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Wongtrakool C, Ma J, Jarrell ZR, Liu KH, Orr M, Tran V, Gauthier TW, Marsit CJ, Jones DP, Go YM, Hu X. Pyrimidine Biosynthesis in Branching Morphogenesis Defects Induced by Prenatal Heavy Metal Exposure. Am J Respir Cell Mol Biol 2024; 71:372-375. [PMID: 39212486 PMCID: PMC11376240 DOI: 10.1165/rcmb.2024-0123le] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Affiliation(s)
- Cherry Wongtrakool
- Emory University Atlanta, Georgia
- Atlanta Veterans Affairs Healthcare System Decatur, Georgia
| | - Jing Ma
- Emory University Atlanta, Georgia
- Atlanta Veterans Affairs Healthcare System Decatur, Georgia
| | | | | | | | | | - Theresa W Gauthier
- Emory University Atlanta, Georgia
- Children's Healthcare of Atlanta Atlanta, Georgia
| | | | | | | | - Xin Hu
- Emory University Atlanta, Georgia
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2
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Jones DP. Redox organization of living systems. Free Radic Biol Med 2024; 217:179-189. [PMID: 38490457 PMCID: PMC11313653 DOI: 10.1016/j.freeradbiomed.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/08/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Redox organization governs an underlying simplicity in living systems. Critically, redox reactions enable the essential characteristics of life: extraction of energy from the environment, use of energy to support metabolic and structural organization, use of dynamic redox responses to defend against environmental threats, and use of redox mechanisms to direct differentiation of cells and organ systems essential for reproduction. These processes are sustained through a redox context in which electron donor/acceptor couples are poised at substantially different steady-state redox potentials, some with relatively reducing steady states and others with relatively oxidizing steady states. Redox-sensitive thiols of the redox proteome, as well as low molecular weight redox-active molecules, are maintained individually by the kinetics of oxidation-reduction within this redox system. Recent research has revealed opposing network interactions of the metallome, redox proteome, metabolome and transcriptome, which appear to be an evolved redox response structure to maintain stability of an organism in the presence of variable oxidative environments. Considerable opportunity exists to improve human health through detailed understanding of these redox networks so that targeted interventions can be developed to support new avenues for redox medicine.
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Affiliation(s)
- Dean P Jones
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Whitehead Biomedical Research Building, 615 Michael St, RM205P, Atlanta, GA, 30322, USA.
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3
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Staitieh BS, Hu X, Yeligar SM, Auld SC. Paired ATAC- and RNA-seq offer insight into the impact of HIV on alveolar macrophages: a pilot study. Sci Rep 2023; 13:15276. [PMID: 37714998 PMCID: PMC10504379 DOI: 10.1038/s41598-023-42644-7] [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: 05/23/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023] Open
Abstract
People with HIV remain at greater risk for both infectious and non-infectious pulmonary diseases even after antiretroviral therapy initiation and CD4 cell count recovery. These clinical risks reflect persistent HIV-mediated defects in innate and adaptive immunity, including in the alveolar macrophage, a key innate immune effector in the lungs. In this proof-of-concept pilot study, we leveraged paired RNA-seq and ATAC-seq analyses of human alveolar macrophages obtained with research bronchoscopy from people with and without HIV to highlight the potential for recent methodologic advances to generate novel hypotheses about biological pathways that may contribute to impaired pulmonary immune function in people with HIV. In addition to 35 genes that were differentially expressed in macrophages from people with HIV, gene set enrichment analysis identified six gene sets that were differentially regulated. ATAC-seq analysis revealed 115 genes that were differentially accessible for people with HIV. Data-driven integration of the findings from these complementary, high-throughput techniques using xMWAS identified distinct clusters involving lipoprotein lipase and inflammatory pathways. By bringing together transcriptional and epigenetic data, this analytic approach points to several mechanisms, including previously unreported pathways, that warrant further exploration as potential mediators of the increased risk of pulmonary disease in people with HIV.
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Affiliation(s)
- Bashar S Staitieh
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA
- Grady Health System, Atlanta, GA, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Samantha M Yeligar
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA
- Veterans Affairs Atlanta Healthcare System, Decatur, GA, USA
| | - Sara C Auld
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, School of Medicine, Emory University, 615 Michael St NE, Ste 200, Atlanta, GA, 30322, USA.
- Departments of Epidemiology and Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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4
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Taibl KR, Dunlop AL, Barr DB, Li YY, Eick SM, Kannan K, Ryan PB, Schroder M, Rushing B, Fennell T, Chang CJ, Tan Y, Marsit CJ, Jones DP, Liang D. Newborn metabolomic signatures of maternal per- and polyfluoroalkyl substance exposure and reduced length of gestation. Nat Commun 2023; 14:3120. [PMID: 37253729 DOI: 10.1038/s41467-023-38710-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/10/2023] [Indexed: 06/01/2023] Open
Abstract
Marginalized populations experience disproportionate rates of preterm birth and early term birth. Exposure to per- and polyfluoroalkyl substances (PFAS) has been reported to reduce length of gestation, but the underlying mechanisms are unknown. In the present study, we characterized the molecular signatures of prenatal PFAS exposure and gestational age at birth outcomes in the newborn dried blood spot metabolome among 267 African American dyads in Atlanta, Georgia between 2016 and 2020. Pregnant people with higher serum perfluorooctanoic acid and perfluorohexane sulfonic acid concentrations had increased odds of an early birth. After false discovery rate correction, the effect of prenatal PFAS exposure on reduced length of gestation was associated with 8 metabolomic pathways and 52 metabolites in newborn dried blood spots, which suggested perturbed tissue neogenesis, neuroendocrine function, and redox homeostasis. These mechanisms explain how prenatal PFAS exposure gives rise to the leading cause of infant death in the United States.
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Affiliation(s)
- Kaitlin R Taibl
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Anne L Dunlop
- Department of Gynecology and Obstetrics, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Dana Boyd Barr
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Yuan-Yuan Li
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Stephanie M Eick
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Kurunthachalam Kannan
- Department of Pediatrics, New York University School of Medicine, New York, NY, USA
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, USA
| | - P Barry Ryan
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Madison Schroder
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Blake Rushing
- Metabolomics and Exposome Laboratory, Nutrition Research Institute, University of North Carolina, Chapel Hill, NC, USA
| | - Timothy Fennell
- Analytical Chemistry and Pharmaceuticals, RTI International, Research Triangle Park, Durham, NC, USA
| | - Che-Jung Chang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Youran Tan
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dean P Jones
- Division of Pulmonary, Allergy, and Critical Care Medicine, Department of Medicine, School of Medicine, Emory University, Atlanta, GA, USA
| | - Donghai Liang
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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Fernandes J, Uppal K, Liu KH, Hu X, Orr M, Tran V, Go YM, Jones DP. Antagonistic Interactions in Mitochondria ROS Signaling Responses to Manganese. Antioxidants (Basel) 2023; 12:804. [PMID: 37107179 PMCID: PMC10134992 DOI: 10.3390/antiox12040804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/29/2023] Open
Abstract
Antagonistic interaction refers to opposing beneficial and adverse signaling by a single agent. Understanding opposing signaling is important because pathologic outcomes can result from adverse causative agents or the failure of beneficial mechanisms. To test for opposing responses at a systems level, we used a transcriptome-metabolome-wide association study (TMWAS) with the rationale that metabolite changes provide a phenotypic readout of gene expression, and gene expression provides a phenotypic readout of signaling metabolites. We incorporated measures of mitochondrial oxidative stress (mtOx) and oxygen consumption rate (mtOCR) with TMWAS of cells with varied manganese (Mn) concentration and found that adverse neuroinflammatory signaling and fatty acid metabolism were connected to mtOx, while beneficial ion transport and neurotransmitter metabolism were connected to mtOCR. Each community contained opposing transcriptome-metabolome interactions, which were linked to biologic functions. The results show that antagonistic interaction is a generalized cell systems response to mitochondrial ROS signaling.
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Affiliation(s)
- Jolyn Fernandes
- Section of Neonatal-Perinatal Medicine, Department of Pediatrics, College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Karan Uppal
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ken H. Liu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Xin Hu
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Orr
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - ViLinh Tran
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Dean P. Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA
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6
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Zahid A, Yu Y, Zhou S, Xie X, Yin F. Antiparasitic effect of copper alloy mesh on tomont stage of Cryptocaryon irritans in aquaculture. JOURNAL OF FISH DISEASES 2023; 46:181-188. [PMID: 36453691 DOI: 10.1111/jfd.13732] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 06/17/2023]
Abstract
Copper alloy sheets have been shown to prevent cryptocaryoniasis. Therefore, we studied the potential efficiency of copper alloy mesh (CAM) in aquaculture tanks to prevent cryptocaryoniasis outbreaks. The effectivenesses of CAM against the tomont stage of Cryptocaryon irritans and in protecting fish from cryptocaryoniasis were tested both in vitro and in vivo. The mortality rate of C. irritans tomonts increased as the contact time with CAM rose and peaked at 70 min (100% of mortality). Morphological changes were observed such as the shrinking of the protoplasm of the treated tomonts, resulting in a larger gap between the cytoplasm and the cyst wall. Mitochondrial dysfunction due to shrinkage in the inner portion, outer and inner mitochondrial membrane damage and cytoplasmic vacuolation was revealed by ultrastructural analysis. The use of CAM effectively preventing reinfection was also provided. In comparison with group B (infected fish without CAM), both groups A (uninfected fish as a control group) and C (infected fish treated with CAM) had a 100% survival rate until the end of the trial. CAM has the same anticryptocaryoniasis effect as copper alloy sheets but is more advantageous due to its lightweight, reduced labor cost and lower purchase cost. It is noticeable that CAM exposure also prevents the excessive accumulation of copper ions in aquaculture sea water.
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Affiliation(s)
- Aysha Zahid
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products; School of Marine Sciences, Ningbo University, Ningbo, China
| | - Youbin Yu
- Key Laboratory of Ocean Fishing Vessel and Equipment, Ministry of Agriculture and Rural Affairs, Fishery Machinery and Instrument Research institute, Chinese Academy of Fishery Sciences, Shanghai, China
| | - Suming Zhou
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products; School of Marine Sciences, Ningbo University, Ningbo, China
| | - Xiao Xie
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products; School of Marine Sciences, Ningbo University, Ningbo, China
| | - Fei Yin
- Key Laboratory of Applied Marine Biotechnology, Ministry of Education; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products; School of Marine Sciences, Ningbo University, Ningbo, China
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7
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Sies H, Belousov VV, Chandel NS, Davies MJ, Jones DP, Mann GE, Murphy MP, Yamamoto M, Winterbourn C. Defining roles of specific reactive oxygen species (ROS) in cell biology and physiology. Nat Rev Mol Cell Biol 2022; 23:499-515. [PMID: 35190722 DOI: 10.1038/s41580-022-00456-z] [Citation(s) in RCA: 609] [Impact Index Per Article: 304.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2022] [Indexed: 02/06/2023]
Abstract
'Reactive oxygen species' (ROS) is a generic term that defines a wide variety of oxidant molecules with vastly different properties and biological functions that range from signalling to causing cell damage. Consequently, the description of oxidants needs to be chemically precise to translate research on their biological effects into therapeutic benefit in redox medicine. This Expert Recommendation article pinpoints key issues associated with identifying the physiological roles of oxidants, focusing on H2O2 and O2.-. The generic term ROS should not be used to describe specific molecular agents. We also advocate for greater precision in measurement of H2O2, O2.- and other oxidants, along with more specific identification of their signalling targets. Future work should also consider inter-organellar communication and the interactions of redox-sensitive signalling targets within organs and whole organisms, including the contribution of environmental exposures. To achieve these goals, development of tools that enable site-specific and real-time detection and quantification of individual oxidants in cells and model organisms are needed. We also stress that physiological O2 levels should be maintained in cell culture to better mimic in vivo redox reactions associated with specific cell types. Use of precise definitions and analytical tools will help harmonize research among the many scientific disciplines working on the common goal of understanding redox biology.
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Affiliation(s)
- Helmut Sies
- Institute for Biochemistry and Molecular Biology I, Faculty of Medicine, Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.
- Leibniz Research Institute for Environmental Medicine, Düsseldorf, Germany.
| | - Vsevolod V Belousov
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow, Russia
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow, Russia
| | - Navdeep S Chandel
- Division of Pulmonary & Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Michael J Davies
- Department of Biomedical Sciences, Panum Institute, University of Copenhagen, Copenhagen, Denmark
| | - Dean P Jones
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Giovanni E Mann
- King's British Heart Foundation Centre of Research Excellence, School of Cardiovascular Medicine and Sciences, King's College London, London, UK
| | - Michael P Murphy
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Masayuki Yamamoto
- Department of Medical Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Christine Winterbourn
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
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8
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Killilea DW, Killilea AN. Mineral requirements for mitochondrial function: A connection to redox balance and cellular differentiation. Free Radic Biol Med 2022; 182:182-191. [PMID: 35218912 DOI: 10.1016/j.freeradbiomed.2022.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 02/16/2022] [Accepted: 02/21/2022] [Indexed: 12/20/2022]
Abstract
Professor Bruce Ames demonstrated that nutritional recommendations should be adjusted in order to 'tune-up' metabolism and reduce mitochondria decay, a hallmark of aging and many disease processes. A major subset of tunable nutrients are the minerals, which despite being integral to every aspect of metabolism are often deficient in the typical Western diet. Mitochondria are particularly rich in minerals, where they function as essential cofactors for mitochondrial physiology and overall cellular health. Yet substantial knowledge gaps remain in our understanding of the form and function of these minerals needed for metabolic harmony. Some of the minerals have known activities in the mitochondria but with incomplete regulatory detail, whereas other minerals have no established mitochondrial function at all. A comprehensive metallome of the mitochondria is needed to fully understand the patterns and relationships of minerals within metabolic processes and cellular development. This brief overview serves to highlight the current progress towards understanding mineral homeostasis in the mitochondria and to encourage more research activity in key areas. Future work may likely reveal that adjusting the amounts of specific nutritional minerals has longevity benefits for human health.
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Affiliation(s)
- David W Killilea
- Office of Research, University of California, San Francisco, CA, USA.
| | - Alison N Killilea
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, USA
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Ruiz LM, Libedinsky A, Elorza AA. Role of Copper on Mitochondrial Function and Metabolism. Front Mol Biosci 2021; 8:711227. [PMID: 34504870 PMCID: PMC8421569 DOI: 10.3389/fmolb.2021.711227] [Citation(s) in RCA: 216] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/05/2021] [Indexed: 12/21/2022] Open
Abstract
Copper is essential for life processes like energy metabolism, reactive oxygen species detoxification, iron uptake, and signaling in eukaryotic organisms. Mitochondria gather copper for the assembly of cuproenzymes such as the respiratory complex IV, cytochrome c oxidase, and the antioxidant enzyme superoxide dismutase 1. In this regard, copper plays a role in mitochondrial function and signaling involving bioenergetics, dynamics, and mitophagy, which affect cell fate by means of metabolic reprogramming. In mammals, copper homeostasis is tightly regulated by the liver. However, cellular copper levels are tissue specific. Copper imbalances, either overload or deficiency, have been associated with many diseases, including anemia, neutropenia, and thrombocytopenia, as well as tumor development and cancer aggressivity. Consistently, new pharmacological developments have been addressed to reduce or exacerbate copper levels as potential cancer therapies. This review goes over the copper source, distribution, cellular uptake, and its role in mitochondrial function, metabolic reprograming, and cancer biology, linking copper metabolism with the field of regenerative medicine and cancer.
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Affiliation(s)
- Lina M Ruiz
- Institute of Biomedical Sciences, Faculty of Health Sciences, Universidad Autónoma de Chile, Santiago, Chile
| | - Allan Libedinsky
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
| | - Alvaro A Elorza
- Institute of Biomedical Sciences, Faculty of Medicine and Faculty of Life Sciences, Universidad Andres Bello, Santiago, Chile.,Millennium Institute on Immunology and Immunotherapy, Santiago, Chile
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10
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Kim JH, Yan Q, Uppal K, Cui X, Ling C, Walker DI, Heck JE, von Ehrenstein OS, Jones DP, Ritz B. Metabolomics analysis of maternal serum exposed to high air pollution during pregnancy and risk of autism spectrum disorder in offspring. ENVIRONMENTAL RESEARCH 2021; 196:110823. [PMID: 33548296 PMCID: PMC9059845 DOI: 10.1016/j.envres.2021.110823] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/27/2021] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Previously, numerous epidemiologic studies reported an association between autism spectrum disorder (ASD) and exposure to air pollution during pregnancy. However, there have been no metabolomics studies investigating the impact of pregnancy pollution exposure to ASD risk in offspring. OBJECTIVES To identify differences in maternal metabolism that may reflect a biological response to exposure to high air pollution in pregnancies of offspring who later did or did not develop ASD. METHODS We obtained stored mid-pregnancy serum from 214 mothers who lived in California's Central Valley and experienced the highest levels of air pollution during early pregnancy. We estimated each woman's average traffic-related air pollution exposure (carbon monoxide, nitric oxides, and particulate matter <2.5 μm) during the first trimester using the California Line Source Dispersion Model, version 4 (CALINE4). By utilizing liquid chromatography-high resolution mass spectrometry, we identified the metabolic profiles of maternal serum for 116 mothers with offspring who later developed ASD and 98 control mothers. Partial least squares discriminant analysis (PLS-DA) was employed to select metabolic features associated with air pollution exposure or autism risk in offspring. We also conducted extensive pathway enrichment analysis to elucidate potential ASD-related changes in the metabolome of pregnant women. RESULTS We extracted 4022 and 4945 metabolic features from maternal serum samples in hydrophilic interaction (HILIC) chromatography (positive ion mode) and C18 (negative ion mode) columns, respectively. After controlling for potential confounders, we identified 167 and 222 discriminative features (HILIC and C18, respectively). Pathway enrichment analysis to discriminate metabolic features associated with ASD risk indicated various metabolic pathway perturbations linked to the tricarboxylic acid (TCA) cycle and mitochondrial function, including carnitine shuttle, amino acid metabolism, bile acid metabolism, and vitamin A metabolism. CONCLUSION Using high resolution metabolomics, we identified several metabolic pathways disturbed in mothers with ASD offspring among women experiencing high exposure to traffic-related air pollution during pregnancy that were associated with mitochondrial dysfunction. These findings provide us with a better understanding of metabolic disturbances involved in the development of ASD under adverse environmental conditions.
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Affiliation(s)
- Ja Hyeong Kim
- Department of Pediatrics, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, 44033, South Korea.
| | - Qi Yan
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.
| | - Karan Uppal
- Computational Systems Medicine & Metabolomics Laboratory, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA, 30322, USA.
| | - Xin Cui
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA; Perinatal Epidemiology and Health Outcomes Research Unit, Division of Neonatology, Department of Pediatrics, Stanford University School of Medicine and Lucile Packard Children's Hospital, Palo Alto, CA, 94304, USA; California Perinatal Quality Care Collaborative, Palo Alto, CA, 94305, USA.
| | - Chenxiao Ling
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.
| | - Douglas I Walker
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Julia E Heck
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.
| | - Ondine S von Ehrenstein
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA; Department of Community Health Sciences, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA.
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, and Critical Care Medicine, School of Medicine, Emory University, Atlanta, GA, 30322, USA.
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA; Department of Community Health Sciences, Fielding School of Public Health, University of California, Los Angeles, CA, 90095, USA; Department of Neurology, Geffen School of Medicine, University of California, Los Angeles, CA, 90095, USA.
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11
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Gong T, Wang W, Xu H, Yang Y, Chen X, Meng L, Xu Y, Li Z, Wan S, Mu Q. Longitudinal Expression of Testicular TAS1R3 from Prepuberty to Sexual Maturity in Congjiang Xiang Pigs. Animals (Basel) 2021; 11:ani11020437. [PMID: 33567555 PMCID: PMC7916009 DOI: 10.3390/ani11020437] [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: 12/02/2020] [Revised: 01/05/2021] [Accepted: 01/29/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary Taste receptor type 1 subunit 3 (T1R3), a sweet/umami taste receptor, is widely expressed from the tongue to the testis, and testis expression is associated with male sterility. In Congjiang Xiang pigs, T1R3 is expressed in elongating/elongated spermatids and Leydig cells in a stage-dependent manner during postnatal development and the spermatogenic cycle. T1R3 may contribute to regulation of spermatid differentiation and Leydig cell function, and may therefore help limit the incidence of various male reproductive pathologies. Abstract Testicular expression of taste receptor type 1 subunit 3 (T1R3), a sweet/umami taste receptor, has been implicated in spermatogenesis and steroidogenesis in mice. We explored the role of testicular T1R3 in porcine postnatal development using the Congjiang Xiang pig, a rare Chinese miniature pig breed. Based on testicular weights, morphology, and testosterone levels, four key developmental stages were identified in the pig at postnatal days 15–180 (prepuberty: 30 day; early puberty: 60 day; late puberty: 90 day; sexual maturity: 120 day). During development, testicular T1R3 exhibited stage-dependent and cell-specific expression patterns. In particular, T1R3 levels increased significantly from prepuberty to puberty (p < 0.05), and expression remained high until sexual maturity (p < 0.05), similar to results for phospholipase Cβ2 (PLCβ2). The strong expressions of T1R3/PLCβ2 were observed at the cytoplasm of elongating/elongated spermatids and Leydig cells. In the eight-stage cycle of the seminiferous epithelium in pigs, T1R3/PLCβ2 levels were higher in the spermatogenic epithelium at stages II–VI than at the other stages, and the strong expressions were detected in elongating/elongated spermatids and residual bodies. The message RNA (mRNA) levels of taste receptor type 1 subunit 1 (T1R1) in the testis showed a similar trend to levels of T1R3. These data indicate a possible role of T1R3 in the regulation of spermatid differentiation and Leydig cell function.
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Affiliation(s)
- Ting Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Weiyong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Houqiang Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
- Correspondence: ; Tel.: +86-0851-88298005
| | - Yi Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Xiang Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Lijie Meng
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Yongjian Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in The Plateau Mountainous Region, Ministry of Education, Guizhou University, Guiyang 550025, China; (T.G.); (W.W.); (Y.Y.); (X.C.); (L.M.); (Y.X.)
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Guiyang 550025, China
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Ziqing Li
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Sufang Wan
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
| | - Qi Mu
- College of Animal Science, Guizhou University, Guiyang 550025, China; (Z.L.); (S.W.); (Q.M.)
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12
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Smith MR, Jarrell ZR, Orr M, Liu KH, Go YM, Jones DP. Metabolome-wide association study of flavorant vanillin exposure in bronchial epithelial cells reveals disease-related perturbations in metabolism. ENVIRONMENT INTERNATIONAL 2021; 147:106323. [PMID: 33360165 PMCID: PMC7856097 DOI: 10.1016/j.envint.2020.106323] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
Electronic cigarettes (e-cig) are an increasingly popular alternative to traditional smoking but have been in use for too short of a period of time to fully understand health risks. Furthermore, associated health risks are difficult to evaluate because of a large range of flavoring agents and their combinations for use with e-cig. Many flavoring agents are generally regarded as safe but have limited studies for effects on lung. Vanillin, an aromatic aldehyde, is one of the most commonly used flavoring agents in e-cig. Vanillin is electrophilic and can be redox active, with chemical properties expected to interact within biologic systems. Because accumulating lung metabolomics studies have identified metabolic disruptions associated with idiopathic pulmonary fibrosis, asthma and acute respiratory distress syndrome, we used human bronchial epithelial cells (BEAS-2B) with high-resolution metabolomics analysis to determine whether these disease-associated pathways are impacted by vanillin over the range used in e-cig. A metabolome-wide association study showed that vanillin perturbed specific energy, amino acid, antioxidant and sphingolipid pathways previously associated with human disease. Analysis of a small publicly available human dataset showed associations with several of the same pathways. Because vanillin is a common and high-abundance flavorant in e-cig, these results show that vanillin has potential to be mechanistically important in lung diseases and warrants in vivo toxicity testing in the context of e-cig use.
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Affiliation(s)
- Matthew Ryan Smith
- Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Zachery R Jarrell
- Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Michael Orr
- Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Ken H Liu
- Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA 30322, USA
| | - Young-Mi Go
- Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA 30322, USA.
| | - Dean P Jones
- Division of Pulmonary, Allergy and Critical Care Medicine, Emory University, Atlanta, GA 30322, USA.
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13
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Towards a systems-level understanding of mitochondrial biology. Cell Calcium 2021; 95:102364. [PMID: 33601101 DOI: 10.1016/j.ceca.2021.102364] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 01/22/2021] [Accepted: 01/23/2021] [Indexed: 11/21/2022]
Abstract
Human mitochondria are complex and highly dynamic biological systems, comprised of over a thousand parts and evolved to fully integrate into the specialized intracellular signaling networks and metabolic requirements of each cell and organ. Over the last two decades, several complementary, top-down computational and experimental approaches have been developed to identify, characterize and modulate the human mitochondrial system, demonstrating the power of integrating classical reductionist and discovery-driven analyses in order to de-orphanize hitherto unknown molecular components of mitochondrial machineries and pathways. To this goal, systematic, multiomics-based surveys of proteome composition, protein networks, and phenotype-to-pathway associations at the tissue, cell and organellar level have been largely exploited to predict the full complement of mitochondrial proteins and their functional interactions, therefore catalyzing data-driven hypotheses. Collectively, these multidisciplinary and integrative research approaches hold the potential to propel our understanding of mitochondrial biology and provide a systems-level framework to unraveling mitochondria-mediated and disease-spanning pathomechanisms.
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14
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Jaiswal S, Kumar M, Mandeep, Sunita, Singh Y, Shukla P. Systems Biology Approaches for Therapeutics Development Against COVID-19. Front Cell Infect Microbiol 2020; 10:560240. [PMID: 33194800 PMCID: PMC7655984 DOI: 10.3389/fcimb.2020.560240] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/29/2020] [Indexed: 12/13/2022] Open
Abstract
Understanding the systems biology approaches for promoting the development of new therapeutic drugs is attaining importance nowadays. The threat of COVID-19 outbreak needs to be vanished for global welfare, and every section of research is focusing on it. There is an opportunity for finding new, quick, and accurate tools for developing treatment options, including the vaccine against COVID-19. The review at this moment covers various aspects of pathogenesis and host factors for exploring the virus target and developing suitable therapeutic solutions through systems biology tools. Furthermore, this review also covers the extensive details of multiomics tools i.e., transcriptomics, proteomics, genomics, lipidomics, immunomics, and in silico computational modeling aiming towards the study of host-virus interactions in search of therapeutic targets against the COVID-19.
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Affiliation(s)
- Shweta Jaiswal
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Mohit Kumar
- Soil Microbial Ecology and Environmental Toxicology Laboratory, Department of Zoology, University of Delhi, Delhi, India
- Department of Zoology, Hindu College, University of Delhi, Delhi, India
| | - Mandeep
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
| | - Sunita
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Yogendra Singh
- Bacterial Pathogenesis Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak, India
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15
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Trevisan R, Uzochukwu D, Di Giulio RT. PAH SORPTION TO NANOPLASTICS AND THE TROJAN HORSE EFFECT AS DRIVERS OF MITOCHONDRIAL TOXICITY AND PAH LOCALIZATION IN ZEBRAFISH. FRONTIERS IN ENVIRONMENTAL SCIENCE 2020; 8:78. [PMID: 34322495 PMCID: PMC8315355 DOI: 10.3389/fenvs.2020.00078] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Plastics are world-wide pollutants that pose a potential threat to wildlife and human health. Small plastic particles, such as microplastics and nanoplastics, are easily ingested, and can act as a Trojan Horse by carrying microorganisms and pollutants. This study investigated the potential role of the Trojan Horse effect in the toxicity of nanoplastics to the vertebrate model organism, zebrafish (Danio rerio). First, we investigated if this effect could affect the toxicity of nanoplastics. Second, we analyzed if it could contribute to the biodistribution of the associated contaminants. And third, we focused on its effect on the mitochondrial toxicity of nanoplastics. We incubated 44 nm polystyrene nanoparticles with a real-world mixture of polycyclic aromatic hydrocarbons (PAHs) for 7 days and removed the free PAHs by ultrafiltration. We dosed embryos with 1 ppm of nanoplastics (NanoPS) or PAH-sorbed nanoplastics (PAH-NanoPS). Neither type of plastic particle caused changes in embryonic and larval development. Fluorescence microscopy and increased EROD activity suggested the uptake of PAHs in larvae exposed to PAH-NanoPS. This coincided with higher concentrations in the yolk sac and the brain. However, PAH-only exposure leads to their accumulation in the yolk sac but not in the brain, suggesting that that the spatial distribution of bioaccumulated PAHs can differ depending on their source of exposure. Both nanoplastic particles affected mitochondrial energy metabolism but caused different adverse effects. While NanoPS decreased NADH production, PAH-NanoPS decreased mitochondrial coupling efficiency and spare respiratory capacity. In summary, the addition of PAHs to the surface of nanoplastics did not translate into increased developmental toxicity. Low levels of PAHs were accumulated in the organisms, and the transfer of PAHs seems to happen in tissues and possibly organelles where nanoplastics accumulate. Disruption of the energy metabolism in the mitochondria may be a key factor in the toxicity of nanoplastics, and the Trojan Horse effect may amplify this effect.
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Affiliation(s)
- Rafael Trevisan
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Daniel Uzochukwu
- Nicholas School of the Environment, Duke University, Durham, NC, USA
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16
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Sung AY, Floyd BJ, Pagliarini DJ. Systems Biochemistry Approaches to Defining Mitochondrial Protein Function. Cell Metab 2020; 31:669-678. [PMID: 32268114 PMCID: PMC7176052 DOI: 10.1016/j.cmet.2020.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/06/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023]
Abstract
Defining functions for the full complement of proteins is a grand challenge in the post-genomic era and is essential for our understanding of basic biology and disease pathogenesis. In recent times, this endeavor has benefitted from a combination of modern large-scale and classical reductionist approaches-a process we refer to as "systems biochemistry"-that helps surmount traditional barriers to the characterization of poorly understood proteins. This strategy is proving to be particularly effective for mitochondria, whose well-defined proteome has enabled comprehensive analyses of the full mitochondrial system that can position understudied proteins for fruitful mechanistic investigations. Recent systems biochemistry approaches have accelerated the identification of new disease-related mitochondrial proteins and of long-sought "missing" proteins that fulfill key functions. Collectively, these studies are moving us toward a more complete understanding of mitochondrial activities and providing a molecular framework for the investigation of mitochondrial pathogenesis.
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Affiliation(s)
- Andrew Y Sung
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Brendan J Floyd
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA; Department of Pediatrics, Stanford School of Medicine, Stanford, CA, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, USA; Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
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17
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Jones DP, Cohn BA. A vision for exposome epidemiology: The pregnancy exposome in relation to breast cancer in the Child Health and Development Studies. Reprod Toxicol 2020; 92:4-10. [PMID: 32197999 PMCID: PMC7306421 DOI: 10.1016/j.reprotox.2020.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Etiology of complex diseases, such as breast cancer, involves multiple genetic, behavioral and environmental factors. Gene sequencing enabled detection of genetic risks with relatively small effect size, and high-resolution metabolomics (HRM) to provide omics level data for exposures is poised to do the same for environmental epidemiology. Coupling HRM to the Child Health and Development Studies (CHDS) cohort combines two unique resources to create a prototype for exposome epidemiology, in which omics scale measures of exposure are used for study of distribution and determinants of health and disease. Using this approach, exposures and biologic responses during pregnancy have been linked to breast cancer in the CHDS. With improved chemical coverage and extension to larger populations and other disease processes, development of exposome epidemiology portends discovery of new disease-associated environment factors with small effect size as well as new capabilities to disentangle these from behavioral and other risk factors.
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Affiliation(s)
- Dean P Jones
- Department of Medicine, School of Medicine, Emory University, Atlanta, GA 30322, USA.
| | - Barbara A Cohn
- Child Health and Development Studies, Public Health Institute, 1683 Shattuck Avenue, Suite B, Berkeley, CA 94709, USA
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