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Daiber A, Rajagopalan S, Kuntic M, Münzel T. Cardiovascular risk posed by the exposome. Atherosclerosis 2025; 405:119222. [PMID: 40339362 DOI: 10.1016/j.atherosclerosis.2025.119222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Revised: 04/13/2025] [Accepted: 04/15/2025] [Indexed: 05/10/2025]
Abstract
Chronic non-communicable diseases (NCDs) account for 2/3 of global deaths annually, primarily due to an aging population and external risk factors such as air/water/soil pollution, traffic noise, mental stress, and climate change emanating from the environment. These factors contribute to premature deaths and loss of healthy life years, as reflected by disability-adjusted life years. The exposome concept was proposed 16 years ago as a new research field to investigate environment-health associations, also by considering the underlying pathophysiological pathways. The exposome describes lifelong environmental exposures, besides pollutants also socioeconomic and lifestyle factors, aiming to explain the associated diseases and deaths. The exposome can be divided into the specific and general external environment and further subcategories such as organ-specific exposomes as well as spatially and temporally restricted pollutomes. The exposome also shows considerable interaction with genetic predisposition and pre-established chronic diseases, characteristics of the vulnerable groups. The present overview provides background information on the impact of the environment on health and disease by considering recent data of the Global Burden of Disease Study. We also explain the exposome concept with the help of selected studies, briefly describe how the exposome is measured, and discuss biomarkers identified by exposomic research and their impact on the development and progression of atherosclerosis. Major pathophysiological pathways comprise exacerbated stress hormone signaling, oxidative stress, inflammation and circadian rhythm dysregulation promoting impairment of cardiometabolic function. The present overview highlights the relevance of the exposome for future health research and preventive medicine, especially concerning cardiovascular diseases and therapy.
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Affiliation(s)
- Andreas Daiber
- Department of Cardiology - Cardiology I, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; German Centre for Cardiovascular Research (DZHK), partner site Rhine-Main, Mainz, Germany.
| | - Sanjay Rajagopalan
- Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Marin Kuntic
- Department of Cardiology - Cardiology I, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; German Centre for Cardiovascular Research (DZHK), partner site Rhine-Main, Mainz, Germany
| | - Thomas Münzel
- Department of Cardiology - Cardiology I, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany; German Centre for Cardiovascular Research (DZHK), partner site Rhine-Main, Mainz, Germany
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2
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Alvarenga L, Ribeiro M, Cardozo LFMF, Borges NA, Stenvinkel P, Mafra D. The Exposome and the Kidney: A Silent Dialogue Shaping Chronic Kidney Disease. J Xenobiot 2025; 15:73. [PMID: 40407537 PMCID: PMC12101341 DOI: 10.3390/jox15030073] [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: 04/09/2025] [Revised: 04/30/2025] [Accepted: 05/07/2025] [Indexed: 05/26/2025] Open
Abstract
Genetic predisposition accounts for less than 20% of the global disease burden, highlighting the substantial role of environmental factors in health outcomes. In chronic kidney disease (CKD), a growing global prevalence, understanding the interplay between genes and the environment is crucial. Emerging research in the exposome and genome underscores how environmental exposures interact with genetic variants to influence the development and progression of CKD. The term "exposome" encompasses a variety of factors, including personal behaviors like smoking, a sedentary lifestyle, and making specific dietary choices (such as consuming ultra-processed foods, sugar, or fat). It also includes broader determinants such as pesticides, air, water, and soil pollution, nanoplastics, global warming, stressful life events, and socioeconomic status. Research on the exposome significantly increases our understanding of toxicological processes and individual variations in susceptibility to environmental stressors. This narrative review aims to explore the exposome associated with CKD, highlight key environmental exposures in its development, and discuss potential preventive and therapeutic strategies informed by these exposure-related factors.
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Affiliation(s)
- Livia Alvarenga
- Department of Cardiopneumology, Faculty of Medicine, University of São Paulo (FMUSP), São Paulo 05403-903, Brazil;
- Graduate Program in Nutrition Science, Federal Fluminense University, Niterói 24220-900, Brazil;
| | - Marcia Ribeiro
- Graduate Program in Biological Sciences—Physiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil;
| | - Ludmila F. M. F. Cardozo
- Graduate Program in Nutrition Science, Federal Fluminense University, Niterói 24220-900, Brazil;
- Graduate Program in Cardiovascular Sciences, Federal Fluminense University, Niterói 24220-900, Brazil
| | - Natália A. Borges
- Graduate Program in Food, Nutrition and Health—Institute of Nutrition, State University of Rio de Janeiro (UERJ), Rio de Janeiro 20950-000, Brazil;
| | - Peter Stenvinkel
- Division of Renal Medicine and Baxter Novum, Department of Clinical Science, Technology and Intervention, Karolinska Institutet, 171 77 Stockholm, Sweden;
| | - Denise Mafra
- Graduate Program in Nutrition Science, Federal Fluminense University, Niterói 24220-900, Brazil;
- Graduate Program in Biological Sciences—Physiology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro 21941-901, Brazil;
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Nkya S, Nzunda C, Saukiwa E, Kaywanga F, Buchard E, Solomon D, Christopher H, Ngowi D, Johansen J, Urio F, Mgaya J, Kindole C, Yonazi M, Karim S, Alimohamed MZ, Sangeda RZ, Chamba C, Dandara C, Novelli E, Chimusa ER, Makani J. Exploring pharmacogenetic factors influencing hydroxyurea response in tanzanian sickle cell disease patients: a genomic medicine approach. THE PHARMACOGENOMICS JOURNAL 2025; 25:11. [PMID: 40268903 DOI: 10.1038/s41397-025-00372-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 04/02/2025] [Accepted: 04/17/2025] [Indexed: 04/25/2025]
Abstract
In sub-Saharan Africa, sickle cell disease (SCD) remains a significant public health challenge. Despite the discovery of SCD over a century ago, progress in developing and accessing effective treatments has been limited. Hydroxyurea is the primary drug used for managing SCD and associated with improving clinical outcomes. However, up to 30% of patients do not respond to hydroxyurea, likely due to genetic factors. This study involved 148 individuals with SCD investigated the association of hydroxyurea response with genetic variants across 13 loci associated with HbF synthesis and drug metabolism, focusing on MYB, HBB, HBG1, HBG2, BCL11A, KLF10, HAO2, NOS1, ARG2, SAR1A, CYP2C9, and CYP2E1. Significant associations with hydroxyurea response were identified in CYP2C9, CYP2E1, KLF10, BCL11A, ARG2, HBG1, SAR1A, MYB, and NOS1 loci. Furthermore, pathway enrichment and gene-gene interaction analyses provide deeper insights into the genetic mechanisms underlying hydroxyurea treatment response, highlighting potential avenues for personalized therapy in SCD management.
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Affiliation(s)
- Siana Nkya
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Biochemistry and Molecular Biology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Dar es Salaam, Tanzania
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Collin Nzunda
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania.
| | - Emmanuel Saukiwa
- Department of Biochemistry and Molecular Biology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Frida Kaywanga
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Dar es Salaam, Tanzania
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eliud Buchard
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - David Solomon
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Heavenlight Christopher
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Doreen Ngowi
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Julieth Johansen
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Florence Urio
- Department of Biochemistry and Molecular Biology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Josephine Mgaya
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Mbonea Yonazi
- Muhimbili National Hospital, Dar es Salaam, Tanzania
| | - Salman Karim
- Department of Biochemistry and Molecular Biology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Mohamed Zahir Alimohamed
- Department of Biochemistry and Molecular Biology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Dar es Salaam, Tanzania
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Raphael Z Sangeda
- Tanzania Human Genetics Organisation, Dar es Salaam, Tanzania
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department Pharmaceutical Microbiology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Clara Chamba
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Collet Dandara
- Division of Human Genetics, Department of Pathology & Institute of Infectious Disease and Molecular Medicine (IDM), University of Cape Town, Cape Town, South Africa
- Pharmacogenomics Research and Translation Unit, South African Medical Research Council, Cape Town, South Africa
| | - Enrico Novelli
- Vascular Medicine Institute, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Emile R Chimusa
- Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle, Tyne and Wear, UK
| | - Julie Makani
- Department of Haematology and Blood Transfusion,, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Tanzania Human Genetics Organisation, Dar es Salaam, Tanzania
- Sickle Cell Program, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- SickleInAfrica, Cape Town, South Africa
- Imperial College London, London, UK
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Teeny S, Jarrell ZR, Krigbaum NY, Cirillo PM, Go YM, Cohn BA, Jones DP. Environmental basis for early onset breast cancer. Reprod Toxicol 2025; 133:108866. [PMID: 40015485 PMCID: PMC11996058 DOI: 10.1016/j.reprotox.2025.108866] [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: 11/14/2024] [Revised: 02/11/2025] [Accepted: 02/24/2025] [Indexed: 03/01/2025]
Abstract
Pregnancy provokes a heightened amino acid requirement, especially in the third trimester. Alterations to late pregnancy amino acid metabolism have been associated with environmental breast carcinogen exposures, including DDT and PFAS. This project examined whether maternal serum amino acids in late pregnancy are associated with subsequent breast cancer risk. Archival third-trimester serum samples from 172 women who were later diagnosed with breast cancer were compared to samples from 351 women without known breast cancer. A prospective metabolome-wide association study (MWAS) for breast cancer cases showed that associated amino acid pathways included lysine, arginine, proline, aspartate, asparagine, alanine, tyrosine, tryptophan, histidine and branched-chain amino acids. Lower mean concentrations of individual amino acids, including histidine, threonine, lysine, and proline, were associated with an increased risk of breast cancer, and network analyses showed that these amino acids were negatively associated with protective breast cancer risk factors. Prospective MWAS for breast cancer cases diagnosed within 15 years of sample collection showed pathway associations for tryptophan, histidine, lysine methionine, and cysteine metabolism. Nutrient stresses caused by low amino acid levels impair immunosurveillance and activate oncogenic mechanisms of cell survival, thereby providing mechanisms by which environmental exposures in late pregnancy can contribute to breast cancer risk.
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Affiliation(s)
- Sami Teeny
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, United States
| | - Zachery R Jarrell
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, United States
| | - Nickilou Y Krigbaum
- Child Health and Development Studies, Public Health Institute, Berkeley, CA 94709, United States
| | - Piera M Cirillo
- Child Health and Development Studies, Public Health Institute, Berkeley, CA 94709, United States
| | - Young-Mi Go
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, United States
| | - Barbara A Cohn
- Child Health and Development Studies, Public Health Institute, Berkeley, CA 94709, United States.
| | - Dean P Jones
- Clinical Biomarkers Laboratory, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, United States.
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Petit P, Vuillerme N. Global research trends on the human exposome: a bibliometric analysis (2005-2024). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2025; 32:7808-7833. [PMID: 40056347 PMCID: PMC11953191 DOI: 10.1007/s11356-025-36197-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/24/2025] [Indexed: 03/10/2025]
Abstract
Exposome represents one of the most pressing issues in the environmental science research field. However, a comprehensive summary of worldwide human exposome research is lacking. We aimed to explore the bibliometric characteristics of scientific publications on the human exposome. A bibliometric analysis of human exposome publications from 2005 to December 2024 was conducted using the Web of Science in accordance with PRISMA guidelines. Trends/hotspots were investigated with keyword frequency, co-occurrence, and thematic map. Sex disparities in terms of publications and citations were examined. From 2005 to 2024, 931 publications were published in 363 journals and written by 4529 authors from 72 countries. The number of publications tripled during the last 5 years. Publications written by females (51% as first authors and 34% as last authors) were cited fewer times (13,674) than publications written by males (22,361). Human exposome studies mainly focused on air pollution, metabolomics, chemicals (e.g., per- and polyfluoroalkyl substances (PFAS), endocrine-disrupting chemicals, pesticides), early-life exposure, biomarkers, microbiome, omics, cancer, and reproductive disorders. Social and built environment factors, occupational exposure, multi-exposure, digital exposure (e.g., screen use), climate change, and late-life exposure received less attention. Our results uncovered high-impact countries, institutions, journals, references, authors, and key human exposome research trends/hotspots. The use of digital exposome technologies (e.g., sensors, and wearables) and data science (e.g., artificial intelligence) has blossomed to overcome challenges and could provide valuable knowledge toward precision prevention. Exposome risk scores represent a promising research avenue.
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Affiliation(s)
- Pascal Petit
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France.
- Laboratoire AGEIS, Université Grenoble Alpes, Bureau 315, Bâtiment Jean Roget, UFR de Médecine, Domaine de La Merci, 38706, La Tronche Cedex, France.
| | - Nicolas Vuillerme
- AGEIS, Université Grenoble Alpes, 38000, Grenoble, France
- Institut Universitaire de France, Paris, France
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le Maire A, Bourguet W. What Structural Biology Tells Us About the Mode of Action and Detection of Toxicants. Annu Rev Pharmacol Toxicol 2025; 65:529-546. [PMID: 39107041 DOI: 10.1146/annurev-pharmtox-061724-080642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2024]
Abstract
The study of the adverse effects of chemical substances on living organisms is an old and intense field of research. However, toxicological and environmental health sciences have long been dominated by descriptive approaches that enable associations or correlations but relatively few robust causal links and molecular mechanisms. Recent achievements have shown that structural biology approaches can bring this added value to the field. By providing atomic-level information, structural biology is a powerful tool to decipher the mechanisms by which toxicants bind to and alter the normal function of essential cell components, causing adverse effects. Here, using endocrine-disrupting chemicals as illustrative examples, we describe recent advances in the structure-based understanding of their modes of action and how this knowledge can be exploited to develop computational tools aimed at predicting properties of large collections of compounds.
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Affiliation(s)
- Albane le Maire
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, Inserm, Montpellier, France; ,
| | - William Bourguet
- Centre de Biologie Structurale (CBS), Univ Montpellier, CNRS, Inserm, Montpellier, France; ,
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Hernandez C, Viscomi B, Faria G, Vasconcelos R, Schneider C, Moreno J, Muniz M. Multilayer Technique Using Calcium Hydroxylapatite Biostimulation With Different Dilutions in the Lateral Face. Aesthet Surg J Open Forum 2024; 6:ojae049. [PMID: 40007596 PMCID: PMC11852247 DOI: 10.1093/asjof/ojae049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2025] Open
Abstract
Background There seems to be an interdependency of superficial structures on deeper layers, so that aging-related changes in 1 layer may lead to changes to the adjacent layers. Following the same rationale, treatment of 1 area may influence other neighboring aesthetic units. A more holistic approach would encompass soft-tissue repositioning and regenerative biostimulation, aiming for improvement of skin quality by increasing skin's collagen content. Objectives To describe the use of calcium hydroxylapatite (CaHA) in different presentations for soft-tissue repositioning and improvement of skin quality in the same session. Methods Males or females between 40 and 60 years of age, with normal BMI, mild facial laxity, underwent supraperiosteal injection of undiluted CaHA for focal biostimulation along the zygomatic arch, in the mandible angle and in the prejowl area, followed by treatment of diluted CaHA in the posterior temporal area, and the remainder in the premasseteric area in the same session, with follow-up pf at least 90 days. Investigator assessment was evaluated using the Global Aesthetic Improvement Scale. Results Out of 6 treated patients (median age of 44.5 years), 66% were deemed as improved (Grade 3) for the treatment of upper third of the face, whereas 83% of the patients were assessed as having at least improved for the mid and lower thirds of the face. Only mild adverse events were reported. Conclusions The technique described in this pilot study provides a full-face approach with CaHA based on the current concepts of the line of ligaments and facial biomechanics. Further studies are needed to validate the results. Level of Evidence 4
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Affiliation(s)
| | - Bianca Viscomi
- Corresponding Author: Dr Bianca Viscomi, Rua Diogo Jacome, 270 suite 91, São Paulo 04512-000, Brazil. E-mail:
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Pilz F, Burkhardt T, Scherer G, Scherer M, Pluym N. Identification of Specific Hemoglobin Adduct Patterns in Users of Different Tobacco/nicotine Products by Nontargeted GC-MS/MS Analysis. Chem Res Toxicol 2024; 37:1884-1902. [PMID: 39405427 DOI: 10.1021/acs.chemrestox.4c00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2024]
Abstract
Tobacco smoke contains several electrophilic constituents which are capable of forming adducts with nucleophilic sites in DNA and proteins like hemoglobin (Hb) and albumin. New nicotine and tobacco products are discussed as less harmful forms of tobacco use compared to smoking combustible cigarettes (CC) due to reduced exposure to harmful constituents. Hence, the adduct profile in users of various tobacco/nicotine products is expected to differ characteristically. In this article, we present a novel nontargeted screening strategy using GC-MS/MS for Hb adducts based on the analysis of the respective derivatized N-terminal valine adducts after modified Edman degradation. We analyzed blood samples from a clinical study with habitual users of CCs, electronic cigarettes, heated tobacco products (HTPs), oral tobacco, nicotine replacement therapy products and nonusers of any tobacco/nicotine products. Our nontargeted approach revealed significant differences in the Hb adduct profiles of the investigated tobacco/nicotine product user groups. Adduct identification was performed by means of an internal database, retention time estimations based on the theoretical boiling points, as well as in-house synthesized reference compounds. Several chemicals that form adducts with Hb could be identified: methylating and ethylating agents, ethylene oxide, acrylonitrile, acrylamide, glycidamide and 4-hydroxybenzaldehyde. Levels were elevated in smokers compared to all other groups for Hb adducts from methylating agents, ethylene oxide, acrylonitrile, acrylamide and glycidamide. Our approach revealed higher concentrations of Hb adducts formed by ethylation, acrylamide and glycidamide in users of HTPs compared to nonusers. However, concentrations for the latter two were still lower than in smokers. Due to their long half-lives, Hb adducts related to acrylonitrile, acrylamide (glycidamide), and ethylene oxide exposure may be useful for the biochemical verification of subjects̀ compliance in longitudinal and cross-sectional studies with respect to smoking and HTP use/abstinence.
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Affiliation(s)
- Fabian Pilz
- ABF, Analytisch-Biologisches Forschungslabor GmbH, Semmelweisstr. 5, Planegg 82152, Germany
| | - Therese Burkhardt
- ABF, Analytisch-Biologisches Forschungslabor GmbH, Semmelweisstr. 5, Planegg 82152, Germany
| | - Gerhard Scherer
- ABF, Analytisch-Biologisches Forschungslabor GmbH, Semmelweisstr. 5, Planegg 82152, Germany
| | - Max Scherer
- ABF, Analytisch-Biologisches Forschungslabor GmbH, Semmelweisstr. 5, Planegg 82152, Germany
| | - Nikola Pluym
- ABF, Analytisch-Biologisches Forschungslabor GmbH, Semmelweisstr. 5, Planegg 82152, Germany
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Chang CW, Hsu JY, Hsiao PZ, Sung PS, Liao PC. Optimized analytical strategy based on high-resolution mass spectrometry for unveiling associations between long-term chemical exposome in hair and Alzheimer's disease. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 284:116955. [PMID: 39213755 DOI: 10.1016/j.ecoenv.2024.116955] [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: 06/06/2024] [Revised: 08/24/2024] [Accepted: 08/25/2024] [Indexed: 09/04/2024]
Abstract
Exposure to environmental pollutants or contaminants is correlated with detrimental effects on human health, such as neurodegenerative diseases. Adopting hair as a biological matrix for biomonitoring is a significant innovation, since it can reflect the long-term chemical exposome, spanning months to years. However, only a limited number of studies have developed analytical strategies for profiling the chemical exposome in this heterogeneous biological matrix. In this study, a systematic investigation of the chemical extraction procedure from human hair was conducted, using a design of experiments and a high-resolution mass spectrometry (HRMS)-based suspect screening approach. The PlackettBurman (PB) design was applied to identify the significant variables influencing the number of detected features. Then, a central composite design was implemented to optimize the levels of each identified significant variable. Under the optimal conditions-15-minute pulverization, 25 mg of hair weight, 40 min of sonication, and a sonication temperature of 35 °C-approximately 32,000 and 15,000 aligned features were detected in positive and negative ion modes, respectively. This optimized analytical procedure was applied to hair samples from patients with Alzheimer's disease (AD) and individuals with normal cognitive function. Overall, 307 chemicals were identified using the suspect screening approach, with 37 chemicals differentiating patients with AD from controls. This study not only optimized an analytical procedure for characterizing the long-term chemical exposome in human hair but also explored the associations between AD and environmental factors.
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Affiliation(s)
- Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Jen-Yi Hsu
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Ping-Zu Hsiao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Pi-Shan Sung
- Department of Neurology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan; Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan.
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Maguire G, McGee ST. NeoGenesis MB-1 with CRISPR Technology Reduces the Effects of the Viruses (Phages) Associated with Acne - Case Report. Integr Med (Encinitas) 2024; 23:34-38. [PMID: 39355416 PMCID: PMC11441580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
We present a case of acne successfully treated with a topical spray containing live bacteria. The live bacteria used in the spray contain CRISPR, and adaptive immune system in the bacteria that are used to disable viral replication. Because acne skin contains bacteria in the microbiome where a shift toward non-CRISPR bacteria occurs, these bacteria are susceptible to bacteriophage infection and lysogeny. Normalizing the bacterial microbiome to one containing more CRISPR-containing bacteria renormalizes the microbiome by killing inflammation-causing bacteriophage infecting the non-CRISPR bacteria associated with acne.
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Affiliation(s)
- Greg Maguire
- California Physiological Society and Neogenesis, Inc.
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11
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Arnold C. The Base Hit: Neurological Diseases and Genetic Susceptibilities to Pesticide Exposures. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:94001. [PMID: 39240787 PMCID: PMC11379126 DOI: 10.1289/ehp15412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/25/2024] [Indexed: 09/08/2024]
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12
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Amini P, Okeme JO. Tear Fluid as a Matrix for Biomonitoring Environmental and Chemical Exposures. Curr Environ Health Rep 2024; 11:340-355. [PMID: 38967858 DOI: 10.1007/s40572-024-00454-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2024] [Indexed: 07/06/2024]
Abstract
PURPOSE Exposures to hazardous chemicals have been linked to many detrimental health effects and it is therefore critical to have effective biomonitoring methods to better evaluate key environmental exposures that increase the risk of chronic disease and death. Traditional biomonitoring utilizing blood and urine is limited due to the specialized skills and invasiveness of collecting these fluid samples. This systematic review focuses on tear fluid, which is largely under-researched, as a promising complementary matrix to the traditional fluids used for biomonitoring. The objective is to evaluate the practicability of using human tear fluid for biomonitoring environmental exposures, highlighting potential pitfalls and opportunities. RECENT FINDING Tear fluid biomonitoring represents a promising method for assessing exposures because it can be collected with minimal invasiveness and tears contain exposure markers from both the external and internal environments. Tear fluid uniquely interfaces with the external environment at the air-tear interface, providing a surface for airborne chemicals to diffuse into the ocular environment and interact with biomolecules. Tear fluid also contains molecules from the internal environment that have travelled from the blood to tears by crossing the blood-tear barrier. This review demonstrates that tear fluid can be used to identify hazardous chemicals from the external environment and differentiate exposure groups.
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Affiliation(s)
- Parshawn Amini
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Ontario, L8S 4L8, Canada
| | - Joseph O Okeme
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, ON, Ontario, L8S 4L8, Canada.
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Hossain MZ, Feuerstein ML, Gu Y, Warth B. Scaling up a targeted exposome LC-MS/MS biomonitoring method by incorporating veterinary drugs and pesticides. Anal Bioanal Chem 2024; 416:4369-4382. [PMID: 38937289 PMCID: PMC11271401 DOI: 10.1007/s00216-024-05374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024]
Abstract
Humans are exposed to a cocktail of food-related and environmental contaminants, potentially contributing to the etiology of chronic diseases. Better characterizing the "exposome" is a challenging task and requires broad human biomonitoring (HBM). Veterinary drugs (VDs)/antibiotics, widely used and regulated in food and animal production, however, are typically not yet included in exposomics workflows. Therefore, in this work, a previously established multianalyte liquid chromatography-tandem mass spectrometry (LC-MS/MS) method covering >80 diverse xenobiotics was expanded by >40 VDs/antibiotics and pesticides. It was investigated if the generic workflow allowed for the successful integration of a high number of new analytes in a proof-of-principle study. The expanded method was successfully in-house validated and specificity, matrix effects, linearity, intra- and inter-day precision, accuracy, limits of quantification, and detection were evaluated. The optimized method demonstrated satisfactory recovery (81-120%) for most of the added analytes with acceptable RSDs (<20%) at three spiking levels. The majority of VDs/antibiotics and pesticides (69%) showed matrix effects within a range of 50-140%. Moreover, sensitivity was excellent with median LODs and LOQs of 0.10 ng/mL and 0.31 ng/mL, respectively. In total, the expanded method can be used to detect and quantify more than 120 highly diverse analytes in a single analytical run. To the best of the authors' knowledge, this work represents the first targeted biomonitoring method integrating VDs with various other classes of pollutants including plasticizers, PFAS, bisphenols, mycotoxins, and personal care products. It demonstrates the potential to expand targeted multianalyte methods towards additional groups of potentially toxic chemicals.
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Affiliation(s)
- Md Zakir Hossain
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
| | - Max L Feuerstein
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
- Exposome Austria, Research Infrastructure and National EIRENE Node, Vienna, Austria
| | - Yunyun Gu
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria
- Vienna Doctoral School of Chemistry, University of Vienna, Währinger Straße 42, 1090, Vienna, Austria
| | - Benedikt Warth
- Department of Food Chemistry and Toxicology, Faculty of Chemistry, University of Vienna, Währinger Str. 38, 1090, Vienna, Austria.
- Exposome Austria, Research Infrastructure and National EIRENE Node, Vienna, Austria.
- Vienna Doctoral School of Chemistry, University of Vienna, Währinger Straße 42, 1090, Vienna, Austria.
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14
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Matus P, Sepúlveda-Peñaloza A, Page K, Rodríguez C, Cárcamo M, Bustamante F, Garrido M, Urquidi C. The Chilean exposome-based system for ecosystems (CHiESS): a framework for national data integration and analytics platform. Front Public Health 2024; 12:1407514. [PMID: 39114513 PMCID: PMC11303229 DOI: 10.3389/fpubh.2024.1407514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
The double burden of diseases and scarce resources in developing countries highlight the need to change the conceptualization of health problems and translational research. Contrary to the traditional paradigm focused on genetics, the exposome paradigm proposed in 2005 that complements the genome is an innovative theory. It involves a holistic approach to understanding the complexity of the interactions between the human being’s environment throughout their life and health. This paper outlines a scalable framework for exposome research, integrating diverse data sources for comprehensive public health surveillance and policy support. The Chilean exposome-based system for ecosystems (CHiESS) project proposes a conceptual model based on the ecological and One Health approaches, and the development of a technological dynamic platform for exposome research, which leverages available administrative data routinely collected by national agencies, in clinical records, and by biobanks. CHiESS considers a multilevel exposure for exposome operationalization, including the ecosystem, community, population, and individual levels. CHiESS will include four consecutive stages for development into an informatic platform: (1) environmental data integration and harmonization system, (2) clinical and omics data integration, (3) advanced analytical algorithm development, and (4) visualization interface development and targeted population-based cohort recruitment. The CHiESS platform aims to integrate and harmonize available secondary administrative data and provide a complete geospatial mapping of the external exposome. Additionally, it aims to analyze complex interactions between environmental stressors of the ecosystem and molecular processes of the human being and their effect on human health. Moreover, by identifying exposome-based hotspots, CHiESS allows the targeted and efficient recruitment of population-based cohorts for translational research and impact evaluation. Utilizing advanced technologies such as Artificial Intelligence (AI), Internet of Things (IoT), and blockchain, this framework enhances data security, real-time monitoring, and predictive analytics. The CHiESS model is adaptable for international use, promoting global health collaboration and supporting sustainable development goals.
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Affiliation(s)
| | | | | | | | | | | | | | - Cinthya Urquidi
- Department of Epidemiology and Health Studies, Medicine Faculty, Universidad de los Andes, Santiago, Chile
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15
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Drago G, Aloi N, Ruggieri S, Longo A, Contrino ML, Contarino FM, Cibella F, Colombo P, Longo V. Guardians under Siege: Exploring Pollution's Effects on Human Immunity. Int J Mol Sci 2024; 25:7788. [PMID: 39063030 PMCID: PMC11277414 DOI: 10.3390/ijms25147788] [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: 06/20/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Chemical pollution poses a significant threat to human health, with detrimental effects on various physiological systems, including the respiratory, cardiovascular, mental, and perinatal domains. While the impact of pollution on these systems has been extensively studied, the intricate relationship between chemical pollution and immunity remains a critical area of investigation. The focus of this study is to elucidate the relationship between chemical pollution and human immunity. To accomplish this task, this study presents a comprehensive review that encompasses in vitro, ex vivo, and in vivo studies, shedding light on the ways in which chemical pollution can modulate human immunity. Our aim is to unveil the complex mechanisms by which environmental contaminants compromise the delicate balance of the body's defense systems going beyond the well-established associations with defense systems and delving into the less-explored link between chemical exposure and various immune disorders, adding urgency to our understanding of the underlying mechanisms and their implications for public health.
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Affiliation(s)
- Gaspare Drago
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.D.); (N.A.); (S.R.); (A.L.); (F.C.); (V.L.)
| | - Noemi Aloi
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.D.); (N.A.); (S.R.); (A.L.); (F.C.); (V.L.)
| | - Silvia Ruggieri
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.D.); (N.A.); (S.R.); (A.L.); (F.C.); (V.L.)
| | - Alessandra Longo
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.D.); (N.A.); (S.R.); (A.L.); (F.C.); (V.L.)
| | - Maria Lia Contrino
- Azienda Sanitaria Provinciale di Siracusa, Corso Gelone 17, 96100 Siracusa, Italy; (M.L.C.); (F.M.C.)
| | - Fabio Massimo Contarino
- Azienda Sanitaria Provinciale di Siracusa, Corso Gelone 17, 96100 Siracusa, Italy; (M.L.C.); (F.M.C.)
| | - Fabio Cibella
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.D.); (N.A.); (S.R.); (A.L.); (F.C.); (V.L.)
| | - Paolo Colombo
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.D.); (N.A.); (S.R.); (A.L.); (F.C.); (V.L.)
| | - Valeria Longo
- Institute for Biomedical Research and Innovation, National Research Council of Italy (IRIB-CNR), Via Ugo La Malfa 153, 90146 Palermo, Italy; (G.D.); (N.A.); (S.R.); (A.L.); (F.C.); (V.L.)
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16
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Panduro A, Ojeda-Granados C, Ramos-Lopez O, Roman S. Editorial: Genome-based nutrition strategies for preventing diet-related chronic diseases: where genes, diet, and food culture meet. Front Nutr 2024; 11:1441685. [PMID: 38978697 PMCID: PMC11228323 DOI: 10.3389/fnut.2024.1441685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 07/10/2024] Open
Affiliation(s)
- Arturo Panduro
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - Claudia Ojeda-Granados
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia, ” University of Catania, Catania, Italy
| | - Omar Ramos-Lopez
- Medicine and Psychology School, Autonomous University of Baja California, Tijuana, Baja California, Mexico
| | - Sonia Roman
- Department of Genomic Medicine in Hepatology, Civil Hospital of Guadalajara, Guadalajara, Jalisco, Mexico
- Health Sciences Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
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17
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Apostolopoulos Y, Sönmez S, Thiese MS, Olufemi M, Gallos LK. A blueprint for a new commercial driving epidemiology: An emerging paradigm grounded in integrative exposome and network epistemologies. Am J Ind Med 2024; 67:515-531. [PMID: 38689533 DOI: 10.1002/ajim.23588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/29/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024]
Abstract
Excess health and safety risks of commercial drivers are largely determined by, embedded in, or operate as complex, dynamic, and randomly determined systems with interacting parts. Yet, prevailing epidemiology is entrenched in narrow, deterministic, and static exposure-response frameworks along with ensuing inadequate data and limiting methods, thereby perpetuating an incomplete understanding of commercial drivers' health and safety risks. This paper is grounded in our ongoing research that conceptualizes health and safety challenges of working people as multilayered "wholes" of interacting work and nonwork factors, exemplified by complex-systems epistemologies. Building upon and expanding these assumptions, herein we: (a) discuss how insights from integrative exposome and network-science-based frameworks can enhance our understanding of commercial drivers' chronic disease and injury burden; (b) introduce the "working life exposome of commercial driving" (WLE-CD)-an array of multifactorial and interdependent work and nonwork exposures and associated biological responses that concurrently or sequentially impact commercial drivers' health and safety during and beyond their work tenure; (c) conceptualize commercial drivers' health and safety risks as multilayered networks centered on the WLE-CD and network relational patterns and topological properties-that is, arrangement, connections, and relationships among network components-that largely govern risk dynamics; and (d) elucidate how integrative exposome and network-science-based innovations can contribute to a more comprehensive understanding of commercial drivers' chronic disease and injury risk dynamics. Development, validation, and proliferation of this emerging discourse can move commercial driving epidemiology to the frontier of science with implications for policy, action, other working populations, and population health at large.
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Affiliation(s)
| | - Sevil Sönmez
- College of Business, University of Central Florida, Orlando, Florida, USA
| | - Matthew S Thiese
- Rocky Mountain Center for Occupational and Environmental Health, University of Utah, Salt Lake City, Utah, USA
| | - Mubo Olufemi
- Rocky Mountain Center for Occupational and Environmental Health, University of Utah, Salt Lake City, Utah, USA
| | - Lazaros K Gallos
- DIMACS, Center for Discrete Mathematics & Theoretical Computer Science, Rutgers University, Piscataway, New Jersey, USA
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18
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Inaç Y, D'Hooghe S, Van Dyck D, Dury S, Vandevijvere S, Deforche B, De Clercq EM, Van de Weghe N, De Ridder K. Associations between the objective and perceived food environment and eating behavior in relation to socioeconomic status among adults in peri-urban settings: results from the CIVISANO study in Flanders, Belgium. Int J Health Geogr 2024; 23:10. [PMID: 38724949 PMCID: PMC11080110 DOI: 10.1186/s12942-024-00369-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 04/10/2024] [Indexed: 05/13/2024] Open
Abstract
Obesity, a significant public health concern, disproportionately affects people with lower socioeconomic status (SES). Food environments have been identified as part of the causal chain of this disparity. This study investigated variations in the food environment across groups with different SES profiles residing in peri-urban municipal settings. In addition, it examined the association of the perceived and objective food environments with eating behaviour and assessed if these associations were moderated by SES. Utilizing GIS and survey data (n = 497, aged 25-65), results showed differences in the objective and perceived food environments based on SES. Respondents with higher SES perceived their food environments as better but resided farther from all food outlets compared to respondents with lower SES. However, there was no difference in outlet density or mRFEI between SES groups. SES moderated associations between the objective and perceived food environments and most eating behavior outcomes except fast food consumption frequency. For fruits and vegetables, SES moderated the association between neighborhood availability and consumption frequency (β0.23,CI0.03;0.49). Stratified analysis revealed a positive association for both lower (β0.15, CI0.03;0.27) and higher (β0.37, CI 0.12;0.63) SES groups. For snack foods, SES moderated the association between healthy outlet density and consumption frequency (β-0.60, CI-0.94; -0.23), showing statistical significance only for respondents with higher SES (β0.36,CI 0.18;0.55). Similarly, for sugar-sweetened beverages, a statistically significant interaction was observed between unhealthy outlet density in the 1000m buffer and consumption frequency (β 0.06, CI 0.02; 0.11). However, this association was only statistically significant for respondents with higher SES (β-0.02,CI -0.05;-0.0002). These results emphasize the significance of SES as a crucial element in comprehending the connection between the food environment and eating behaviour. Indicating the need for policymakers to take SES into account when implementing food environment interventions, particularly when focusing on the neighborhood food environment without considering residents' SES and their perceptions.
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Affiliation(s)
- Yasemin Inaç
- Sciensano, Department of Epidemiology and Public Health, Brussels, Belgium.
- Faculty of Psychology and Educational Sciences, Adult Educational Sciences, Vrije Universiteit Brussel, Brussels, Belgium.
- Faculty of Medicine and Health Sciences, Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium.
| | - Suzannah D'Hooghe
- Sciensano, Department of Epidemiology and Public Health, Brussels, Belgium
- Faculty of Medicine and Health Sciences, Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
- Faculty of Psychology and Educational Sciences, Adult Educational Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Delfien Van Dyck
- Faculty of Medicine and Health Sciences, Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Sarah Dury
- Faculty of Psychology and Educational Sciences, Adult Educational Sciences, Vrije Universiteit Brussel, Brussels, Belgium
- Society and Ageing Research Lab (SARLab), Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Benedicte Deforche
- Faculty of Medicine and Health Sciences, Department of Public Health and Primary Care, Ghent University, Ghent, Belgium
- Faculty of Physical Education and Physiotherapy, Department of Movement and Sport Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Eva M De Clercq
- Sciensano, Department of Chemical and Physical Health Risks, Brussels, Belgium
| | - Nico Van de Weghe
- Faculty of Sciences, Department of Geography, Ghent University, Ghent, Belgium
| | - Karin De Ridder
- Sciensano, Department of Epidemiology and Public Health, Brussels, Belgium
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19
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Kosnik MB, Antczak P, Fantke P. Data-Driven Characterization of Genetic Variability in Disease Pathways and Pesticide-Induced Nervous System Disease in the United States Population. ENVIRONMENTAL HEALTH PERSPECTIVES 2024; 132:57003. [PMID: 38752992 PMCID: PMC11098008 DOI: 10.1289/ehp14108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024]
Abstract
BACKGROUND Genetic susceptibility to chemicals is incompletely characterized. However, nervous system disease development following pesticide exposure can vary in a population, implying some individuals may have higher genetic susceptibility to pesticide-induced nervous system disease. OBJECTIVES We aimed to build a computational approach to characterize single-nucleotide polymorphisms (SNPs) implicated in chemically induced adverse outcomes and used this framework to assess the link between differential population susceptibility to pesticides and human nervous system disease. METHODS We integrated publicly available datasets of Chemical-Gene, Gene-Pathway, and SNP-Disease associations to build Chemical-Pathway-Gene-SNP-Disease linkages for humans. As a case study, we integrated these linkages with spatialized pesticide application data for the US from 1992 to 2018 and spatialized nervous system disease rates for 2018. Through this, we characterized SNPs that may be important in states with high disease occurrence based on the pesticides used there. RESULTS We found that the number of SNP hits per pesticide in US states positively correlated with disease incidence and prevalence for Alzheimer's disease, Parkinson disease, and multiple sclerosis. We performed frequent itemset mining to differentiate pesticides used over time in states with high and low disease occurrence and found that only 19% of pesticide sets overlapped between 10 states with high disease occurrence and 10 states with low disease occurrence rates, and more SNPs were implicated in pathways in high disease occurrence states. Through a cross-validation of subsets of five high and low disease occurrence states, we characterized SNPs, genes, pathways, and pesticides more frequently implicated in high disease occurrence states. DISCUSSION Our findings support that pesticides contribute to nervous system disease, and we developed priority lists of SNPs, pesticides, and pathways for further study. This data-driven approach can be adapted to other chemicals, diseases, and locations to characterize differential population susceptibility to chemical exposures. https://doi.org/10.1289/EHP14108.
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Affiliation(s)
- Marissa B. Kosnik
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
- Department of Environmental Toxicology, Swiss Federal Institute of Aquatic Science and Technology, Dübendorf, Switzerland
| | - Philipp Antczak
- Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
- Cluster of Excellence on Cellular Stress Responses in Aging-associated Diseases (CECAD), University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University of Cologne, Cologne, Germany
| | - Peter Fantke
- Quantitative Sustainability Assessment, Department of Environmental and Resource Engineering, Technical University of Denmark, Kgs. Lyngby, Denmark
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20
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Lefèvre-Arbogast S, Chaker J, Mercier F, Barouki R, Coumoul X, Miller GW, David A, Samieri C. Assessing the contribution of the chemical exposome to neurodegenerative disease. Nat Neurosci 2024; 27:812-821. [PMID: 38684891 DOI: 10.1038/s41593-024-01627-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Over the past few decades, numerous environmental chemicals from solvents to pesticides have been suggested to be involved in the development and progression of neurodegenerative diseases. Most of the evidence has accumulated from occupational or cohort studies in humans or laboratory research in animal models, with a range of chemicals being implicated. What has been missing is a systematic approach analogous to genome-wide association studies, which have identified dozens of genes involved in Alzheimer's disease, Parkinson's disease and other neurodegenerative diseases. Fortunately, it is now possible to study hundreds to thousands of chemical features under the exposome framework. This Perspective explores how advances in mass spectrometry make it possible to generate exposomic data to complement genomic data and thereby better understand neurodegenerative diseases.
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Affiliation(s)
- S Lefèvre-Arbogast
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, France
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - J Chaker
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - F Mercier
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - R Barouki
- Université Paris Cité, T3S, INSERM UMR-S 1124, Paris, France
| | - X Coumoul
- Université Paris Cité, T3S, INSERM UMR-S 1124, Paris, France
| | - G W Miller
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - A David
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail) - UMR_S 1085, Rennes, France
| | - C Samieri
- University of Bordeaux, Inserm, Bordeaux Population Health Research Center, UMR 1219, Bordeaux, France.
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21
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Lester BM, Camerota M, Everson TM, Shuster CL, Marsit CJ. Toward a more holistic approach to the study of exposures and child outcomes. Epigenomics 2024; 16:635-651. [PMID: 38482639 PMCID: PMC11157992 DOI: 10.2217/epi-2023-0424] [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: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 06/09/2024] Open
Abstract
Aim: The current work was designed to demonstrate the application of the exposome framework in examining associations between exposures and children's long-term neurodevelopmental and behavioral outcomes. Methods: Longitudinal data were collected from birth through age 6 from 402 preterm infants. Three statistical methods were utilized to demonstrate the exposome framework: exposome-wide association study, cumulative exposure and machine learning models, with and without epigenetic data. Results: Each statistical approach answered a distinct research question regarding the impact of exposures on longitudinal child outcomes. Findings highlight associations between exposures, epigenetics and executive function. Conclusion: Findings demonstrate how an exposome-based approach can be utilized to understand relationships between internal (e.g., DNA methylation) and external (e.g., prenatal risk) exposures and long-term developmental outcomes in preterm children.
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Affiliation(s)
- Barry M Lester
- Department of Pediatrics, Brown Alpert Medical School & Women & Infants Hospital, Providence, RI 02905, USA
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School & Women & Infants Hospital, Providence, RI 02905, USA
- Department of Psychiatry & Human Behavior, Brown Alpert Medical School, Providence, RI 02905, USA
| | - Marie Camerota
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School & Women & Infants Hospital, Providence, RI 02905, USA
- Department of Psychiatry & Human Behavior, Brown Alpert Medical School, Providence, RI 02905, USA
| | - Todd M Everson
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
| | - Coral L Shuster
- Department of Pediatrics, Brown Alpert Medical School & Women & Infants Hospital, Providence, RI 02905, USA
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School & Women & Infants Hospital, Providence, RI 02905, USA
| | - Carmen J Marsit
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA 30322, USA
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22
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Apostolopoulos Y, Sönmez S, Thiese MS, Gallos LK. The indispensable whole of work and population health: How the working life exposome can advance empirical research, policy, and action. Scand J Work Environ Health 2024; 50:83-95. [PMID: 37952240 PMCID: PMC10927210 DOI: 10.5271/sjweh.4130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Indexed: 11/14/2023] Open
Abstract
OBJECTIVES The thesis of this paper is that health and safety challenges of working people can only be fully understood by examining them as wholes with interacting parts. This paper unravels this indispensable whole by introducing the working life exposome and elucidating how associated epistemologies and methodologies can enhance empirical research. METHODS Network and population health scientists have initiated an ongoing discourse on the state of empirical work-health-safety-well-being research. RESULTS Empirical research has not fully captured the totality and complexity of multiple and interacting work and nonwork factors defining the health of working people over their life course. We challenge the prevailing paradigm by proposing to expand it from narrow work-related exposures and associated monocausal frameworks to the holistic study of work and population health grounded in complexity and exposome sciences. Health challenges of working people are determined by, embedded in, and/or operate as complex systems comprised of multilayered and interdependent components. One can identify many potentially causal factors as sufficient and component causes where removal of one or more of these can impact disease progression. We, therefore, cannot effectively study them by an a priori determination of a set of components and/or properties to be examined separately and then recombine partial approaches, attempting to form a picture of the whole. Instead, we must examine these challenges as wholes from the start, with an emphasis on interactions among their multifactorial components and their emergent properties. Despite various challenges, working-life-exposome-grounded frameworks and associated innovations have the potential to accomplish that. CONCLUSIONS This emerging paradigm shift can move empirical work-health-safety-well-being research to cutting-edge science and enable more impactful policies and actions.
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Affiliation(s)
| | - Sevil Sönmez
- University of Central Florida College of Business, Orlando, Florida, USA.
| | - Matthew S Thiese
- Rocky Mountain Center for Occupational and Environmental Health, University of Utah School of Medicine and Weber State University, Salt Lake City, Utah, USA
| | - Lazaros K Gallos
- DIMACS, Center for Discrete Mathematics & Theoretical Computer Science, Rutgers University, Piscataway, New Jersey, USA
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23
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Yang W, Li X, Li X, Hu B, Xu S, Zhang H, Wang Y, Jin T, He Y. Impact of missense TSBP1 variants on the susceptibility to coronary heart disease. Gene 2024; 896:148042. [PMID: 38042215 DOI: 10.1016/j.gene.2023.148042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023]
Abstract
BACKGROUND A genome-wide association study has recognized C6orf10-BTNL2 polymorphism in coronary artery disease. The goal of this study was to explore the potential correlation of nine missense TSBP1 variants with coronary heart disease (CHD) risk in the Chinese Han population. METHODS Nine TSBP1 missense single nucleotide polymorphisms (SNPs) were selected for genotyping by the Agena MassARRAY platform. Odds ratios (ORs) with 95% confidence intervals (CIs) were calculated to analyze the contribution of TSBP1 SNPs to CHD predisposition by logistic regression models adjusted by age, sex, drinking, and smoking. The correlation of TSBP1 variants with clinical data in CHD patients was examined by Kruskal-Wallis test. RESULTS rs9268368-C (p = 0.039, OR = 1.18, 95 % CI: 1.01-1.38) was related to an increased risk of CHD, while rs3749966-C (p = 0.032, OR = 0.49, 95 % CI: 0.25-0.96) and rs3129941-A (p = 0.011, OR = 0.74, 95 % CI: 0.59-0.93) might be protective factors against CHD occurrence in the Chinese Han population. We also observed the effects of demographic characteristics (age, sex, alcohol consumption, and smoking) and complications (hypertension and diabetes) on the interactive association of TSBP1 polymorphisms with CHD susceptibility. rs139993810 was related to the levels of high-density lipoprotein cholesterol (HDL-C, p = 0.030). CONCLUSIONS Our findings determined the association of TSBP1 rs9268368, rs3749966, and rs3129941 with CHD occurrence in the Chinese Han population, and highlighted the influence of demographic characteristics and complications on the interactive association of TSBP1 polymorphisms with CHD risk.
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Affiliation(s)
- Wei Yang
- Department of Emergency, the Affiliated Hospital of Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Xuguang Li
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Xuemei Li
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Baoping Hu
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Department of Anesthesia, the Affiliated Hospital of Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Shilin Xu
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Department of Clinical Laboratory, the Affiliated Hospital of Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Hengxun Zhang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Department of Healthcare, the Affiliated Hospital of Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Yuhe Wang
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Department of Clinical Laboratory, the Affiliated Hospital of Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Tianbo Jin
- School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China.
| | - Yongjun He
- Key Laboratory of Molecular Mechanism and Intervention Research for Plateau Diseases of Tibet Autonomous Region, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China; Key Laboratory of High Altitude Hypoxia Environment and Life Health, School of Medicine, Xizang Minzu University, Xianyang 712082, Shaanxi, China.
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Deru LS, Gipson EZ, Hales KE, Bikman BT, Davidson LE, Horne BD, LeCheminant JD, Tucker LA, Bailey BW. The Effects of a High-Carbohydrate versus a High-Fat Shake on Biomarkers of Metabolism and Glycemic Control When Used to Interrupt a 38-h Fast: A Randomized Crossover Study. Nutrients 2024; 16:164. [PMID: 38201992 PMCID: PMC10780935 DOI: 10.3390/nu16010164] [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: 11/10/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/12/2024] Open
Abstract
This study aimed to determine the impact of various fast-interrupting shakes on markers of glycemic control including glucose, β-hydroxybutyrate (BHB), insulin, glucagon, GLP-1, and GIP. Twenty-seven sedentary adults (twelve female, fifteen male) with overweight or obesity completed this study. One condition consisted of a 38-h water-only fast, and the other two conditions repeated this, but the fasts were interrupted at 24 h by either a high carbohydrate/low fat (HC/LF) shake or an isovolumetric and isocaloric low carbohydrate/high fat (LC/HF) shake. The water-only fast resulted in 135.3% more BHB compared to the HC/LF condition (p < 0.01) and 69.6% more compared to the LC/HF condition (p < 0.01). The LC/HF condition exhibited a 38.8% higher BHB level than the HC/LF condition (p < 0.01). The area under the curve for glucose was 14.2% higher in the HC/LF condition than in the water condition (p < 0.01) and 6.9% higher compared to the LC/HF condition (p < 0.01), with the LC/HF condition yielding 7.8% more glucose than the water condition (p < 0.01). At the 25-h mark, insulin and glucose-dependent insulinotropic polypeptide (GIP) were significantly elevated in the HC/LF condition compared to the LC/HF condition (p < 0.01 and p = 0.02, respectively) and compared to the water condition (p < 0.01). Furthermore, insulin, GLP-1, and GIP were increased in the LC/HF condition compared to the water condition at 25 h (p < 0.01, p = 0.015, and p < 0.01, respectively). By the 38-h time point, no differences were observed among the conditions for any of the analyzed hormones. While a LC/HF shake does not mimic a fast completely, it does preserve some of the metabolic changes including elevated BHB and glucagon, and decreased glucose and insulin compared to a HC/LF shake, implying a potential for improved metabolic health.
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Affiliation(s)
- Landon S. Deru
- Department of Exercise Science, Brigham Young University, Provo, UT 84602, USA
- Division of Physical Activity and Weight Management, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Elizabeth Z. Gipson
- Department of Exercise Science, Brigham Young University, Provo, UT 84602, USA
| | - Katelynn E. Hales
- Department of Exercise Science, Brigham Young University, Provo, UT 84602, USA
| | - Benjamin T. Bikman
- Department of Cellular Biology and Physiology, Brigham Young University, Provo, UT 84602, USA
| | - Lance E. Davidson
- Department of Exercise Science, Brigham Young University, Provo, UT 84602, USA
| | - Benjamin D. Horne
- Intermountain Heart Institute, Intermountain Medical Center, Salt Lake City, UT 84107, USA;
| | - James D. LeCheminant
- Department of Nutrition, Dietetics and Food Science, Brigham Young University, Provo, UT 84602, USA;
| | - Larry A. Tucker
- Department of Exercise Science, Brigham Young University, Provo, UT 84602, USA
| | - Bruce W. Bailey
- Department of Exercise Science, Brigham Young University, Provo, UT 84602, USA
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Protti G, Rubbi L, Gören T, Sabirli R, Civlan S, Kurt Ö, Türkçüer İ, Köseler A, Pellegrini M. The methylome of buccal epithelial cells is influenced by age, sex, and physiological properties. Physiol Genomics 2023; 55:618-633. [PMID: 37781740 DOI: 10.1152/physiolgenomics.00063.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/05/2023] [Accepted: 09/27/2023] [Indexed: 10/03/2023] Open
Abstract
Epigenetic modifications, particularly DNA methylation, have emerged as regulators of gene expression and are implicated in various biological processes and disease states. Understanding the factors influencing the epigenome is essential for unraveling its complexity. In this study, we aimed to identify how the methylome of buccal epithelial cells, a noninvasive and easily accessible tissue, is associated with demographic and health-related variables commonly used in clinical settings, such as age, sex, blood immune composition, hemoglobin levels, and others. We developed a model to assess the association of multiple factors with the human methylome and identify the genomic loci significantly impacted by each trait. We demonstrated that DNA methylation variation is accurately modeled by several factors. We confirmed the well-known impact of age and sex and unveiled novel clinical factors associated with DNA methylation, such as blood neutrophils, hemoglobin, red blood cell distribution width, high-density lipoprotein cholesterol, and urea. Genomic regions significantly associated with these traits were enriched in relevant transcription factors, drugs, and diseases. Among our findings, we showed that neutrophil-impacted loci were involved in neutrophil functionality and maturation. Similarly, hemoglobin-influenced sites were associated with several diseases, including aplastic anemia, and the genomic loci affected by urea were related to congenital anomalies of the kidney and urinary tract. Our findings contribute to a better understanding of the human methylome plasticity and provide insights into novel factors shaping DNA methylation patterns, highlighting their potential clinical implications as biomarkers and the importance of considering these physiological traits in future medical epigenomic investigations.NEW & NOTEWORTHY We have developed a quantitative model to assess how the human methylome is associated with several factors and to identify the genomic loci significantly impacted by each trait. We reported novel health-related factors driving DNA methylation patterns and new site-specific regulations that further elucidate methylome dynamics. Our study contributes to a better understanding of the plasticity of the human methylome and unveils novel physiological traits with a potential role in future medical epigenomic investigations.
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Affiliation(s)
- Giulia Protti
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
| | - Tarik Gören
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Ramazan Sabirli
- Emergency Department, Bakircay University Faculty of Medicine Cigli Training and Research Hospital, Izmir, Turkey
| | - Serkan Civlan
- Department of Neurosurgery, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Özgür Kurt
- Department of Microbiology, Acibadem Mehmet Ali Aydinlar University School of Medicine, Istanbul, Turkey
| | - İbrahim Türkçüer
- Emergency Department, Pamukkale University Medical Faculty, Denizli, Turkey
| | - Aylin Köseler
- Department of Biophysics, Pamukkale University Faculty of Medicine, Denizli, Turkey
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California, Los Angeles, California, United States
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Glassmeyer ST, Burns EE, Focazio MJ, Furlong ET, Gribble MO, Jahne MA, Keely SP, Kennicutt AR, Kolpin DW, Medlock Kakaley EK, Pfaller SL. Water, Water Everywhere, but Every Drop Unique: Challenges in the Science to Understand the Role of Contaminants of Emerging Concern in the Management of Drinking Water Supplies. GEOHEALTH 2023; 7:e2022GH000716. [PMID: 38155731 PMCID: PMC10753268 DOI: 10.1029/2022gh000716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 09/21/2023] [Accepted: 09/21/2023] [Indexed: 12/30/2023]
Abstract
The protection and management of water resources continues to be challenged by multiple and ongoing factors such as shifts in demographic, social, economic, and public health requirements. Physical limitations placed on access to potable supplies include natural and human-caused factors such as aquifer depletion, aging infrastructure, saltwater intrusion, floods, and drought. These factors, although varying in magnitude, spatial extent, and timing, can exacerbate the potential for contaminants of concern (CECs) to be present in sources of drinking water, infrastructure, premise plumbing and associated tap water. This monograph examines how current and emerging scientific efforts and technologies increase our understanding of the range of CECs and drinking water issues facing current and future populations. It is not intended to be read in one sitting, but is instead a starting point for scientists wanting to learn more about the issues surrounding CECs. This text discusses the topical evolution CECs over time (Section 1), improvements in measuring chemical and microbial CECs, through both analysis of concentration and toxicity (Section 2) and modeling CEC exposure and fate (Section 3), forms of treatment effective at removing chemical and microbial CECs (Section 4), and potential for human health impacts from exposure to CECs (Section 5). The paper concludes with how changes to water quantity, both scarcity and surpluses, could affect water quality (Section 6). Taken together, these sections document the past 25 years of CEC research and the regulatory response to these contaminants, the current work to identify and monitor CECs and mitigate exposure, and the challenges facing the future.
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Affiliation(s)
- Susan T. Glassmeyer
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | | | - Michael J. Focazio
- Retired, Environmental Health ProgramEcosystems Mission AreaU.S. Geological SurveyRestonVAUSA
| | - Edward T. Furlong
- Emeritus, Strategic Laboratory Sciences BranchLaboratory & Analytical Services DivisionU.S. Geological SurveyDenverCOUSA
| | - Matthew O. Gribble
- Gangarosa Department of Environmental HealthRollins School of Public HealthEmory UniversityAtlantaGAUSA
| | - Michael A. Jahne
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | - Scott P. Keely
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
| | - Alison R. Kennicutt
- Department of Civil and Mechanical EngineeringYork College of PennsylvaniaYorkPAUSA
| | - Dana W. Kolpin
- U.S. Geological SurveyCentral Midwest Water Science CenterIowa CityIAUSA
| | | | - Stacy L. Pfaller
- U.S. Environmental Protection AgencyOffice of Research and DevelopmentCincinnatiOHUSA
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27
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Chen YC, Hsu JF, Chang CW, Li SW, Yang YC, Chao MR, Chen HJC, Liao PC. Connecting chemical exposome to human health using high-resolution mass spectrometry-based biomonitoring: Recent advances and future perspectives. MASS SPECTROMETRY REVIEWS 2023; 42:2466-2486. [PMID: 36062854 DOI: 10.1002/mas.21805] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 06/15/2023]
Abstract
Compared with the rapid advances in genomics leading to broad understanding of human disease, the linkage between chemical exposome and diseases is still under investigation. High-resolution mass spectrometry (HRMS) is expected to accelerate the process via relatively accurate and precise biomonitoring of human exposome. This review covers recent advancements in biomonitoring of exposed environmental chemicals (chemical exposome) using HRMS described in the 124 articles that resulted from a systematic literature search on Medline and Web of Science databases. The analytical strategic aspects, including the selection of specimens, sample preparation, instrumentation, untargeted versus targeted analysis, and workflows for MS-based biomonitoring to explore the environmental chemical space of human exposome, are deliberated. Applications of HRMS in human exposome investigation are presented by biomonitoring (1) exposed chemical compounds and their biotransformation products; (2) DNA/protein adducts; and (3) endogenous compound perturbations. Challenges and future perspectives are also discussed.
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Affiliation(s)
- Yuan-Chih Chen
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Jing-Fang Hsu
- National Institute of Environmental Health Sciences, National Health Research Institutes, Miaoli, Taiwan
| | - Chih-Wei Chang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Shih-Wen Li
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Ya-Chi Yang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hauh-Jyun C Chen
- Department of Chemistry and Biochemistry, National Chung Cheng University, Chiayi, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University, Tainan, 704, Taiwan
- Department of Food Safety/Hygiene and Risk Management, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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28
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Münzel T, Sørensen M, Hahad O, Nieuwenhuijsen M, Daiber A. The contribution of the exposome to the burden of cardiovascular disease. Nat Rev Cardiol 2023; 20:651-669. [PMID: 37165157 DOI: 10.1038/s41569-023-00873-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/12/2023]
Abstract
Large epidemiological and health impact assessment studies at the global scale, such as the Global Burden of Disease project, indicate that chronic non-communicable diseases, such as atherosclerosis and diabetes mellitus, caused almost two-thirds of the annual global deaths in 2020. By 2030, 77% of all deaths are expected to be caused by non-communicable diseases. Although this increase is mainly due to the ageing of the general population in Western societies, other reasons include the increasing effects of soil, water, air and noise pollution on health, together with the effects of other environmental risk factors such as climate change, unhealthy city designs (including lack of green spaces), unhealthy lifestyle habits and psychosocial stress. The exposome concept was established in 2005 as a new strategy to study the effect of the environment on health. The exposome describes the harmful biochemical and metabolic changes that occur in our body owing to the totality of different environmental exposures throughout the life course, which ultimately lead to adverse health effects and premature deaths. In this Review, we describe the exposome concept with a focus on environmental physical and chemical exposures and their effects on the burden of cardiovascular disease. We discuss selected exposome studies and highlight the relevance of the exposome concept for future health research as well as preventive medicine. We also discuss the challenges and limitations of exposome studies.
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Affiliation(s)
- Thomas Münzel
- Department of Cardiology, Cardiology I, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany.
| | - Mette Sørensen
- Danish Cancer Society, Copenhagen, Denmark
- Department of Natural Science and Environment, Roskilde University, Roskilde, Denmark
| | - Omar Hahad
- Department of Cardiology, Cardiology I, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Mark Nieuwenhuijsen
- Institute for Global Health (ISGlobal), Barcelona Biomedical Research Park (PRBB), Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), PRBB building (Mar Campus), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid, Spain
| | - Andreas Daiber
- Department of Cardiology, Cardiology I, University Medical Center of the Johannes Gutenberg-University, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
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29
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Cerdeña JP, Tsai JW, Warpinski C, Rosencrans RF, Gravlee CC. Racial, Gender, and Size Bias in a Medical Graphical Abstract Gallery: A Content Analysis. Health Equity 2023; 7:631-643. [PMID: 37786527 PMCID: PMC10541937 DOI: 10.1089/heq.2023.0026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/13/2023] [Indexed: 10/04/2023] Open
Abstract
Introduction Graphical abstracts may enhance dissemination of scientific and medical research but are also prone to reductionism and bias. We conducted a systematic content analysis of the Journal of Internal Medicine (JIM) Graphical Abstract Gallery to assess for evidence of bias. Materials and Methods We analyzed 140 graphical abstracts published by JIM between February 2019 and May 2020. Using a combination of inductive and deductive approaches, we developed a set of codes and code definitions for thematic, mixed-methods analysis. Results We found that JIM graphical abstracts disproportionately emphasized male (59.5%) and light-skinned (91.3%) bodies, stigmatized large body size, and overstated genetic and behavioral causes of disease, even relative to the articles they purportedly represented. Whereas 50.7% of the graphical surface area was coded as representing genetic factors, just 0.4% represented the social environment. Discussion Our analysis suggests evidence of bias and reductionism promoting normative white male bodies, linking large bodies with disease and death, conflating race with genetics, and overrepresenting genes while underrepresenting the environment as a driver of health and illness. These findings suggest that uncritical use of graphical abstracts may distort rather than enhance our understanding of disease; harm patients who are minoritized by race, gender, or body size; and direct attention away from dismantling the structural barriers to health equity. Conclusion We recommend that journals develop standards for mitigating bias in the publication of graphical abstracts that (1) ensure diverse skin tone and gender representation, (2) mitigate weight bias, (3) avoid racial or ethnic essentialism, and (4) attend to sociostructural contributors to disease.
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Affiliation(s)
- Jessica P. Cerdeña
- Department of Family Medicine, Middlesex Health, Middletown, Connecticut, USA
- Institute for Collaboration on Health, Implementation, and Policy (InCHIP), University of Connecticut, Storrs, Connecticut, USA
- Department of Anthropology, University of Connecticut, Storrs, Connecticut, USA
| | - Jennifer W. Tsai
- Department of Emergency Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Chloe Warpinski
- Department of Anthropology, University of Florida, Gainesville, Florida, USA
- MD-PhD Training Program, University of Florida College of Medicine, Gainesville, Florida, USA
| | - Robert F. Rosencrans
- Medical Scientist Training Program, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Clarence C. Gravlee
- Department of Anthropology, University of Florida, Gainesville, Florida, USA
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30
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Buckley TJ, Egeghy PP, Isaacs K, Richard AM, Ring C, Sayre RR, Sobus JR, Thomas RS, Ulrich EM, Wambaugh JF, Williams AJ. Cutting-edge computational chemical exposure research at the U.S. Environmental Protection Agency. ENVIRONMENT INTERNATIONAL 2023; 178:108097. [PMID: 37478680 PMCID: PMC10588682 DOI: 10.1016/j.envint.2023.108097] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/05/2023] [Accepted: 07/12/2023] [Indexed: 07/23/2023]
Abstract
Exposure science is evolving from its traditional "after the fact" and "one chemical at a time" approach to forecasting chemical exposures rapidly enough to keep pace with the constantly expanding landscape of chemicals and exposures. In this article, we provide an overview of the approaches, accomplishments, and plans for advancing computational exposure science within the U.S. Environmental Protection Agency's Office of Research and Development (EPA/ORD). First, to characterize the universe of chemicals in commerce and the environment, a carefully curated, web-accessible chemical resource has been created. This DSSTox database unambiguously identifies >1.2 million unique substances reflecting potential environmental and human exposures and includes computationally accessible links to each compound's corresponding data resources. Next, EPA is developing, applying, and evaluating predictive exposure models. These models increasingly rely on data, computational tools like quantitative structure activity relationship (QSAR) models, and machine learning/artificial intelligence to provide timely and efficient prediction of chemical exposure (and associated uncertainty) for thousands of chemicals at a time. Integral to this modeling effort, EPA is developing data resources across the exposure continuum that includes application of high-resolution mass spectrometry (HRMS) non-targeted analysis (NTA) methods providing measurement capability at scale with the number of chemicals in commerce. These research efforts are integrated and well-tailored to support population exposure assessment to prioritize chemicals for exposure as a critical input to risk management. In addition, the exposure forecasts will allow a wide variety of stakeholders to explore sustainable initiatives like green chemistry to achieve economic, social, and environmental prosperity and protection of future generations.
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Affiliation(s)
- Timothy J Buckley
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States.
| | - Peter P Egeghy
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Kristin Isaacs
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Ann M Richard
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Caroline Ring
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Risa R Sayre
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Jon R Sobus
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Russell S Thomas
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Elin M Ulrich
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - John F Wambaugh
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
| | - Antony J Williams
- U.S. Environmental Protection Agency, Office of Research & Development, Center for Computational Toxicology & Exposure (CCTE), 109 TW Alexander Drive, Research Triangle Park, NC 27711, United States
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31
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Kolli A, Sekimitsu S, Wang J, Segre A, Friedman D, Elze T, Pasquale LR, Wiggs J, Zebardast N. Background polygenic risk modulates the association between glaucoma and cardiopulmonary diseases and measures: an analysis from the UK Biobank. Br J Ophthalmol 2023; 107:1112-1118. [PMID: 35361574 PMCID: PMC9522920 DOI: 10.1136/bjophthalmol-2021-320305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 03/13/2022] [Indexed: 12/27/2022]
Abstract
AIMS To assess whether associations of cardiopulmonary conditions and markers with glaucoma differ by background genetic risk for primary open angle glaucoma (POAG). METHODS We constructed a POAG polygenic risk score (PRS) using genome-wide association study summary statistics from a large cross-ancestry meta-analysis. History of glaucoma (including self-report and codes for POAG, 'other glaucoma' or unspecified glaucoma), history of common cardiopulmonary conditions and cardiopulmonary measures were assessed in the UK Biobank. Stratifying by PRS decile 1 (lowest risk) versus decile 10 (highest risk), separate multivariable models were estimated to assess the associations of cardiopulmonary diseases or factors with glaucoma, adjusting for age, sex, smoking and medication use. A Bonferroni correction was used to adjust p values for multiple comparisons. RESULTS Individuals in POAG PRS decile 1 (417 cases, 44 458 controls; mean age 56.8 years) and decile 10 (2135 cases, 42 413 controls; mean age 56.7 years) were included. Within decile 1, glaucoma cases had significantly higher glycated haemoglobin (38.5 vs 35.9 mmol/mol) and higher prevalence of diabetes (17.5% vs 6.5%), dyslipidaemia (31.2% vs 18.3%) and chronic kidney disease (CKD) (6.7% vs 2.0%) than controls (adjusted p<0.0013 for each). Within decile 10, glaucoma was associated with higher prevalence of dyslipidaemia (27.7% vs 17.3%, p=6.9E-05). The magnitude of association between glaucoma and diabetes, CKD and glycated haemoglobin differed between deciles 1 and 10 (contrast test p value for difference <0.05). CONCLUSION The relations between systemic conditions and glaucoma vary by underlying genetic predisposition to POAG, with larger associations among those who developed glaucoma despite low genetic risk.
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Affiliation(s)
- Ajay Kolli
- Ophthalmology and Visual Science, University of Michigan, Ann Arbor, Michigan, USA
- Harvard University T H Chan School of Public Health, Boston, Massachusetts, USA
| | | | - Jiali Wang
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Ayellet Segre
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
- Schepens Eye Research Institute, Harvard Medical School, Boston, Massachusetts, USA
- Ocular Genomics Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - David Friedman
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
| | - Tobias Elze
- Schepens Eye Research Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Louis R Pasquale
- Department of Ophthalmology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Janey Wiggs
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
- Ocular Genomics Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Nazlee Zebardast
- Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts, USA
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Huang H, Liu J, Liang X, Fang L, Yang C, Ke K, Bai H, Xu W, Li W, Meng F, Chen C. Trends in the prevalence of elevated cardiovascular risk and the control of its risk factors Among US adults, 2001-2020. Front Cardiovasc Med 2023; 10:1153926. [PMID: 37456815 PMCID: PMC10347386 DOI: 10.3389/fcvm.2023.1153926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/21/2023] [Indexed: 07/18/2023] Open
Abstract
Background An accurate assessment of current trends in cardiovascular risks could inform public health policy. This study aims to determine 20-year trends in the prevalence of elevated cardiovascular risk and its risk factors' control among US adults. Methods In this serial cross-sectional analysis of 23,594 adults, aged 40-79 years, without clinical atherosclerotic cardiovascular disease (ASCVD) in the National Health and Nutrition Examination Survey from 2001 to 2020, we calculated the prevalence of elevated cardiovascular risk (10-year ASCVD risk ≥ 7.5%) for all participants and subgroups with their risk factors controlled for diabetes, hypertension, or dyslipidemia. Results The age- and sex-adjusted prevalence of elevated cardiovascular risk slightly decreased from 41.5% (95% CI, 39.7-43.3%) in 2001-2004 to 38.6% (95% CI, 36.1-41.1%) in 2017-2020 (P for trend = 0.169) while the respective sex-adjusted prevalence significantly increased from 34.4% (95% CI, 32.8-36.0%) to 39.5% (95% CI, 37.0-42.0%; P for trend <0.001). Sex and race continued to show disparities in cardiovascular risk. Furthermore, a worsening disparity in age- and sex-adjusted prevalence of elevated cardiovascular risk between young and old and a narrowing gap among different education and poverty index levels (all P trend for interaction <0.05). Differential decomposition analysis found that demographic changes (primarily population aging) led to an 8.8% increase in the prevalence of elevated cardiovascular risk from 2001 to 2004 to 2017-2020, while risk factor control led to a 3.8% decrease. The rate of individuals receiving treatment for diabetes, hypertension, or dyslipidemia increased significantly between 2001 and 2020 (all P for trend <0.05). The rate of participants with hypertension who achieved blood pressure under 130/80 mmHg and those with dyslipidemia who achieved a non-high-density lipoprotein cholesterol level under 130 mg/dl increased significantly (all P for trend <0.001). Conclusions There is a slight reduction in the prevalence of age- and sex-adjusted elevated cardiovascular risk among US adults without clinical ASCVD between 2001 and 2020, while the sex-adjusted prevalence significantly increased. The decrease in elevated cardiovascular risk prevalence was mainly attributed to risk factor control, while demographic changes contributed to an increase.
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Affiliation(s)
- Haitao Huang
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Jianhong Liu
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Xiao Liang
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Lingyan Fang
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Chenhui Yang
- Key Laboratory of Environment and Health, Ministries of Education and Environmental Protection, And State Key Laboratory of Environmental Health (Incubation), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Kangling Ke
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Hemanyun Bai
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Weize Xu
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Weiyan Li
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- The First Clinical College, Guangdong Medical University, Zhanjiang, China
| | - Fanji Meng
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Can Chen
- Department of Cardiology, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
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Daiber A, Hahad O, Münzel T. Editorial: Special issue: "Impact of lifestyle und behavioral risk factors on endothelial function and vascular biology"-how lifestyle and behavioral risk factors affect the vasculature. Pflugers Arch 2023:10.1007/s00424-023-02826-8. [PMID: 37270741 DOI: 10.1007/s00424-023-02826-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/05/2023]
Affiliation(s)
- Andreas Daiber
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany.
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany.
| | - Omar Hahad
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Thomas Münzel
- Department of Cardiology, Cardiology I, University Medical Center Mainz, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
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Hulsen T, Friedecký D, Renz H, Melis E, Vermeersch P, Fernandez-Calle P. From big data to better patient outcomes. Clin Chem Lab Med 2023; 61:580-586. [PMID: 36539928 DOI: 10.1515/cclm-2022-1096] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Among medical specialties, laboratory medicine is the largest producer of structured data and must play a crucial role for the efficient and safe implementation of big data and artificial intelligence in healthcare. The area of personalized therapies and precision medicine has now arrived, with huge data sets not only used for experimental and research approaches, but also in the "real world". Analysis of real world data requires development of legal, procedural and technical infrastructure. The integration of all clinical data sets for any given patient is important and necessary in order to develop a patient-centered treatment approach. Data-driven research comes with its own challenges and solutions. The Findability, Accessibility, Interoperability, and Reusability (FAIR) Guiding Principles provide guidelines to make data findable, accessible, interoperable and reusable to the research community. Federated learning, standards and ontologies are useful to improve robustness of artificial intelligence algorithms working on big data and to increase trust in these algorithms. When dealing with big data, the univariate statistical approach changes to multivariate statistical methods significantly shifting the potential of big data. Combining multiple omics gives previously unsuspected information and provides understanding of scientific questions, an approach which is also called the systems biology approach. Big data and artificial intelligence also offer opportunities for laboratories and the In Vitro Diagnostic industry to optimize the productivity of the laboratory, the quality of laboratory results and ultimately patient outcomes, through tools such as predictive maintenance and "moving average" based on the aggregate of patient results.
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Affiliation(s)
- Tim Hulsen
- Department of Hospital Services & Informatics, Philips Research, Eindhoven, The Netherlands
| | - David Friedecký
- Department of Clinical Biochemistry, Laboratory for Inherited Metabolic Disorders, University Hospital Olomouc and Faculty of Medicine and Dentistry, Palacký University in Olomouc, Olomouc, Czech Republic
| | - Harald Renz
- Institute of Laboratory Medicine, member of the German Center for Lung Research (DZL), and the Universities of Giessen and Marburg Lung Center (UGMLC), Philipps University Marburg, Marburg, Germany
- Department of Clinical Immunology and Allergy, Laboratory of Immunopathology, I.M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Els Melis
- Ortho Clinical Diagnostics, Zaventem, Belgium
| | - Pieter Vermeersch
- Clinical Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
- European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Milan, Italy
| | - Pilar Fernandez-Calle
- European Federation of Clinical Chemistry and Laboratory Medicine (EFLM), Milan, Italy
- Department of Laboratory Medicine, Hospital Universitario La Paz, Madrid, Spain
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35
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Olatunji SO, Alsheikh N, Alnajrani L, Alanazy A, Almusairii M, Alshammasi S, Alansari A, Zaghdoud R, Alahmadi A, Basheer Ahmed MI, Ahmed MS, Alhiyafi J. Comprehensible Machine-Learning-Based Models for the Pre-Emptive Diagnosis of Multiple Sclerosis Using Clinical Data: A Retrospective Study in the Eastern Province of Saudi Arabia. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:4261. [PMID: 36901273 PMCID: PMC10002108 DOI: 10.3390/ijerph20054261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/22/2023] [Accepted: 02/24/2023] [Indexed: 06/18/2023]
Abstract
Multiple Sclerosis (MS) is characterized by chronic deterioration of the nervous system, mainly the brain and the spinal cord. An individual with MS develops the condition when the immune system begins attacking nerve fibers and the myelin sheathing that covers them, affecting the communication between the brain and the rest of the body and eventually causing permanent damage to the nerve. Patients with MS (pwMS) might experience different symptoms depending on which nerve was damaged and how much damage it has sustained. Currently, there is no cure for MS; however, there are clinical guidelines that help control the disease and its accompanying symptoms. Additionally, no specific laboratory biomarker can precisely identify the presence of MS, leaving specialists with a differential diagnosis that relies on ruling out other possible diseases with similar symptoms. Since the emergence of Machine Learning (ML) in the healthcare industry, it has become an effective tool for uncovering hidden patterns that aid in diagnosing several ailments. Several studies have been conducted to diagnose MS using ML and Deep Learning (DL) models trained using MRI images, achieving promising results. However, complex and expensive diagnostic tools are needed to collect and examine imaging data. Thus, the intention of this study is to implement a cost-effective, clinical data-driven model that is capable of diagnosing pwMS. The dataset was obtained from King Fahad Specialty Hospital (KFSH) in Dammam, Saudi Arabia. Several ML algorithms were compared, namely Support Vector Machine (SVM), Decision Tree (DT), Logistic Regression (LR), Random Forest (RF), Extreme Gradient Boosting (XGBoost), Adaptive Boosting (AdaBoost), and Extra Trees (ET). The results indicated that the ET model outpaced the rest with an accuracy of 94.74%, recall of 97.26%, and precision of 94.67%.
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Affiliation(s)
- Sunday O. Olatunji
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Nawal Alsheikh
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Lujain Alnajrani
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Alhatoon Alanazy
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Meshael Almusairii
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Salam Alshammasi
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Aisha Alansari
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Rim Zaghdoud
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Alaa Alahmadi
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Mohammed Imran Basheer Ahmed
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Mohammed Salih Ahmed
- College of Computer Science and Information Technology, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Jamal Alhiyafi
- Department of Computer Science, Kettering University, Flint, MI 48504, USA
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36
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Gago-Ferrero P, Ghassabian A, Lamoree M, Toms LM. The Exposome and Human Health: A New Virtual and Special Issue in ES&T. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:2272-2273. [PMID: 36745693 DOI: 10.1021/acs.est.3c00622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Affiliation(s)
- Pablo Gago-Ferrero
- Institute of Environmental Assessment and Water Research (IDAEA-CSIC) , 08034 Barcelona, Spain
| | | | - Marja Lamoree
- Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Leisa-Maree Toms
- Queensland University of Technology (QUT), Brisbane 4000, Australia
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37
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A clinically validated human saliva metatranscriptomic test for global systems biology studies. Biotechniques 2023; 74:31-44. [PMID: 36622006 DOI: 10.2144/btn-2022-0104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
The authors report here the development of a high-throughput, automated, inexpensive and clinically validated saliva metatranscriptome test that requires less than 100 μl of saliva. RNA is preserved at the time of sample collection, allowing for ambient-temperature transportation and storage for up to 28 days. Critically, the RNA preservative is also able to inactivate pathogenic microorganisms, rendering the samples noninfectious and allowing for safe and easy shipping. Given the unique set of convenience, low cost, safety and technical performance, this saliva metatranscriptomic test can be integrated into longitudinal, global-scale systems biology studies that will lead to an accelerated development of precision medicine, diagnostic and therapeutic tools.
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38
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Srivastava R. Applications of artificial intelligence multiomics in precision oncology. J Cancer Res Clin Oncol 2023; 149:503-510. [PMID: 35796775 DOI: 10.1007/s00432-022-04161-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 06/17/2022] [Indexed: 02/06/2023]
Abstract
Cancer is the second leading worldwide disease that depends on oncogenic mutations and non-mutated genes for survival. Recent advancements in next-generation sequencing (NGS) have transformed the health care sector with big data and machine learning (ML) approaches. NGS data are able to detect the abnormalities and mutations in the oncogenes. These multi-omics analyses are used for risk prediction, early diagnosis, accurate prognosis, and identification of biomarkers in cancer patients. The availability of these cancer data and their analysis may provide insights into the biology of the disease, which can be used for the personalized treatment of cancer patients. Bioinformatics tools are delivering this promise by managing, integrating, and analyzing these complex datasets. The clinical outcomes of cancer patients are improved by the use of various innovative methods implicated particularly for diagnosis and therapeutics. ML-based artificial intelligence (AI) applications are solving these issues to a great extent. AI techniques are used to update the patients on a personalized basis about their treatment procedures, progress, recovery, therapies used, dietary changes in lifestyles patterns along with the survival summary of previously recovered cancer patients. In this way, the patients are becoming more aware of their diseases and the entire clinical treatment procedures. Though the technology has its own advantages and disadvantages, we hope that the day is not so far when AI techniques will provide personalized treatment to cancer patients tailored to their needs in much quicker ways.
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Affiliation(s)
- Ruby Srivastava
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India.
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Vryonidis E, Karlsson I, Aasa J, Carlsson H, Motwani HV, Pedersen M, Eriksson J, Törnqvist MÅ. Pathways to Identify Electrophiles In Vivo Using Hemoglobin Adducts: Hydroxypropanoic Acid Valine Adduct and Its Possible Precursors. Chem Res Toxicol 2022; 35:2227-2240. [PMID: 36395356 PMCID: PMC9768813 DOI: 10.1021/acs.chemrestox.2c00208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Analytical methods and tools for the characterization of the human exposome by untargeted mass spectrometry approaches are advancing rapidly. Adductomics methods have been developed for untargeted screening of short-lived electrophiles, in the form of adducts to proteins or DNA, in vivo. The identification of an adduct and its precursor electrophile in the blood is more complex than that of stable chemicals. The present work aims to illustrate procedures for the identification of an adduct to N-terminal valine in hemoglobin detected with adductomics, and pathways for the tracing of its precursor and possible exposure sources. Identification of the adduct proceeded via preparation and characterization of standards of adduct analytes. Possible precursor(s) and exposure sources were investigated by measurements in blood of adduct formation by precursors in vitro and adduct levels in vivo. The adduct was identified as hydroxypropanoic acid valine (HPA-Val) by verification with a synthesized reference. The HPA-Val was measured together with other adducts (from acrylamide, glycidamide, glycidol, and acrylic acid) in human blood (n = 51, schoolchildren). The HPA-Val levels ranged between 6 and 76 pmol/g hemoglobin. The analysis of reference samples from humans and rodents showed that the HPA-Val adduct was observed in all studied samples. No correlation of the HPA-Val level with the other studied adducts was observed in humans, nor was an increase in tobacco smokers observed. A small increase was observed in rodents exposed to glycidol. The formation of the HPA-Val adduct upon incubation of blood with glycidic acid (an epoxide) was shown. The relatively high adduct levels observed in vivo in relation to the measured reactivity of the epoxide, and the fact that the epoxide is not described as naturally occurring, suggest that glycidic acid is not the only precursor of the HPA-Val adduct identified in vivo. Another endogenous electrophile is suspected to contribute to the in vivo HPA-Val adduct level.
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Affiliation(s)
- Efstathios Vryonidis
- Department
of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Isabella Karlsson
- Department
of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Jenny Aasa
- Department
of Risk and Benefit Assessment, Swedish
Food Agency, SE-751 26 Uppsala, Sweden
| | - Henrik Carlsson
- Department
of Medical Sciences, Clinical Chemistry, Uppsala University, SE-751
85 Uppsala, Sweden
| | - Hitesh V. Motwani
- Department
of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Marie Pedersen
- Department
of Public Health, University of Copenhagen, DK-1353 Copenhagen, Denmark
| | - Johan Eriksson
- Department
of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Margareta Å. Törnqvist
- Department
of Environmental Science, Stockholm University, SE-106 91 Stockholm, Sweden,
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Ding E, Wang Y, Liu J, Tang S, Shi X. A review on the application of the exposome paradigm to unveil the environmental determinants of age-related diseases. Hum Genomics 2022; 16:54. [DOI: 10.1186/s40246-022-00428-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 10/29/2022] [Indexed: 11/11/2022] Open
Abstract
AbstractAge-related diseases account for almost half of all diseases among adults worldwide, and their incidence is substantially affected by the exposome, which is the sum of all exogenous and endogenous environmental exposures and the human body’s response to these exposures throughout the entire lifespan. Herein, we perform a comprehensive review of the epidemiological literature to determine the key elements of the exposome that affect the development of age-related diseases and the roles of aging hallmarks in this process. We find that most exposure assessments in previous aging studies have used a reductionist approach, whereby the effect of only a single environmental factor or a specific class of environmental factors on the development of age-related diseases has been examined. As such, there is a lack of a holistic and unbiased understanding of the effect of multiple environmental factors on the development of age-related diseases. To address this, we propose several research strategies based on an exposomic framework that could advance our understanding—in particular, from a mechanistic perspective—of how environmental factors affect the development of age-related diseases. We discuss the statistical methods and other methods that have been used in exposome-wide association studies, with a particular focus on multiomics technologies. We also address future challenges and opportunities in the realm of multidisciplinary approaches and genome–exposome epidemiology. Furthermore, we provide perspectives on precise public health services for vulnerable populations, public communications, the integration of risk exposure information, and the bench-to-bedside translation of research on age-related diseases.
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Daiber A, Frenis K, Kuntic M, Li H, Wolf E, Kilgallen AB, Lecour S, Van Laake LW, Schulz R, Hahad O, Münzel T. Redox Regulatory Changes of Circadian Rhythm by the Environmental Risk Factors Traffic Noise and Air Pollution. Antioxid Redox Signal 2022; 37:679-703. [PMID: 35088601 PMCID: PMC9618394 DOI: 10.1089/ars.2021.0272] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 12/31/2021] [Indexed: 12/13/2022]
Abstract
Significance: Risk factors in the environment such as air pollution and traffic noise contribute to the development of chronic noncommunicable diseases. Recent Advances: Epidemiological data suggest that air pollution and traffic noise are associated with a higher risk for cardiovascular, metabolic, and mental disease, including hypertension, heart failure, myocardial infarction, diabetes, arrhythmia, stroke, neurodegeneration, depression, and anxiety disorders, mainly by activation of stress hormone signaling, inflammation, and oxidative stress. Critical Issues: We here provide an in-depth review on the impact of the environmental risk factors air pollution and traffic noise exposure (components of the external exposome) on cardiovascular health, with special emphasis on the role of environmentally triggered oxidative stress and dysregulation of the circadian clock. Also, a general introduction on the contribution of circadian rhythms to cardiovascular health and disease as well as a detailed mechanistic discussion of redox regulatory pathways of the circadian clock system is provided. Future Directions: Finally, we discuss the potential of preventive strategies or "chrono" therapy for cardioprotection. Antioxid. Redox Signal. 37, 679-703.
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Affiliation(s)
- Andreas Daiber
- Molecular Cardiology, Department of Cardiology 1, Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Katie Frenis
- Molecular Cardiology, Department of Cardiology 1, Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Marin Kuntic
- Molecular Cardiology, Department of Cardiology 1, Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Huige Li
- Department of Pharmacology, Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Eva Wolf
- Structural Chronobiology, Institute of Molecular Physiology, Johannes Gutenberg University, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Aoife B. Kilgallen
- Division Heart and Lungs, Regenerative Medicine Centre, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sandrine Lecour
- Hatter Institute for Cardiovascular Research in Africa, University of Cape Town, Cape Town, South Africa
| | - Linda W. Van Laake
- Division Heart and Lungs, Regenerative Medicine Centre, University Medical Centre Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rainer Schulz
- Institute for Physiology, Justus-Liebig University Giessen, Giessen, Germany
| | - Omar Hahad
- Molecular Cardiology, Department of Cardiology 1, Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
| | - Thomas Münzel
- Molecular Cardiology, Department of Cardiology 1, Medical Center of the Johannes Gutenberg University, Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Partner Site Rhine-Main, Mainz, Germany
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Senay E, Levine R, Shepherd JM, Rizzo A, Yitshak-Sade M, Carrión D, Liu B, Lewis J, Wright R, Sorensen C, Wortzel J, Pinsky E, Hudson K, Katz C, Gore K, Basu G, Duritz N, Wright R, Sheffield P. Mental Health and Well-Being for Patients and Clinicians: Proceedings of the Fourth Annual Clinical Climate Change Meeting, January 7, 2022. J Occup Environ Med 2022; 64:e661-e666. [PMID: 36179344 DOI: 10.1097/jom.0000000000002655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Emily Senay
- From the Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, New York (Dr Senay, Dr Yitshak-Sade, Dr Liu, Dr Rosalind Wright, Dr Robert Wright, Dr Sheffield); Assistant Secretary for Health, Department of Health and Human Services, Washington, District of Columbia (Dr Levine); Department of Geography and the College of Engineering, University of Georgia, Athens, Georgia (Dr Shepherd); American Lung Association, Chicago, Illinois (Dr Rizzo); Yale School of Public Health and Yale Center on Climate Change and Health, New Haven, Connecticut (Dr Carrión); University of Rochester, Rochester, New York (Dr Lewis, Dr Wortzel); Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York (Dr Rosalind Wright); Mailman School of Public Health, Columbia University, New York, New York (Dr Sorensen); Massachusetts General Hospital, Boston, Massachusetts (Dr Pinsky); Center for Anxiety and Related Disorders, Boston University, Boston, Massachusetts (Dr Hudson); Departments of Psychiatry, Medical Education, and Health System Design & Global Health, Icahn School of Medicine at Mount Sinai, New York, New York (Dr Katz); Union Theological Seminary, New York, New York (Dr Gore); Center for Climate Health and the Global Environment, Harvard TH Chan School of Public Health, Boston, Massachusetts (Dr Basu); The Medical Society Consortium on Climate & Health, Center for Climate Change Communication, George Mason University, Fairfax, Virginia (Dr Duritz, Dr Robert Wright)
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43
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Koelmel JP, Xie H, Price EJ, Lin EZ, Manz KE, Stelben P, Paige MK, Papazian S, Okeme J, Jones DP, Barupal D, Bowden JA, Rostkowski P, Pennell KD, Nikiforov V, Wang T, Hu X, Lai Y, Miller GW, Walker DI, Martin JW, Godri Pollitt KJ. An actionable annotation scoring framework for gas chromatography-high-resolution mass spectrometry. EXPOSOME 2022; 2:osac007. [PMID: 36483216 PMCID: PMC9719826 DOI: 10.1093/exposome/osac007] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 04/16/2023]
Abstract
Omics-based technologies have enabled comprehensive characterization of our exposure to environmental chemicals (chemical exposome) as well as assessment of the corresponding biological responses at the molecular level (eg, metabolome, lipidome, proteome, and genome). By systematically measuring personal exposures and linking these stimuli to biological perturbations, researchers can determine specific chemical exposures of concern, identify mechanisms and biomarkers of toxicity, and design interventions to reduce exposures. However, further advancement of metabolomics and exposomics approaches is limited by a lack of standardization and approaches for assigning confidence to chemical annotations. While a wealth of chemical data is generated by gas chromatography high-resolution mass spectrometry (GC-HRMS), incorporating GC-HRMS data into an annotation framework and communicating confidence in these assignments is challenging. It is essential to be able to compare chemical data for exposomics studies across platforms to build upon prior knowledge and advance the technology. Here, we discuss the major pieces of evidence provided by common GC-HRMS workflows, including retention time and retention index, electron ionization, positive chemical ionization, electron capture negative ionization, and atmospheric pressure chemical ionization spectral matching, molecular ion, accurate mass, isotopic patterns, database occurrence, and occurrence in blanks. We then provide a qualitative framework for incorporating these various lines of evidence for communicating confidence in GC-HRMS data by adapting the Schymanski scoring schema developed for reporting confidence levels by liquid chromatography HRMS (LC-HRMS). Validation of our framework is presented using standards spiked in plasma, and confident annotations in outdoor and indoor air samples, showing a false-positive rate of 12% for suspect screening for chemical identifications assigned as Level 2 (when structurally similar isomers are not considered false positives). This framework is easily adaptable to various workflows and provides a concise means to communicate confidence in annotations. Further validation, refinements, and adoption of this framework will ideally lead to harmonization across the field, helping to improve the quality and interpretability of compound annotations obtained in GC-HRMS.
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Affiliation(s)
- Jeremy P Koelmel
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Hongyu Xie
- Department of Environmental Science, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Elliott J Price
- RECETOX, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic
| | - Elizabeth Z Lin
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | | | - Paul Stelben
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Matthew K Paige
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Stefano Papazian
- Department of Environmental Science, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- National Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Joseph Okeme
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
| | - Dean P Jones
- School of Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Dinesh Barupal
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
| | - John A Bowden
- Department of Physiological Sciences, Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL, USA
- Department of Chemistry, University of Florida, Gainesville, FL, USA
| | | | - Kurt D Pennell
- School of Engineering, Brown University, Providence, RI, USA
| | | | - Thanh Wang
- MTM Research Centre, Örebro University, Örebro, Sweden
| | - Xin Hu
- School of Medicine, Department of Medicine, Emory University, Atlanta, GA, USA
| | - Yunjia Lai
- Mailman School of Public Health, Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Gary W Miller
- Mailman School of Public Health, Department of Environmental Health Sciences, Columbia University, New York, NY, USA
| | - Douglas I Walker
- Icahn School of Medicine at Mount Sinai, Department of Environmental Medicine and Public Health, New York, NY, USA
| | - Jonathan W Martin
- Department of Environmental Science, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- National Facility for Exposomics, Metabolomics Platform, Science for Life Laboratory, Stockholm University, Solna 171 65, Sweden
| | - Krystal J Godri Pollitt
- Department of Environmental Health Science, Yale School of Public Health, New Haven, CT, USA
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44
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Thornton LL, Carlson DE, Wiesner MR. Predicting emerging chemical content in consumer products using machine learning. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 834:154849. [PMID: 35405240 DOI: 10.1016/j.scitotenv.2022.154849] [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: 12/20/2021] [Revised: 03/20/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Chemical ingredients in consumer products are continually changing. To understand our exposure to chemicals and their consequent risk, we need to know their concentrations in products, or chemical weight fractions. Unfortunately, manufacturers rarely report comprehensive weight fraction data on product labels. The goal of this study was to evaluate the utility of machine learning strategies for predicting weight fractions when chemical constituent data are limited. A "data-poor" framework was developed and tested using a small dataset on consumer products containing engineered nanomaterials to represent emerging substances. A second, more traditional framework was applied to a "data-rich" product dataset comprised of bulk-scale organic chemicals for comparison purposes. Feature variables included chemical properties, functional use categories (e.g., antimicrobial), product categories (e.g., makeup), product matrix categories, and whether weight fractions were manufacturer-reported or experimentally obtained. Classification into three weight fraction bins was done using a random forest or nonlinear support vector classifier. An ablation study revealed that functional use data improved predictive performance when included alongside chemical property data, suggesting the utility of functional use categories in evaluating the safety and sustainability of emerging chemicals. Models could roughly stratify material-product observations into order of magnitude weight fractions with moderate success; the best of these achieved an average balanced accuracy of 73% on the nanomaterials product data. Framework comparisons also revealed a positive trend in sample size versus average balanced accuracy, suggesting great promise for machine learning approaches with continued investment in chemical data collection.
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Affiliation(s)
- Luka Lila Thornton
- Duke University, Department of Civil and Environmental Engineering, 121 Hudson Hall, Durham, NC 27708, USA; Center for the Environmental Implications of NanoTechnology (CEINT), USA.
| | - David E Carlson
- Duke University, Department of Civil and Environmental Engineering, 121 Hudson Hall, Durham, NC 27708, USA; Duke University, Department of Biostatistics and Bioinformatics, Duke University Medical Center, 2424 Erwin Road, Suite 1102 Hock Plaza, Durham, NC 27710, USA
| | - Mark R Wiesner
- Duke University, Department of Civil and Environmental Engineering, 121 Hudson Hall, Durham, NC 27708, USA; Center for the Environmental Implications of NanoTechnology (CEINT), USA
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45
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Davies TC. The position of geochemical variables as causal co-factors of diseases of unknown aetiology. SN APPLIED SCIENCES 2022; 4:236. [PMID: 35909942 PMCID: PMC9326422 DOI: 10.1007/s42452-022-05113-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/06/2022] [Indexed: 11/28/2022] Open
Abstract
Abstract The term diseases of unknown aetiology (DUA) or idiopathic diseases is used to describe diseases that are of uncertain or unknown cause or origin. Among plausible geoenvironmental co-factors in causation of DUA, this article focusses on the entry of trace elements, including metals and metalloids into humans, and their involvement in humoral and cellular immune responses, representing potentially toxic agents with implications as co-factors for certain DUA. Several trace elements/metals/metalloids (micronutrients) play vital roles as co-factors for essential enzymes and antioxidant molecules, thus, conferring protection against disease. However, inborn errors of trace element/metal/metalloid metabolisms can occur to produce toxicity, such as when there are basic defects in the element transport mechanism. Ultimately, it is the amount of trace element, metal or metalloid that is taken up, its mode of accumulation in human tissues, and related geomedical attributes such as the chemical form and bioavailability that decisively determine whether the exerted effects are toxic or beneficial. Several case descriptions of DUA that are common worldwide are given to illustrate our knowledge so far of how trace element/metal/metalloid interactions in the immune system may engender its dysregulation and be implicated as causal co-factors of DUA. Article highlights The importance of a proper understanding of geochemical perturbations in human metabolisms is emphasisedIt is proferred that such an understanding would aid greatly in the decipherment of diseases of unknown aetiology (DUA)The thesis presented may pave the way towards better diagnosis and therapy of DUA.
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Affiliation(s)
- Theophilus C. Davies
- Present Address: Faculty of Natural Sciences, Mangosuthu University of Technology, 511 Mangosuthu Highway, 4031, KwaZulu Natal, South Africa
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46
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Schor J, Scheibe P, Bernt M, Busch W, Lai C, Hackermüller J. AI for predicting chemical-effect associations at the chemical universe level-deepFPlearn. Brief Bioinform 2022; 23:6645490. [PMID: 35849097 PMCID: PMC9487703 DOI: 10.1093/bib/bbac257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 05/17/2022] [Accepted: 06/02/2022] [Indexed: 11/20/2022] Open
Abstract
Many chemicals are present in our environment, and all living species are exposed to them. However, numerous chemicals pose risks, such as developing severe diseases, if they occur at the wrong time in the wrong place. For the majority of the chemicals, these risks are not known. Chemical risk assessment and subsequent regulation of use require efficient and systematic strategies. Lab-based methods—even if high throughput—are too slow to keep up with the pace of chemical innovation. Existing computational approaches are designed for specific chemical classes or sub-problems but not usable on a large scale. Further, the application range of these approaches is limited by the low amount of available labeled training data. We present the ready-to-use and stand-alone program deepFPlearn that predicts the association between chemical structures and effects on the gene/pathway level using a combined deep learning approach. deepFPlearn uses a deep autoencoder for feature reduction before training a deep feed-forward neural network to predict the target association. We received good prediction qualities and showed that our feature compression preserves relevant chemical structural information. Using a vast chemical inventory (unlabeled data) as input for the autoencoder did not reduce our prediction quality but allowed capturing a much more comprehensive range of chemical structures. We predict meaningful—experimentally verified—associations of chemicals and effects on unseen data. deepFPlearn classifies hundreds of thousands of chemicals in seconds. We provide deepFPlearn as an open-source and flexible tool that can be easily retrained and customized to different application settings at https://github.com/yigbt/deepFPlearn.
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Affiliation(s)
- Jana Schor
- Department Computational Biology, Helmholtz Centre for environmental research - UFZ, Permoserstr. 15, 04318 Leipzig, Saxony, Germany
| | - Patrick Scheibe
- Department of Neurophysics, Max Planck Institute for Human Cognitive and Brain Sciences, Stephanstraβe 1a, 04103 Leipzig, Saxony, Germany
| | - Matthias Bernt
- Department Computational Biology, Helmholtz Centre for environmental research - UFZ, Permoserstr. 15, 04318 Leipzig, Saxony, Germany
| | - Wibke Busch
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for environmental research - UFZ, Permoserstr. 15, 04318 Leipzig, Saxony, Germany
| | - Chih Lai
- Graduate Program in Software & School of Engineering, University of St. Thomas, 2115 Summit Ave, St. Paul, MN 55105, Minnesota, USA
| | - Jörg Hackermüller
- Department Computational Biology, Helmholtz Centre for environmental research - UFZ, Permoserstr. 15, 04318 Leipzig, Saxony, Germany.,Department of Computer Science, Leipzig University, Augustuspl. 10, 04109 Leipzig, Saxony, Germany
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47
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Zhou G, Pang Z, Lu Y, Ewald J, Xia J. OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics. Nucleic Acids Res 2022; 50:W527-W533. [PMID: 35639733 PMCID: PMC9252810 DOI: 10.1093/nar/gkac376] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/21/2022] [Accepted: 05/05/2022] [Indexed: 12/17/2022] Open
Abstract
Researchers are increasingly seeking to interpret molecular data within a multi-omics context to gain a more comprehensive picture of their study system. OmicsNet (www.omicsnet.ca) is a web-based tool developed to allow users to easily build, visualize, and analyze multi-omics networks to study rich relationships among lists of ‘omics features of interest. Three major improvements have been introduced in OmicsNet 2.0, which include: (i) enhanced network visual analytics with eleven 2D graph layout options and a novel 3D module layout; (ii) support for three new ‘omics types: single nucleotide polymorphism (SNP) list from genetic variation studies; taxon list from microbiome profiling studies, as well as liquid chromatography–mass spectrometry (LC–MS) peaks from untargeted metabolomics; and (iii) measures to improve research reproducibility by coupling R command history with the release of the companion OmicsNetR package, and generation of persistent links to share interactive network views. We performed a case study using the multi-omics data obtained from a recent large-scale investigation on inflammatory bowel disease (IBD) and demonstrated that OmicsNet was able to quickly create meaningful multi-omics context to facilitate hypothesis generation and mechanistic insights.
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Affiliation(s)
- Guangyan Zhou
- Institute of Parasitology, McGill University, Quebec, Canada
| | - Zhiqiang Pang
- Institute of Parasitology, McGill University, Quebec, Canada
| | - Yao Lu
- Department of Microbiology and Immunology, McGill University, Quebec, Canada
| | - Jessica Ewald
- Department of Natural Resource Sciences, McGill University, Quebec, Canada
| | - Jianguo Xia
- Institute of Parasitology, McGill University, Quebec, Canada.,Department of Microbiology and Immunology, McGill University, Quebec, Canada
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48
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Scholz S, Brack W, Escher BI, Hackermüller J, Liess M, von Bergen M, Wick LY, Zenclussen AC, Altenburger R. The EU chemicals strategy for sustainability: an opportunity to develop new approaches for hazard and risk assessment. Arch Toxicol 2022; 96:2381-2386. [PMID: 35543751 PMCID: PMC9217765 DOI: 10.1007/s00204-022-03313-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Stefan Scholz
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany.
| | - Werner Brack
- Faculty Biological Sciences, Goethe University Frankfurt, Max-von-der-Laue-Straße 13, 60438, Frankfurt, Germany
- Department of effect directed analysis, Helmholtz Centre for Environmental Research - UFZ, 04318, Leipzig, Germany
| | - Beate I Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- Center for Applied Geoscience, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
| | - Jörg Hackermüller
- Department Computational Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- Faculty of Mathematics and Informatics, University of Leipzig, 04109, Leipzig, Germany
| | - Matthias Liess
- Department Systems Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- RWTH Aachen University, Institute for Environmental Research (Biology V), Aachen, Germany
| | - Martin von Bergen
- Department Molecular Systems Biology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- Faculty of Life Sciences, Institute of Biochemistry, University of Leipzig, Brüderstraße 34, 04103, Leipzig, Germany
| | - Lukas Y Wick
- Department Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
| | - Ana C Zenclussen
- Department Environmental Immunology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- Perinatal Immunology, Saxonian Incubator for Clinical Translation (SIKT), Medical Faculty, Leipzig University, Philipp-Rosenthal-Str. 55, 04103, Leipzig, Germany
| | - Rolf Altenburger
- Department of Bioanalytical Ecotoxicology, Helmholtz Centre for Environmental Research-UFZ, Permoserstr. 15, 04318, Leipzig, Germany
- RWTH Aachen University, Institute for Environmental Research (Biology V), Aachen, Germany
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49
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Rueter K, Siafarikas A, Palmer DJ, Prescott SL. Pre- and Postnatal Vitamin D Status and Allergy Outcomes in Early Childhood. Biomedicines 2022; 10:biomedicines10050933. [PMID: 35625670 PMCID: PMC9139153 DOI: 10.3390/biomedicines10050933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/16/2022] Open
Abstract
The dramatic increase in the prevalence of allergic disease in recent decades reflects environmental and behavioural changes that have altered patterns of early immune development. The very early onset of allergic diseases points to the specific vulnerability of the developing immune system to environmental changes and the development of primary intervention strategies is crucial to address this unparalleled burden. Vitamin D is known to have immunomodulatory functions. While allergic disease is multifactorial, associations with reduced sunlight exposure have led to the hypothesis that suboptimal vitamin D levels during critical early periods may be one possible explanation. Interventions to improve vitamin D status, especially in early life, may be the key to allergic disease prevention.
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Affiliation(s)
- Kristina Rueter
- School of Medicine, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia; (A.S.); (D.J.P.); (S.L.P.)
- Department of Immunology, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands 6009, Australia
- inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), 6010 Park Ave, West New York, NJ 07093, USA
- Correspondence:
| | - Aris Siafarikas
- School of Medicine, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia; (A.S.); (D.J.P.); (S.L.P.)
- Telethon Kids Institute, The University of Western Australia, 15 Hospital Avenue, Nedlands 6009, Australia
- Department of Endocrinology, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands 6009, Australia
- Institute for Health Research, University of Notre Dame, Fremantle 6160, Australia
| | - Debra J. Palmer
- School of Medicine, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia; (A.S.); (D.J.P.); (S.L.P.)
- Telethon Kids Institute, The University of Western Australia, 15 Hospital Avenue, Nedlands 6009, Australia
| | - Susan L. Prescott
- School of Medicine, The University of Western Australia, 35 Stirling Highway, Crawley 6009, Australia; (A.S.); (D.J.P.); (S.L.P.)
- Department of Immunology, Perth Children’s Hospital, 15 Hospital Avenue, Nedlands 6009, Australia
- inVIVO Planetary Health, Group of the Worldwide Universities Network (WUN), 6010 Park Ave, West New York, NJ 07093, USA
- Telethon Kids Institute, The University of Western Australia, 15 Hospital Avenue, Nedlands 6009, Australia
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50
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Yamamoto T, Taniguchi M, Matsunaga K, Kawata Y, Kawamura M, Okubo K, Yamashiro K, Omori K, Takashiba S. Analysis of subgingival microbiota in monozygotic twins with different severity and progression risk of periodontitis. Clin Case Rep 2022; 10:e05725. [PMID: 35449775 PMCID: PMC9014707 DOI: 10.1002/ccr3.5725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 03/11/2022] [Accepted: 03/27/2022] [Indexed: 11/24/2022] Open
Abstract
The study aims to reveal the composition of subgingival bacteria in monozygotic twins with discordant in severity and progression risk of periodontitis. Microbiome analysis indicated that most bacteria were heritable but differed in their abundance and immune response. The dysbiotic bacteria can be considered as risk markers for periodontitis progression.
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Affiliation(s)
- Tadashi Yamamoto
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | | | - Kazuyuki Matsunaga
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
- Department of Neurology Brain Attack Center Ota Memorial Hospital Fukuyama, Hiroshima Japan
| | - Yusuke Kawata
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | - Mari Kawamura
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | - Keisuke Okubo
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | - Keisuke Yamashiro
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | - Kazuhiro Omori
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
| | - Shogo Takashiba
- Department of Pathophysiology ‐ Periodontal Science Okayama University Graduate School of Medicine Dentistry and Pharmaceutical Sciences Okayama Japan
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