 M NaOH buffer solution using cyclic voltammetry, differential pulse voltammetry, and i-t measurements. A good linear relationship between the peak current and the concentration of H2O2 in the range from 10 to 1800 μM was obtained. The sensitivity of the obtained CuO electrode is 439.19 μA·mM-1. The calculated limit of detection is 1.34 μM, assuming a signal-to-noise ratio of 3. The investigation of the system for sensitivity to interference showed that the most common interfering substances, that is, ascorbic acid, uric acid, dopamine, NaCl, glucose, and acetaminophen, do not affect the electrochemical response. The real milk sample test showed a high recovery rate (more than 95%). According to the obtained results, this sensor is suitable for practical use for the qualitative detection of H2O2 in real samples, as well as for the quantitative determination of its concentration.
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Affiliation(s)
- Irena Mihailova
- G. Liberts' Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1, Daugavpils, LV-5401, Latvia
| | - Vjaceslavs Gerbreders
- G. Liberts' Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1, Daugavpils, LV-5401, Latvia
| | - Marina Krasovska
- G. Liberts' Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1, Daugavpils, LV-5401, Latvia
| | - Eriks Sledevskis
- G. Liberts' Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1, Daugavpils, LV-5401, Latvia
| | - Valdis Mizers
- G. Liberts' Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1, Daugavpils, LV-5401, Latvia
| | - Andrejs Bulanovs
- G. Liberts' Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1, Daugavpils, LV-5401, Latvia
| | - Andrejs Ogurcovs
- G. Liberts' Innovative Microscopy Centre, Department of Technology, Institute of Life Sciences and Technology, Daugavpils University, Parades Street 1, Daugavpils, LV-5401, Latvia
- Institute of Solid State Physics, University of Latvia, Kengaraga street 8, Riga, LV-1063, Latvia
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Acin-Perez R, Benincá C, Shabane B, Shirihai OS, Stiles L. Utilization of Human Samples for Assessment of Mitochondrial Bioenergetics: Gold Standards, Limitations, and Future Perspectives. Life (Basel) 2021; 11:949. [PMID: 34575097 PMCID: PMC8467772 DOI: 10.3390/life11090949] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 08/12/2021] [Accepted: 08/23/2021] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial bioenergetic function is a central component of cellular metabolism in health and disease. Mitochondrial oxidative phosphorylation is critical for maintaining energetic homeostasis, and impairment of mitochondrial function underlies the development and progression of metabolic diseases and aging. However, measurement of mitochondrial bioenergetic function can be challenging in human samples due to limitations in the size of the collected sample. Furthermore, the collection of samples from human cohorts is often spread over multiple days and locations, which makes immediate sample processing and bioenergetics analysis challenging. Therefore, sample selection and choice of tests should be carefully considered. Basic research, clinical trials, and mitochondrial disease diagnosis rely primarily on skeletal muscle samples. However, obtaining skeletal muscle biopsies requires an appropriate clinical setting and specialized personnel, making skeletal muscle a less suitable tissue for certain research studies. Circulating white blood cells and platelets offer a promising primary tissue alternative to biopsies for the study of mitochondrial bioenergetics. Recent advances in frozen respirometry protocols combined with the utilization of minimally invasive and non-invasive samples may provide promise for future mitochondrial research studies in humans. Here we review the human samples commonly used for the measurement of mitochondrial bioenergetics with a focus on the advantages and limitations of each sample.
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Affiliation(s)
- Rebeca Acin-Perez
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Cristiane Benincá
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Byourak Shabane
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Orian S. Shirihai
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Linsey Stiles
- Department of Medicine, Endocrinology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (C.B.); (B.S.); (O.S.S.)
- Metabolism Theme, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
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Bam S, Buchanan E, Mahony C, O'Ryan C. DNA Methylation of PGC-1α Is Associated With Elevated mtDNA Copy Number and Altered Urinary Metabolites in Autism Spectrum Disorder. Front Cell Dev Biol 2021; 9:696428. [PMID: 34381777 PMCID: PMC8352569 DOI: 10.3389/fcell.2021.696428] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex disorder that is underpinned by numerous dysregulated biological pathways, including pathways that affect mitochondrial function. Epigenetic mechanisms contribute to this dysregulation and DNA methylation is an important factor in the etiology of ASD. We measured DNA methylation of peroxisome proliferator-activated receptor-gamma coactivator-1 alpha (PGC-1α), as well as five genes involved in regulating mitochondrial homeostasis to examine mitochondrial dysfunction in an ASD cohort of South African children. Using targeted Next Generation bisulfite sequencing, we found differential methylation (p < 0.05) at six key genes converging on mitochondrial biogenesis, fission and fusion in ASD, namely PGC-1α, STOML2, MFN2, FIS1, OPA1, and GABPA. PGC-1α, the transcriptional regulator of biogenesis, was significantly hypermethylated at eight CpG sites in the gene promoter, one of which contained a putative binding site for CAMP response binding element 1 (CREB1) (p = 1 × 10–6). Mitochondrial DNA (mtDNA) copy number, a marker of mitochondrial function, was elevated (p = 0.002) in ASD compared to controls and correlated significantly with DNA methylation at the PGC-1α promoter and there was a positive correlation between methylation at PGC-1α CpG#1 and mtDNA copy number (Spearman’s r = 0.2, n = 49, p = 0.04) in ASD. Furthermore, DNA methylation at PGC-1α CpG#1 and mtDNA copy number correlated significantly (p < 0.05) with levels of urinary organic acids associated with mitochondrial dysfunction, oxidative stress, and neuroendocrinology. Our data show differential methylation in ASD at six key genes converging on PGC-1α-dependent regulation of mitochondrial biogenesis and function. We demonstrate that methylation at the PGC-1α promoter is associated with elevated mtDNA copy number and metabolomic evidence of mitochondrial dysfunction in ASD. This highlights an unexplored role for DNA methylation in regulating specific pathways involved in mitochondrial biogenesis, fission and fusion contributing to mitochondrial dysfunction in ASD.
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Affiliation(s)
- Sophia Bam
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Erin Buchanan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Caitlyn Mahony
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Colleen O'Ryan
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
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