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Panis C, Lemos B. Pesticide exposure and increased breast cancer risk in women population studies. Sci Total Environ 2024:172988. [PMID: 38710391 DOI: 10.1016/j.scitotenv.2024.172988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
Abstract
Pesticide exposure is emerging as a risk factor for various human diseases. Breast cancer (BC) is a multifactorial disease with known genetic and non-genetic risk factors. Most BC cases are attibutable to non-genetic risk factors, with a history of adverse environmental exposures playing a significant role. Pesticide exposure can occur at higher levels in female populations participating in rural activities such as spraying of pesticides in the field, unprotected handling of pesticides at home, and washing of contaminated clothes. Exposure can also be significant in the drinking water of certain populations. Here, we reviewed the literature on women's exposure to pesticides and the risk of BC. We summarize the main links between pesticide exposure and BC and discuss the role of dose, exposure context, and potential mechanisms. Overall, reports reviewed here have documented stronger associations between higher levels of exposure and BC risk, including documenting direct and acute pesticide exposure in certain female populations. However, discrepancies among studies regarding dose and mode of exposure may result in misunderstandings about the risks posed by pesticide exposure. Plausible mechanisms linking pesticides to breast cancer risk include impacts as endocrine disruptors, as well as roles as genotoxic agents, and modulators of the epigenome. Besides establishing links between pesticide exposure and breast cancer, the literature also highlights the critical need to understand the routes and doses of women's exposure to pesticides and the specific associations and mechanisms that are determinants of disease etiology and prognosis.
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Affiliation(s)
- Carolina Panis
- R Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, United States; Laboratory of Tumor Biology, State University of Western Paraná, UNIOESTE, Francisco Beltrão, Paraná, Brazil.
| | - Bernardo Lemos
- R Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, United States; Coit Center for Longevity and Neurotherapeutics, The University of Arizona, Tucson, AZ, United States.
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Lumour-Mensah T, Lemos B. Evidence of reduced gestational age in response to in utero arsenic exposure and implications for aging trajectories of the newborn. Environ Int 2024; 185:108566. [PMID: 38461780 DOI: 10.1016/j.envint.2024.108566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/09/2024] [Accepted: 03/04/2024] [Indexed: 03/12/2024]
Abstract
Arsenic exposure is associated with a plethora of age-related health outcomes of disparate etiology. However, evidence of the impact of arsenic on aging remains limited. Here, we investigated the utility of epigenetic clocks in two different populations and the impact of maternal arsenic exposure during pregnancy on epigenetic gestational age at birth. To do this, we examined publicly available DNA methylation data and estimated gestational age across five gestational clocks in two unrelated human populations. These populations also differ in the extent of arsenic exposure and the targeted tissue of analysis (cord blood and placental tissue). Our results indicate that same-tissue clocks produce gestational age estimates that are more highly correlated with clinical gestational age. Interestingly, our results also indicate that arsenic exposure is associated with gestational age, with higher arsenic exposures associated with decreased gestational age. We also applied two pediatric clocks to evaluate infant biological age in the same samples. The data is suggestive of higher pediatric age in infants exposed to higher arsenic levels during gestation. Taken altogether, our findings are consistent with past work indicating that that in utero arsenic exposure is associated with decreased gestational maturity as characterized by infant outcomes such as low birthweight and lung underdevelopment and dysfunction in arsenic exposed infants. The findings are also consistent with arsenic exposure setting infants on a trajectory of accelerated epigenetic aging that starts at birth.
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Affiliation(s)
- Tabitha Lumour-Mensah
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, United States
| | - Bernardo Lemos
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, United States; R. Ken Coit College of Pharmacy, Department of Pharmacology and Toxicology, The University of Arizona, Tucson, AZ, United States; Coit Center for Longevity and Neurotherapeutics, The University of Arizona, Tucson, AZ, United States.
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Lumour-Mensah T, Lemos B. Defining high confidence targets of differential CpG methylation in response to in utero arsenic exposure and implications for cancer risk. Toxicol Appl Pharmacol 2024; 482:116768. [PMID: 38030093 PMCID: PMC10889851 DOI: 10.1016/j.taap.2023.116768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 11/11/2023] [Accepted: 11/18/2023] [Indexed: 12/01/2023]
Abstract
Arsenic is a relatively abundant metalloid that impacts DNA methylation and has been implicated in various adverse health outcomes including several cancers and diabetes. However, uncertainty remains about the identity of genomic CpGs that are sensitive to arsenic exposure, in utero or otherwise. Here we identified a high confidence set of CpG sites whose methylation is sensitive to in utero arsenic exposure. To do so, we analyzed methylation of infant CpGs as a function of maternal urinary arsenic in cord blood and placenta from geographically and ancestrally distinct human populations. Independent analyses of these distinct populations were followed by combination of results across sexes and populations/tissue types. Following these analyses, we concluded that both sex and tissue type are important drivers of heterogeneity in methylation response at several CpGs. We also identified 17 high confidence CpGs that were hypermethylated across sex, tissue type and population; 11 of these were located within protein coding genes. This pattern is consistent with hypotheses that arsenic increases cancer risk by inducing the hypermethylation of genic regions. This study represents an opportunity to understand consistent, reproducible patterns of epigenomic responses after in utero arsenic exposure and may aid towards novel biomarkers or signatures of arsenic exposure. Identifying arsenic-responsive sites can also contribute to our understanding of the biological mechanisms by which arsenic exposure can affect biological function and increase risk of cancer and other age-related diseases.
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Affiliation(s)
- Tabitha Lumour-Mensah
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, United States of America
| | - Bernardo Lemos
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, United States of America; R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, United States of America.
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Aquino AM, Alonso-Costa LG, Santos SAA, Rocha VA, Barbisan LF, Bedrat A, Justulin LA, Flaws JA, Lemos B, Scarano WR. Integrated transcriptome and proteome analysis indicates potential biomarkers of prostate cancer in offspring of pregnant rats exposed to a phthalate mixture during gestation and lactation. Chemosphere 2023; 341:140020. [PMID: 37690569 DOI: 10.1016/j.chemosphere.2023.140020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023]
Abstract
As the second leading cause of death for cancer among men worldwide, prostate cancer (PCa) prevention and detection remain a critical challenge. One aspect of PCa research is the identification of common environmental agents that may increase the risk of initiation and progression of PCa. Endocrine disrupting chemicals (EDCs) are strong candidates for risk factors, partially because they alter essential pathways for prostate gland development and oncogenesis. Phthalates correspond to a set of commercially used plasticizers that humans are exposed to ubiquitously. Here, we show that maternal exposure to a phthalate mixture interferes with the expression profile of mRNA and proteins in the ventral prostate of offspring and increases the susceptibility to prostate adenocarcinomas in aged animals. The data highlight Ubxn11, Aldoc, Kif5c, Tubb4a, Tubb3, Tubb2, Rab6b and Rab3b as differentially expressed targets in young and adult offspring descendants (PND22 and PND120). These phthalate-induced targets were enriched for pathways such as: dysregulation in post-translational protein modification (PTPM), cell homeostasis, HSP90 chaperone activity, gap junctions, and kinases. In addition, the Kif5c, Tubb3, Tubb2b and Tubb4a targets were enriched for impairment in cell cycle and GTPase activity. Furthermore, these targets showed strong relationships with 12 transcriptional factors (TF), which regulate the phosphorylation of eight protein kinases. The correlation of TF-kinases is associated with alterations in immune system, RAS/ErbB/VEGF/estrogen/HIF-1 signaling pathways, cellular senescence, cell cycle, autophagy, and apoptosis. Downregulation of KIF5C, TUBB3 and RAB6B targets is associated with poor prognosis in patients diagnosed with adenocarcinoma. Collectively, this integrative investigation establishes the post-transcriptional mechanisms in the prostate that are modulated by maternal exposure to phthalate mixture during gestation and lactation.
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Affiliation(s)
- A M Aquino
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - L G Alonso-Costa
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - S A A Santos
- Cancer Signaling and Epigenetics, Fox Chase Cancer Center, Philadelphia, USA
| | - V A Rocha
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - L F Barbisan
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - A Bedrat
- Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, Massachussets, USA
| | - L A Justulin
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - J A Flaws
- Department of Comparative Biosciences; University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - B Lemos
- Harvard T. H. Chan School of Public Health, Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Boston, Massachussets, USA
| | - W R Scarano
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.
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Reis AHDEO, Figalo LB, Orsini M, Lemos B. The implications of DNA methylation for amyotrophic lateral sclerosis. AN ACAD BRAS CIENC 2023; 95:e20230277. [PMID: 37909610 DOI: 10.1590/0001-3765202320230277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 07/11/2023] [Indexed: 11/03/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a complex and serious neurodegenerative disorder that develops in consequence of the progressive loss of the upper and lower motor neurons. Cases of ALS are classified as sporadic (sALS), or familial (fALS). Over 90% of cases are sALS, while roughly 10% are related to inherited genetic mutations (fALS). Approximately 70% of the genetic mutations that contribute to fALS have been identified. On the other hand, the majority of the sALS cases have an undetermined genetic contributor and few mutations have been described, despite the advanced genetic analysis methods. Also, several factors contribute to the onset and progression of ALS. Numerous lines of evidence indicate that epigenetic changes are linked to aging, as well as neurodegenerative disorders, such as ALS. In most cases, they act as the heritable regulation of transcription by DNA methylation, histone modification and expression of noncoding RNAs. Mechanisms involving aberrant DNA methylation could be relevant to human ALS pathobiology and therapeutic targeting. Despite advances in research to find factors associated with ALS and more effective treatments, this disease remains complex and has low patient survival. Here, we provide a narrative review of the role of DNA methylation for this complex neurodegenerative disorder.
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Affiliation(s)
- Adriana Helena DE Oliveira Reis
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcantara Gomes, Departamento de Genética, Pavilhão Haroldo Lisboa da Cunha, Rua São Francisco Xavier, 524, Sala 501F, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Luna B Figalo
- Universidade do Estado do Rio de Janeiro, Instituto de Biologia Roberto Alcantara Gomes, Departamento de Genética, Pavilhão Haroldo Lisboa da Cunha, Rua São Francisco Xavier, 524, Sala 501F, 20550-900 Rio de Janeiro, RJ, Brazil
| | - Marco Orsini
- Programa de Pós-Graduação em Vigilância em Saúde, Universidade Iguaçu, Av. Abílio Augusto Távora, 2134, 26260-045 Nova Iguaçu, RJ, Brazil
- Universidade Federal do Rio de Janeiro, Departamento de Psiquiatria, Av. Venceslau Brás, 71, Botafogo, 22290-140 Rio de Janeiro, RJ, Brazil
| | - Bernardo Lemos
- Coit Center for longevity and Neurotheraéutics, Departament of pharmacology and toxicology, R Ken Coit College of Pharmacy, University of Arizona, 1703 E. Mabel St. PO Box 210207 Tucson, Arizona, USA
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Zhao T, Sun D, Long K, Lemos B, Zhang Q, Man J, Zhao M, Zhang Z. N 6-methyladenosine upregulates ribosome biogenesis in environmental carcinogenesis. Sci Total Environ 2023; 881:163428. [PMID: 37061066 DOI: 10.1016/j.scitotenv.2023.163428] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/20/2023] [Accepted: 04/06/2023] [Indexed: 06/01/2023]
Abstract
Many trace metal pollutants in surface water, the atmosphere, and soil are carcinogenic, and ribosome biogenesis plays an important role in the carcinogenicity of heavy metals. However, the contradiction between upregulated ribosome biogenesis and decreased ribosomal DNA copy number in environmental carcinogenesis is not fully understood. Here, from a perspective of the most predominant and abundant RNA epigenetic modification, N6-methyladenosine (m6A), we explored the reason behind this contradiction at the post-transcriptional level using arsenite-induced skin carcinogenesis models both in vitro and in vivo. Based on the m6A microarray assay and a series of experiments, we found for the first time that the elevated m6A in arsenite-induced transformation is mainly enriched in the genes regulating ribosome biogenesis. m6A upregulates ribosome biogenesis post-transcriptionally by stabilizing ribosomal proteins and modulating non-coding RNAs targeting ribosomal RNAs and proteins, leading to arsenite-induced skin carcinogenesis. Using multi-omics analysis of human subjects and experimental validation, we identified an unconventional role of a well-known key proliferative signaling node AKT1 as a vital mediator between m6A and ribosome biogenesis in arsenic carcinogenesis. m6A activates AKT1 and transmits proliferative signals to ribosome biogenesis, exacerbating the upregulation of ribosome biogenesis in arsenite-transformed keratinocytes. Similarly, m6A promotes cell proliferation by upregulating ribosome biogenesis in cell transformation induced by carcinogenic heavy metals (chromium and nickel). Importantly, inhibiting m6A reduces ribosome biogenesis. Targeted inhibition of m6A-upregulated ribosome biogenesis effectively prevents cell transformation induced by trace metals (arsenic, chromium, and nickel). Our results reveal the mechanism of ribosome biogenesis upregulated by m6A in the carcinogenesis of trace metal pollutants. From the perspective of RNA epigenetics, our study improves our understanding of the contradiction between upregulated ribosome biogenesis and decreased ribosomal DNA copy number in the carcinogenesis of environmental carcinogens.
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Affiliation(s)
- Tianhe Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Donglei Sun
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Keyan Long
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Bernardo Lemos
- Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston 02108, MA, USA
| | - Qian Zhang
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Jin Man
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Manyu Zhao
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China
| | - Zunzhen Zhang
- Department of Environmental and Occupational Health, West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610000, Sichuan, China.
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Layh S, Nagarajan-Radha V, Lemos B, Dowling DK. Y chromosome-linked variation affects locomotor activity in male Drosophila melanogaster and is robust to differences in thermal environment. Heredity (Edinb) 2023; 130:312-319. [PMID: 36914794 PMCID: PMC10163223 DOI: 10.1038/s41437-023-00604-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 03/16/2023] Open
Abstract
Although containing genes important for sex determination, genetic variation within the Y chromosome was traditionally predicted to contribute little to the expression of sexually dimorphic traits. This prediction was shaped by the assumption that the chromosome harbours few protein-coding genes, and that capacity for Y-linked variation to shape adaptation would be hindered by the chromosome's lack of recombination and holandric inheritance. Consequently, most studies exploring the genotypic contributions to sexually dimorphic traits have focused on the autosomes and X chromosome. Yet, several studies have now demonstrated that the Y chromosome harbours variation affecting male fitness, moderating the expression of hundreds of genes across the nuclear genome. Furthermore, emerging results have shown that expression of this Y-linked variation may be sensitive to environmental heterogeneity, leading to the prediction that Y-mediated gene-by-environment interactions will shape the expression of sexually dimorphic phenotypes. We tested this prediction, investigating whether genetic variation across six distinct Y chromosome haplotypes affects the expression of locomotor activity, at each of two temperatures (20 and 28 °C) in male fruit flies (Drosophila melanogaster). Locomotor activity is a sexually dimorphic trait in this species, previously demonstrated to be under intralocus sexual conflict. We demonstrate Y haplotype effects on male locomotor activity, but the rank order and magnitude of these effects were unaltered by differences in temperature. Our study contributes to a growing number of studies demonstrating Y-linked effects moderating expression of traits evolving under sexually antagonistic selection, suggesting a role for the Y chromosome in shaping outcomes of sexual conflict.
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Affiliation(s)
- Sean Layh
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia
| | - Venkatesh Nagarajan-Radha
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.,Behaviour Ecology and Evolution Lab, School of Life and Environmental Sciences, The University of Sydney, Camperdown, NSW, Australia
| | - Bernardo Lemos
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, VIC, Australia.
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Panis C, Candiotto LZP, Gaboardi SC, Gurzenda S, Cruz J, Castro M, Lemos B. Widespread pesticide contamination of drinking water and impact on cancer risk in Brazil. Environ Int 2022; 165:107321. [PMID: 35691095 DOI: 10.1016/j.envint.2022.107321] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/26/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Pesticides, which are associated with endocrine dysfunction, immunological dysregulation, and cancer, are widespread sources of drinking water contamination. The state of Paraná has a population of 11 million, is the second largest grain producer in Brazil and is a leading consumer of pesticides. In this study, we analyzed the extent of drinking water contamination from 11 proven, probable, or potentially carcinogenic pesticides (alachlor, aldrin-dieldrin, atrazine, chlordane, DDT-DDD-DDE, diuron, glyphosate-AMPA, lindane-γ-HCH, mancozeb-ETU, molinate, and trifluralin) in 127 grain-producing municipalities in the state of Paraná. Extensive contamination of drinking water was found, including legacy pesticides such as aldrin-dieldrin (mean 0.047 ppb), DDT-DDD-DDE (mean: 0.07), chlordane (mean: 0.181), and lindane-HCH (mean: 2.17). Most of the municipalities were significantly above the maximum limits for each one of the currently allowed pesticides (67% for alachlor, 9.44% for atrazine, 96.85% for diuron, 100% for glyphosate-AMPA, 80.31% for mancozeb-ETU, 91.33% for molinate, and 12.6% for trifluralin). Ninety-seven percent of municipalities presented a sum of all pesticides at levels significantly above (189.84 ppb) the European Union preconized limits (<0.5 ppb). Using the mean pesticide concentration in water (ppb), the exposed population for each municipality, and the benchmark cancer risk for pesticides, we estimated the minimum number of cancer cases attributable to pesticide-contaminated drinking water during the period (total of 542 cases). More than 80% were attributed to mancozeb-ETU and diuron. Glyphosate-AMPA and diuron-attributable cases strongly correlated with the total cancer cases in the same period (R = 0.8117 and 0.8138, respectively) as well as with breast cancer cases (R = 0.7695 and 0.7551, respectively). Water contamination was significantly correlated with the sum of the estimated cancer cases for all 11 pesticides detected in each city (R = 0.58 and p < 0.0001). These findings reveal extensive contamination of drinking water in the state of Paraná and suggest that contamination may increase the risk of cancer in this region.
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Affiliation(s)
- Carolina Panis
- Laboratory of Tumor Biology, State University of Western Paraná, UNIOESTE, Francisco Beltrão, Paraná, Brazil; Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States.
| | | | - Shaiane Carla Gaboardi
- Catarinense Federal Institute of Science and Technology, Campus Ibirama, Santa Catarina, Brazil
| | - Susie Gurzenda
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Jurandir Cruz
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States; Faculty of Medicine of the University of São Paulo, São Paulo, Brazil
| | - Marcia Castro
- Department of Global Health and Population, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Bernardo Lemos
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States.
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Mallik S, Grodstein F, Bennett DA, Vavvas DG, Lemos B. Novel Epigenetic Clock Biomarkers of Age-Related Macular Degeneration. Front Med (Lausanne) 2022; 9:856853. [PMID: 35783640 PMCID: PMC9244395 DOI: 10.3389/fmed.2022.856853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/19/2022] [Indexed: 01/05/2023] Open
Abstract
Age-Related Macular Degeneration (AMD) is a bilateral ocular condition resulting in irreversible vision impairment caused by the progressive loss of photoreceptors in the macula, a region at the center of the retina. The progressive loss of photoreceptor is a key feature of dry AMD but not always wet AMD, though both forms of AMD can lead to loss of vision. Regression-based biological age clocks are one of the most promising biomarkers of aging but have not yet been used in AMD. Here we conducted analyses to identify regression-based biological age clocks for the retina and explored their use in AMD using transcriptomic data consisting of a total of 453 retina samples including 105 Minnesota Grading System (MGS) level 1 samples, 175 MGS level 2, 112 MGS level 3 and 61 MGS level 4 samples, as well as 167 fibroblast samples. The clocks yielded good separation among AMD samples with increasing severity score viz., MGS1-4, regardless of whether clocks were trained in retina tissue, dermal fibroblasts, or in combined datasets. Clock application to cultured fibroblasts, embryonic stem cells, and induced Pluripotent Stem Cells (iPSCs) were consistent with age reprograming in iPSCs. Moreover, clock application to in vitro neuronal differentiation suggests broader applications. Interesting, many of the age clock genes identified include known targets mechanistically linked to AMD and aging, such as GDF11, C16ORF72, and FBN2. This study provides new observations for retina age clocks and suggests new applications for monitoring in vitro neuronal differentiation. These clocks could provide useful markers for AMD monitoring and possible intervention, as well as potential targets for in vitro screens.
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Affiliation(s)
- Saurav Mallik
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States
| | - Fran Grodstein
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - Demetrios G. Vavvas
- Ines and Frederick Yeatts Retina Research Laboratory, Retina Service, Department of Ophthalmology, Mass Eye and Ear, Harvard Medical School, Boston, MA, United States
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States,Broad Institute of Harvard and MIT, Cambridge, MA, United States,*Correspondence: Bernardo Lemos,
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Stern RA, Charness ME, Gupta K, Koutrakis P, Linsenmeyer K, Madjarov R, Martins MAG, Lemos B, Dowd SE, Garshick E. Concordance of SARS-CoV-2 RNA in Aerosols From a Nurses Station and in Nurses and Patients During a Hospital Ward Outbreak. JAMA Netw Open 2022; 5:e2216176. [PMID: 35675074 PMCID: PMC9178433 DOI: 10.1001/jamanetworkopen.2022.16176] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
IMPORTANCE Aerosol-borne SARS-CoV-2 has not been linked specifically to nosocomial outbreaks. OBJECTIVE To explore the genomic concordance of SARS-CoV-2 from aerosol particles of various sizes and infected nurses and patients during a nosocomial outbreak of COVID-19. DESIGN, SETTING, AND PARTICIPANTS This cohort study included patients and nursing staff in a US Department of Veterans Affairs inpatient hospital unit and long-term-care facility during a COVID-19 outbreak between December 27, 2020, and January 8, 2021. Outbreak contact tracing was conducted using exposure histories and screening with reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV-2. Size-selective particle samplers were deployed in diverse clinical areas of a multicampus health care system from November 2020 to March 2021. Viral genomic sequences from infected nurses and patients were sequenced and compared with ward nurses station aerosol samples. EXPOSURE SARS-CoV-2. MAIN OUTCOMES AND MEASURES The primary outcome was positive RT-PCR results and genomic similarity between SARS-CoV-2 RNA in aerosols and human samples. Air samplers were used to detect SARS-CoV-2 RNA in aerosols on hospital units where health care personnel were or were not under routine surveillance for SARS-CoV-2 infection. RESULTS A total of 510 size-fractionated air particle samples were collected. Samples representing 3 size fractions (>10 μm, 2.5-10 μm, and <2.5 μm) obtained at the nurses station were positive for SARS-CoV-2 during the outbreak (3 of 30 samples [10%]) and negative during 9 other collection periods. SARS-CoV-2 partial genome sequences for the smallest particle fraction were 100% identical with all 3 human samples; the remaining size fractions shared >99.9% sequence identity with the human samples. Fragments of SARS-CoV-2 RNA were detected by RT-PCR in 24 of 300 samples (8.0%) in units where health care personnel were not under surveillance and 7 of 210 samples (3.3%; P = .03) where they were under surveillance. CONCLUSIONS AND RELEVANCE In this cohort study, the finding of genetically identical SARS-CoV-2 RNA fragments in aerosols obtained from a nurses station and in human samples during a nosocomial outbreak suggests that aerosols may have contributed to hospital transmission. Surveillance, along with ventilation, masking, and distancing, may reduce the introduction of community-acquired SARS-CoV-2 into aerosols on hospital wards, thereby reducing the risk of hospital transmission.
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Affiliation(s)
- Rebecca A. Stern
- Department of Environmental Health, Harvard T.H. Chan School of Public Heath, Boston, Massachusetts
| | - Michael E. Charness
- Veterans Affairs Boston Healthcare System, West Roxbury, Boston, Massachusetts
- Harvard Medical School, Boston, Massachusetts
- Boston University School of Medicine, Boston, Massachusetts
- Department of Neurology, Brigham and Women’s Hospital, Boston, Massachusetts
| | - Kalpana Gupta
- Veterans Affairs Boston Healthcare System, West Roxbury, Boston, Massachusetts
- Boston University School of Medicine, Boston, Massachusetts
| | - Petros Koutrakis
- Department of Environmental Health, Harvard T.H. Chan School of Public Heath, Boston, Massachusetts
| | - Katherine Linsenmeyer
- Veterans Affairs Boston Healthcare System, West Roxbury, Boston, Massachusetts
- Boston University School of Medicine, Boston, Massachusetts
| | - Rebecca Madjarov
- Veterans Affairs Boston Healthcare System, West Roxbury, Boston, Massachusetts
| | - Marco A. G. Martins
- Department of Environmental Health, Harvard T.H. Chan School of Public Heath, Boston, Massachusetts
| | - Bernardo Lemos
- Department of Environmental Health and Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Scot E. Dowd
- Molecular Research LP (MR DNA), Shallowater, Texas
| | - Eric Garshick
- Harvard Medical School, Boston, Massachusetts
- Pulmonary, Allergy, Sleep, and Critical Care Medicine Section, Veterans Affairs Boston Healthcare System, West Roxbury, Boston, Massachusetts
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, Massachusetts
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11
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Santana DA, Bedrat A, Puga RD, Turecki G, Mechawar N, Faria TC, Gigek CO, Payão SL, Smith MA, Lemos B, Chen ES. The role of H3K9 acetylation and gene expression in different brain regions of Alzheimer's disease patients. Epigenomics 2022; 14:651-670. [PMID: 35588246 DOI: 10.2217/epi-2022-0096] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aims: To evaluate H3K9 acetylation and gene expression profiles in three brain regions of Alzheimer's disease (AD) patients and elderly controls, and to identify AD region-specific abnormalities. Methods: Brain samples of auditory cortex, hippocampus and cerebellum from AD patients and controls underwent chromatin immunoprecipitation sequencing, RNA sequencing and network analyses. Results: We found a hyperacetylation of AD cerebellum and a slight hypoacetylation of AD hippocampus. The transcriptome revealed differentially expressed genes in the hippocampus and auditory cortex. Network analysis revealed Rho GTPase-mediated mechanisms. Conclusions: These findings suggest that some crucial mechanisms, such as Rho GTPase activity and cytoskeletal organization, are differentially dysregulated in brain regions of AD patients at the epigenetic and transcriptomic levels, and might contribute toward future research on AD pathogenesis.
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Affiliation(s)
- Daliléia A Santana
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Amina Bedrat
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Renato D Puga
- Hermes Pardini Institute, São Paulo, SP, 04038-030, Brazil
| | - Gustavo Turecki
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, H4H1R3, Canada
| | - Tathyane C Faria
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Carolina O Gigek
- Department of Pathology, Universidade Federal de São Paulo (UNIFESP), São Paulo, SP, 04023-062, Brazil
| | - Spencer Lm Payão
- Department of Genetics, Blood Center, Faculdade de Medicina de Marília (FAMEMA), Marília, SP, 17519-050, Brazil
| | - Marília Ac Smith
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil
| | - Bernardo Lemos
- Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
| | - Elizabeth S Chen
- Department of Morphology & Genetics, Universidade Federal de São Paulo (UNIFESP), São Paulo,SP, 04023-062, Brazil.,Department of Environmental Health & Molecular & Integrative Physiological Sciences Program, Harvard TH Chan School of Public Health, Boston, MA 02115-5810, USA
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12
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Cruz J, Lemos B. Post-transcriptional diversity in riboproteins and RNAs in aging and cancer. Semin Cancer Biol 2021; 76:292-300. [PMID: 34474152 PMCID: PMC8627441 DOI: 10.1016/j.semcancer.2021.08.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 12/19/2022]
Abstract
Post-transcriptional (PtscM) and post-translational (PtrnM) modifications of nucleotides and amino acids are covalent modifications able to change physio-chemical properties of RNAs and proteins. In the ribosome, the adequate assembly of rRNAs and ribosomal protein subunits in the nucleolus ensures suitable translational activity, with protein synthesis tuned according to intracellular demands of energy production, replication, proliferation, and growth. Disruption in the regulatory control of PtscM and PtrnM can impair ribosome biogenesis and ribosome function. Ribosomal impairment may, in turn, impact the synthesis of proteins engaged in functions as varied as telomere maintenance, apoptosis, and DNA repair, as well as intersect with mitochondria and telomerase activity. These cellular processes often malfunction in carcinogenesis and senescence. Here we discuss regulatory mechanisms of PtscMs and PtrnMs on ribosomal function. We also address chemical modification in rRNAs and their impacts on cellular metabolism, replication control, and senescence. Further, we highlight similarities and differences of PtscMs and PtrnMs in ribosomal intermediates during aging and carcinogenesis. Understanding these regulatory mechanisms may uncover critical steps for the development of more efficient oncologic and anti-aging therapies.
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Affiliation(s)
- Jurandir Cruz
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Faculdade de Medicina, Universidade de São Paulo, São Paulo, SP 01246, Brazil
| | - Bernardo Lemos
- Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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13
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Grodstein F, Lemos B, Yu L, Klein HU, Iatrou A, Buchman AS, Shireby GL, Mill J, Schneider JA, De Jager PL, Bennett DA. The association of epigenetic clocks in brain tissue with brain pathologies and common aging phenotypes. Neurobiol Dis 2021; 157:105428. [PMID: 34153464 PMCID: PMC8373772 DOI: 10.1016/j.nbd.2021.105428] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/10/2021] [Accepted: 06/16/2021] [Indexed: 10/21/2022] Open
Abstract
Epigenetic clocks are calculated by combining DNA methylation states across select CpG sites to estimate biologic age, and have been noted as the most successful markers of biologic aging to date. Yet, limited research has considered epigenetic clocks calculated in brain tissue. We used DNA methylation states in dorsolateral prefrontal cortex specimens from 721 older participants of the Religious Orders Study and Rush Memory and Aging Project, to calculate DNA methylation age using four established epigenetic clocks: Hannum, Horvath, PhenoAge, GrimAge, and a new Cortical clock. The four established clocks were trained in blood samples (Hannum, PhenoAge, GrimAge) or using 51 human tissue and cell types (Horvath); the recent Cortical clock is the first trained in postmortem cortical tissue. Participants were recruited beginning in 1994 (Religious Orders Study) and 1997 (Memory and Aging Project), and followed annually with questionnaires and clinical evaluations; brain specimens were obtained for 80-90% of participants. Mean age at death was 88.0 (SD 6.7) years. We used linear regression, logistic regression, and linear mixed models, to examine relations of epigenetic clock ages to neuropathologic and clinical aging phenotypes, controlling for chronologic age, sex, education, and depressive symptomatology. Hannum, Horvath, PhenoAge and Cortical clock ages were related to pathologic diagnosis of Alzheimer's disease (AD), as well as to Aβ load (a hallmark pathology of Alzheimer's disease). However, associations were substantially stronger for the Cortical than other clocks; for example, each standard deviation (SD) increase in Hannum, Horvath, and PhenoAge clock age was related to approximately 30% greater likelihood of pathologic AD (all p < 0.05), while each SD increase in Cortical age was related to 90% greater likelihood of pathologic AD (odds ratio = 1.91, 95% confidence interval 1.38, 2.62). Moreover, Cortical age was significantly related to other AD pathology (eg, mean tau tangle density, p = 0.003), and to odds of neocortical Lewy body pathology (for each SD increase in Cortical age, odds ratio = 2.00, 95% confidence 1.27, 3.17), although no clocks were related to cerebrovascular neuropathology. Cortical age was the only epigenetic clock significantly associated with the clinical phenotypes examined, from dementia to cognitive decline (5 specific cognitive systems, and a global cognitive measure averaging 17 tasks) to Parkinsonian signs. Overall, our findings provide evidence of the critical necessity for bespoke clocks of brain aging for advancing research to understand, and eventually prevent, neurodegenerative diseases of aging.
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Affiliation(s)
- Francine Grodstein
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States of America.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States of America
| | - Lei Yu
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Hans-Ulrich Klein
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - Artemis Iatrou
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America
| | - Aron S Buchman
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
| | - Gemma L Shireby
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Julie A Schneider
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America; Department of Pathology, Rush University Medical Center, Chicago, IL, United States of America
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Irving Medical Center, New York, NY, United States of America
| | - David A Bennett
- Rush Alzheimer's Disease Center, Chicago, IL, United States of America; Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States of America
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14
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Lou J, Yu S, Feng L, Guo X, Wang M, Branco AT, Li T, Lemos B. Environmentally induced ribosomal DNA (rDNA) instability in human cells and populations exposed to hexavalent chromium [Cr (VI)]. Environ Int 2021; 153:106525. [PMID: 33774497 PMCID: PMC8477438 DOI: 10.1016/j.envint.2021.106525] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 05/12/2023]
Abstract
Hexavalent Chromium [Cr (VI)] is an established toxicant, carcinogen, and a significant source of public health concern. The multicopy ribosomal DNA (rDNA) array is mechanistically linked to aging and cancer, is the most evolutionarily conserved segment of the human genome, and gives origin to nucleolus, a nuclear organelle where ribosomes are assembled. Here we show that exposure to Cr (VI) induces instability in the rDNA, triggering cycles of rapid, specific, and transient amplification and contraction of the array in human cells. The dynamic of environmentally responsive rDNA copy number (CN) amplification and contraction occurs at doses to which millions of individuals are regularly exposed. Finally, analyses of human populations occupationally exposed to Cr (VI) indicate that environmental exposure history and drinking habits but not age shape extensive naturally occurring rDNA copy number variation. Our observations identify a novel pathway of response to hexavalent chromium exposure and raise the prospect that a suite of environmental determinants of rDNA copy number remain to be discovered.
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Affiliation(s)
- Jianlin Lou
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA; School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Shoukai Yu
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Lingfang Feng
- School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Xinnian Guo
- School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Meng Wang
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Alan T Branco
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Tao Li
- School of Public Health, Hangzhou Medical College, Hangzhou, People's Republic of China; Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, People's Republic of China
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
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15
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O'Sullivan MJ, Jang JH, Panariti A, Bedrat A, Ijpma G, Lemos B, Park JA, Lauzon AM, Martin JG. Airway Epithelial Cells Drive Airway Smooth Muscle Cell Phenotype Switching to the Proliferative and Pro-inflammatory Phenotype. Front Physiol 2021; 12:687654. [PMID: 34295265 PMCID: PMC8290262 DOI: 10.3389/fphys.2021.687654] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022] Open
Abstract
The increased mass of airway smooth muscle (ASM) in the airways of asthmatic patients may contribute to the pathology of this disease by increasing the capacity for airway narrowing. Evidence for the airway epithelium as a participant in ASM remodeling is accruing. To investigate mechanisms by which airway epithelial cells induce ASM cell (ASMC) proliferation, we have employed a co-culture model to explore markers of ASMC proliferative phenotype. Co-culture with epithelial cells led to incorporation of bromodeoxyuridine into ASMCs, indicating augmented proliferation and an associated increase in mRNA of the pro-proliferative co-transcription factor Elk1. Although the mitogen heparin-binding epidermal growth factor (HB-EGF) was augmented in the co-culture supernatant, the ASMC epidermal growth factor receptor (EGFR), an effector of HB-EGF induced proliferation, did not mediate epithelial-induced proliferation. The co-culture increased the expression of ASMC mRNA for the pro-inflammatory cytokines IL-6 and IL-8 as well as the pro-proliferative microRNA miR-210. The transcriptional repressor Max-binding protein (Mnt), a putative target of miR-210, was transcriptionally repressed in co-cultured ASMCs. Together, these data indicate that the airway epithelium-induced proliferative phenotype of ASMCs is not driven by EGFR signaling, but rather may be dependent on miR210 targeting of tumor suppressor Mnt.
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Affiliation(s)
- M J O'Sullivan
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, QC, Canada.,T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - J H Jang
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, QC, Canada
| | - A Panariti
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, QC, Canada
| | - A Bedrat
- T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - G Ijpma
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, QC, Canada
| | - B Lemos
- T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - J A Park
- T.H. Chan School of Public Health, Harvard University, Boston, MA, United States
| | - A M Lauzon
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, QC, Canada
| | - J G Martin
- Meakins-Christie Laboratories, McGill University Health Centre, Montreal, QC, Canada
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16
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Tao T, Shi H, Wang M, Perez-Atayde AR, London WB, Gutierrez A, Lemos B, Durbin AD, Look AT. Ganglioneuromas are driven by activated AKT and can be therapeutically targeted with mTOR inhibitors. J Exp Med 2021; 217:151986. [PMID: 32728700 PMCID: PMC7537400 DOI: 10.1084/jem.20191871] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 04/01/2020] [Accepted: 05/13/2020] [Indexed: 12/13/2022] Open
Abstract
Peripheral sympathetic nervous system tumors are the most common extracranial solid tumors of childhood and include neuroblastoma, ganglioneuroblastoma, and ganglioneuroma. Surgery is the only effective therapy for ganglioneuroma, which may be challenging due to the location of the tumor and involvement of surrounding structures. Thus, there is a need for well-tolerated presurgical therapies that could reduce the size and extent of ganglioneuroma and therefore limit surgical morbidity. Here, we found that an AKT–mTOR–S6 pathway was active in human ganglioneuroma but not neuroblastoma samples. Zebrafish transgenic for constitutively activated myr-Akt2 in the sympathetic nervous system were found to develop ganglioneuroma without progression to neuroblastoma. Inhibition of the downstream AKT target, mTOR, in zebrafish with ganglioneuroma effectively reduced the tumor burden. Our results implicate activated AKT as a tumorigenic driver in ganglioneuroma. We propose a clinical trial of mTOR inhibitors as a means to shrink large ganglioneuromas before resection in order to reduce surgical morbidity.
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Affiliation(s)
- Ting Tao
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Hui Shi
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Meng Wang
- Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA
| | | | - Wendy B London
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Alejandro Gutierrez
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Bernardo Lemos
- Department of Environmental Health & Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Adam D Durbin
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA.,The Broad Institute of MIT and Harvard, Cambridge, MA
| | - A Thomas Look
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
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17
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Stern RA, Koutrakis P, Martins MAG, Lemos B, Dowd SE, Sunderland EM, Garshick E. Characterization of hospital airborne SARS-CoV-2. Respir Res 2021; 22:73. [PMID: 33637076 PMCID: PMC7909372 DOI: 10.1186/s12931-021-01637-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 01/24/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The mechanism for spread of SARS-CoV-2 has been attributed to large particles produced by coughing and sneezing. There is controversy whether smaller airborne particles may transport SARS-CoV-2. Smaller particles, particularly fine particulate matter (≤ 2.5 µm in diameter), can remain airborne for longer periods than larger particles and after inhalation will penetrate deeply into the lungs. Little is known about the size distribution and location of airborne SARS-CoV-2 RNA. METHODS As a measure of hospital-related exposure, air samples of three particle sizes (> 10.0 µm, 10.0-2.5 µm, and ≤ 2.5 µm) were collected in a Boston, Massachusetts (USA) hospital from April to May 2020 (N = 90 size-fractionated samples). Locations included outside negative-pressure COVID-19 wards, a hospital ward not directly involved in COVID-19 patient care, and the emergency department. RESULTS SARS-CoV-2 RNA was present in 9% of samples and in all size fractions at concentrations of 5 to 51 copies m-3. Locations outside COVID-19 wards had the fewest positive samples. A non-COVID-19 ward had the highest number of positive samples, likely reflecting staff congregation. The probability of a positive sample was positively associated (r = 0.95, p < 0.01) with the number of COVID-19 patients in the hospital. The number of COVID-19 patients in the hospital was positively associated (r = 0.99, p < 0.01) with the number of new daily cases in Massachusetts. CONCLUSIONS More frequent detection of positive samples in non-COVID-19 than COVID-19 hospital areas indicates effectiveness of COVID-ward hospital controls in controlling air concentrations and suggests the potential for disease spread in areas without the strictest precautions. The positive associations regarding the probability of a positive sample, COVID-19 cases in the hospital, and cases in Massachusetts suggests that hospital air sample positivity was related to community burden. SARS-CoV-2 RNA with fine particulate matter supports the possibility of airborne transmission over distances greater than six feet. The findings support guidelines that limit exposure to airborne particles including fine particles capable of longer distance transport and greater lung penetration.
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Affiliation(s)
- Rebecca A Stern
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA, USA
| | - Petros Koutrakis
- Department of Environmental Health, Harvard T.H. Chan School of Public Heath, Boston, MA, USA
| | - Marco A G Martins
- Department of Environmental Health, Harvard T.H. Chan School of Public Heath, Boston, MA, USA
| | - Bernardo Lemos
- Department of Environmental Health and Molecular and Integrative Physiological Sciences Program, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Scot E Dowd
- Molecular Research LP (MR DNA), Shallowater, TX, USA
| | - Elsie M Sunderland
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, MA, USA
- Department of Environmental Health, Harvard T.H. Chan School of Public Heath, Boston, MA, USA
| | - Eric Garshick
- Pulmonary, Allergy, Sleep, and Critical Care Medicine Section, VA Boston Healthcare System, 1400 VFW Pkwy, West Roxbury, Boston, MA, 02132, USA.
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
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18
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Grodstein F, Lemos B, Yu L, Iatrou A, De Jager PL, Bennett DA. Characteristics of Epigenetic Clocks Across Blood and Brain Tissue in Older Women and Men. Front Neurosci 2021; 14:555307. [PMID: 33488342 PMCID: PMC7817909 DOI: 10.3389/fnins.2020.555307] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 12/09/2020] [Indexed: 01/22/2023] Open
Abstract
Epigenetic clocks are among the most promising biomarkers of aging. It is particularly important to establish biomarkers of brain aging to better understand neurodegenerative diseases. To advance application of epigenetic clocks-which were largely created with DNA methylation levels in blood samples-for use in brain, we need clearer evaluation of epigenetic clock behavior in brain, including direct comparisons of brain specimens with blood, a more accessible tissue for research. We leveraged data from the Religious Orders Study and Rush Memory and Aging Project to examine three established epigenetic clocks (Horvath, Hannum, PhenoAge clocks) and a newer clock, trained in cortical tissue. We calculated each clock in three different specimens: (1) antemortem CD4+ cells derived from blood (n = 41); (2) postmortem dorsolateral prefrontal cortex (DLPFC, n = 730); and (3) postmortem posterior cingulate cortex (PCC, n = 186), among older women and men, age 66-108 years at death. Across all clocks, epigenetic age calculated from blood and brain specimens was generally lower than chronologic age, although differences were smallest for the Cortical clock when calculated in the brain specimens. Nonetheless, we found that Pearson correlations of epigenetic to chronologic ages in brain specimens were generally reasonable for all clocks; correlations for the Horvath, Hannum, and PhenoAge clocks largely ranged from 0.5 to 0.7 (all p < 0.0001). The Cortical clock outperformed the other clocks, reaching a correlation of 0.83 in the DLFPC (p < 0.0001) for epigenetic vs. chronologic age. Nonetheless, epigenetic age was quite modestly correlated across blood and DLPFC in 41 participants with paired samples [Pearson r from 0.21 (p = 0.2) to 0.32 (p = 0.05)], indicating that broader research in neurodegeneration may benefit from clocks using CpG sites better conserved across blood and brain. Finally, in analyses stratified by sex, by pathologic diagnosis of Alzheimer disease, and by clinical diagnosis of Alzheimer dementia, correlations of epigenetic to chronologic age remained consistently high across all groups. Future research in brain aging will benefit from epigenetic clocks constructed in brain specimens, including exploration of any advantages of focusing on CpG sites conserved across brain and other tissue types.
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Affiliation(s)
- Francine Grodstein
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL, United States
| | - Bernardo Lemos
- Department of Environmental Health, Harvard TH Chan School of Public Health, Boston, MA, United States
| | - Lei Yu
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
| | - Artemis Iatrou
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
| | - Philip L. De Jager
- Department of Neurology and Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Center for Translational and Computational Neuroimmunology, Columbia University Irving Medical Center, New York, NY, United States
| | - David A. Bennett
- Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, IL, United States
- Department of Neurological Sciences, Rush University Medical Center, Chicago, IL, United States
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19
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Kitara DL, Lemos B, Bump JB. Nodding syndrome: an enigmatic neglected tropical disease, a newly recognized neurodegenerative disorder with regional clusters in East Africa; could it be an early-onset Alzheimer’s disease? PAMJ-CM 2021. [DOI: 10.11604/pamj-cm.2021.7.31.29943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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20
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Zhang Y, Wolosker MB, Zhao Y, Ren H, Lemos B. Exposure to microplastics cause gut damage, locomotor dysfunction, epigenetic silencing, and aggravate cadmium (Cd) toxicity in Drosophila. Sci Total Environ 2020; 744:140979. [PMID: 32721682 PMCID: PMC8491431 DOI: 10.1016/j.scitotenv.2020.140979] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Revised: 07/08/2020] [Accepted: 07/13/2020] [Indexed: 04/13/2023]
Abstract
The interactions of microplastics (MPs) with other chemicals and the range of outcomes are of great importance to enhance understanding of their environmental impacts and health risks. Cadmium (Cd) and cadmium compounds are widely used as pigments and stabilizers in plastics, but they readily leach out. Here we addressed the impacts of MPs, Cd, and their joint exposure in a tractable Drosophila melanogaster model. We show that exposure to MPs lead to extensive particle size depended gut damage early in life and an enhancement of Cd-induced inhibition of locomotor-behavioral function in adult flies. In addition, we show that Cd exposure induces epigenetic gene silencing via position-effect variegation (PEV) in somatic tissues that was dramatically enhanced by co-exposure with MPs. The results indicate that MPs can aggravate the toxicity of other environmental contaminants and induce adverse effects across a range of diverse outcomes in a tractable and widely used model organism. These observations raise the prospects of using Drosophila as a tool for the rapid assessment of MP-mediated toxicity.
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Affiliation(s)
- Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China; Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA.
| | - Marina B Wolosker
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yanping Zhao
- School of Environment, Nanjing Normal University, Nanjing 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.
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21
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Rosa-Fernandes L, Barbosa RH, dos Santos MLB, Angeli CB, Silva TP, Melo RCN, de Oliveira GS, Lemos B, Van Eyk JE, Larsen MR, Cardoso CA, Palmisano G. Cellular Imprinting Proteomics Assay: A Novel Method for Detection of Neural and Ocular Disorders Applied to Congenital Zika Virus Syndrome. J Proteome Res 2020; 19:4496-4515. [PMID: 32686424 PMCID: PMC7640952 DOI: 10.1021/acs.jproteome.0c00320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Indexed: 12/24/2022]
Abstract
Congenital Zika syndrome was first described due to increased incidence of congenital abnormalities associated with Zika virus (ZIKV) infection. Since the eye develops as part of the embryo central nervous system (CNS) structure, it becomes a specialized compartment able to display symptoms of neurodegenerative diseases and has been proposed as a noninvasive approach to the early diagnosis of neurological diseases. Ocular lesions result from defects that occurred during embryogenesis and can become apparent in newborns exposed to ZIKV. Furthermore, the absence of microcephaly cannot exclude the occurrence of ocular lesions and other CNS manifestations. Considering the need for surveillance of newborns and infants with possible congenital exposure, we developed a method termed cellular imprinting proteomic assay (CImPA) to evaluate the ocular surface proteome specific to infants exposed to ZIKV during gestation compared to nonexposure. CImPA combines surface cells and fluid capture using membrane disks and a large-scale quantitative proteomics approach, which allowed the first-time report of molecular alterations such as neutrophil degranulation, cell death signaling, ocular and neurological pathways, which are associated with ZIKV infection with and without the development of congenital Zika syndrome, CZS. Particularly, infants exposed to ZIKV during gestation and without early clinical symptoms could be detected using the CImPA method. Lastly, this methodology has broad applicability as it could be translated in the study of several neurological diseases to identify novel diagnostic biomarkers. Data are available via ProteomeXchange with identifier PXD014038.
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Affiliation(s)
- Livia Rosa-Fernandes
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Odense, Denmark
| | - Raquel Hora Barbosa
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
- Molecular
and Integrative Physiological Sciences Program, Department of Environmental
Health, Harvard School of Public Health, Boston, Massachusetts, United States
- Maternal
and Child Department, Faculty of Medicine, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil
- Genetics
Program, National Cancer Institute, Rio de Janeiro, Brazil
| | - Maria Luiza B. dos Santos
- Maternal
and Child Department, Faculty of Medicine, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil
| | - Claudia B. Angeli
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Thiago P. Silva
- Laboratory
of Cellular Biology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Rossana C. N. Melo
- Laboratory
of Cellular Biology, Department of Biology, Federal University of Juiz de Fora, Juiz de Fora, Minas Gerais, Brazil
| | - Gilberto Santos de Oliveira
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
| | - Bernardo Lemos
- Molecular
and Integrative Physiological Sciences Program, Department of Environmental
Health, Harvard School of Public Health, Boston, Massachusetts, United States
| | - Jennifer E Van Eyk
- Advanced
Clinical BioSystems Research Institute, Cedars Sinai Precision Biomarker
Laboratories, Barbra Streisand Women’s Heart Center, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Martin R. Larsen
- Department
of Biochemistry and Molecular Biology, University
of Southern Denmark, Odense, Denmark
| | - Claudete Araújo Cardoso
- Maternal
and Child Department, Faculty of Medicine, Fluminense Federal University, Niteroi, Rio de Janeiro, Brazil
| | - Giuseppe Palmisano
- GlycoProteomics
Laboratory, Department of Parasitology, Institute of Biomedical Sciences, University of Sao Paulo, Sao Paulo, Brazil
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22
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Deng Y, Yan Z, Shen R, Wang M, Huang Y, Ren H, Zhang Y, Lemos B. Microplastics release phthalate esters and cause aggravated adverse effects in the mouse gut. Environ Int 2020; 143:105916. [PMID: 32615348 DOI: 10.1016/j.envint.2020.105916] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/15/2020] [Accepted: 06/15/2020] [Indexed: 05/21/2023]
Abstract
Increasing evidence shows that microplastics (MPs) have the potential to act as carriers and transport contaminants into organisms, as well as induce serious health risks. Here we endeavored to address for the first time whether MPs could transport and release phthalate esters (PAEs) into mouse gut and the consequential toxic effects. As a result, MPs could adsorb PAEs, transport PAEs into the gut and cause intestinal accumulation. The accumulation of PAE in the gut followed the order of DEHP > DBP > DEP > DMP, which was the same order for the adsorption of PAEs on MPs. After exposed to DEHP-contaminated MPs for 30 days, significantly increased intestinal permeability and enhanced intestinal inflammation were induced compared with individual MPs and DEHP according to biochemical and histological analysis. Transcriptomic analysis found that 703 genes were differentially regulated and these genes are involved in oxidative stress, immune response, lipid metabolism, and hormone metabolism. Moreover, gut microbiota analysis found that the combined exposure of MPs and DEHP also caused alterations in gut microbiota composition, especially some energy metabolism and immune function related bacteria were significantly changed in the relative abundance. The aggravated effects on intestinal inflammation and metabolic disorders caused by DEHP-contaminated MPs may attribute to increased DEHP accumulation, changed exposure pathway, and shared toxic mechanisms. Our results provide valuable information for the health risk of MPs and plastic additives.
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Affiliation(s)
- Yongfeng Deng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Zehua Yan
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Ruqin Shen
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Meng Wang
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yichao Huang
- School of Environment, Guangzhou Key Laboratory of Environmental Exposure and Health, and Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, Guangdong 510632, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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23
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Tao T, Shi H, Durbin AD, Wang M, Perez-Atayde AR, London WB, Gutierrez A, Lemos B, Look AT. Abstract 3450: Ganglioneuromas are driven by activated AKT and can be therapeutically targeted with mTOR inhibitors. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-3450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Peripheral sympathetic nervous system tumors are the most common extra-cranial pediatric tumors in children and include neuroblastoma, ganglioneuroblastoma (intermixed and nodular) and ganglioneuroma. The etiology and molecular pathogenesis of ganglioneuromas remains largely unknown. Surgery is the only effective therapy for ganglioneuroma, which can be challenging due to the location of the tumor and involvement of surrounding structures. Thus, there is need for well tolerated presurgical therapies that could reduce the size and extent of ganglioneuroma, and therefore limit surgical morbidity. Here we found high levels of phosphorylated AKT expressed in 10 of 11 patients with ganglioneuroma, but only in 1 of 15 who had poorly differentiated neuroblastoma (p<0.0001, Fisher's exact test). Consistent with these results, zebrafish transgenic for constitutively activated myr-Akt2 in the sympathetic nervous system were found to develop ganglioneuroma without progression to neuroblastoma. Histopathological analysis and whole-transcriptome sequencing revealed that zebrafish ganglioneuroma highly resembles human ganglioneuroma. Inhibition of the downstream AKT target, mTOR, using sirolimus in zebrafish with ganglioneuroma effectively reduced the tumor burden, providing preclinical evidence for efficacy with this well tolerated drug. Our results implicate activated AKT as a tumorigenic driver in ganglioneuroma. We propose a clinical trial of sirolimus as a means to shrink large ganglioneuromas prior to resection in order to reduce surgical morbidity.
Citation Format: Ting Tao, Hui Shi, Adam D. Durbin, Meng Wang, Antonio R. Perez-Atayde, Wendy B. London, Alejandro Gutierrez, Bernardo Lemos, A. Thomas Look. Ganglioneuromas are driven by activated AKT and can be therapeutically targeted with mTOR inhibitors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3450.
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Affiliation(s)
- Ting Tao
- 1Dana-Farber Cancer Institute, Boston, MA
| | - Hui Shi
- 1Dana-Farber Cancer Institute, Boston, MA
| | | | - Meng Wang
- 2Harvard T.H. Chan School of Public Health, Boston, MA
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24
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Feng L, Du J, Yao C, Jiang Z, Li T, Zhang Q, Guo X, Yu M, Xia H, Shi L, Jia J, Tong Y, Ju L, Liu J, Lou J, Lemos B. Ribosomal DNA copy number is associated with P53 status and levels of heavy metals in gastrectomy specimens from gastric cancer patients. Environ Int 2020; 138:105593. [PMID: 32120062 DOI: 10.1016/j.envint.2020.105593] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 02/15/2020] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
The ribosomal DNA (rDNA) can act as a sensor and responder of cancer-associated stress. Here we investigated rDNA copy number in gastric cancers and its association with existing biomarkers and metals exposure. This study was performed on paired tumor and adjacent normal tissues obtained from 65 gastric cancer patients who underwent gastrectomy. Immunohistochemistry was used to assess HER-2, E-cadherin, EGFR, CK (pan), CK20, CK7, TopoⅡ, CAM5.2, P53, and Ki-67 expression. Inductively coupled plasma mass spectrometry (ICP-MS) was used to detect the concentrations of 17 metals in gastric tissues. rDNA copy number was detected by qPCR in genomic DNA isolated from tissue samples. Associations between the expression of existing markers, metal concentrations, and rDNA copy number were evaluated. Within patients with gastric cancer, the copy number of the 45S rDNA components (18S, 5.8S, 28S) and the 5S rDNA in tumor tissues were significantly higher than those in adjacent normal tissues, whereas mitochondrial DNA (mtDNA) copy number was significantly lower in tumor tissues than that in adjacent normal tissues. Further analysis revealed that the increase in 18S, 5.8S, and 28S rDNA copy number in tumor tissues was diminished in the context of EGFR and P53 loss. Moreover, analysis of metals revealed particularly high concentrations of As, Cd, Cr, Cu and Fe in the gastric tissues of these patients. Intriguingly, rDNA copy number variation across individuals was correlated with the concentrations of some metals. The rDNA was amplified in tumor tissues of gastric cancer patients, and its amplification may be associated with metals exposure. The expression of EGFR and P53 may influence rDNA copy number, with diminished amplification of the rDNA in cancers that were negative for these biomarkers. Our observation further our understanding of rDNA copy number in gastric cancer and its potential as a simple and useful marker in gastric cancer monitoring.
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Affiliation(s)
- Lingfang Feng
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Jing Du
- Department of Gastroenterology, Zhejiang Provincial People's Hospital, Hangzhou, China; People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Chunji Yao
- Institute of Hygiene, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Zhaoqiang Jiang
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Tao Li
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Quan Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou, China
| | - Xinnian Guo
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Min Yu
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Hailing Xia
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Li Shi
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Junlin Jia
- Center for Biostatistics, Bioinformatics and Big Data, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Tong
- Affiliated Hangzhou First People's Hospital Zhejiang University School of Medicine, Hangzhou, China
| | - Li Ju
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Jiaqi Liu
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China
| | - Jianlin Lou
- Institute of Occupational Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, China; Hangzhou Medical College, Hangzhou, China.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard University T.H. Chan School of Public Health, Boston, USA
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25
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Faria TC, Maldonado HL, Santos LC, DeLabio R, Payao SLM, Turecki G, Mechawar N, Santana DA, Gigek CO, Lemos B, Smith MAC, Chen ES. Characterization of Cerebellum-Specific Ribosomal DNA Epigenetic Modifications in Alzheimer's Disease: Should the Cerebellum Serve as a Control Tissue After All? Mol Neurobiol 2020; 57:2563-2571. [PMID: 32232768 DOI: 10.1007/s12035-020-01902-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 03/09/2020] [Indexed: 11/26/2022]
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease, known as the most common form of dementia. In AD onset, abnormal rRNA expression has been reported to be linked in pathogenesis. Although region-specific expression patterns have previously been reported in AD, it is not until recently that the cerebellum has come under the spotlight. Specifically, it is unclear whether DNA methylation is the mechanism involved in rRNA expression regulation in AD. Hence, we sought to explore the rDNA methylation pattern of two different brain regions - auditory cortex and cerebellum - from AD and age-/sex-matched controls. Our results showed differential hypermethylation at an upstream CpG region to the rDNA promoter when comparing cerebellum controls to auditory cortex controls. This suggests a possible regulatory region from rDNA expression regulation. Moreover, when comparing between AD and control cerebellum samples, we observed hypermethylation of the rDNA promoter region as well as an increase in rDNA content. In addition, we also observed increased rRNA levels in AD compared to control cerebellum. Although still considered a pathology-free brain region, there are growing findings that continue to suggest otherwise. Indeed, cerebellum from AD has been recently described as affected by the disease, presenting a unique pattern of molecular alterations. Given that we observed that increased rDNA promoter methylation did not silence rDNA gene expression, we suggest that rDNA promoter hypermethylation is playing a protective role in rDNA genomic stability and, therefore, increasing rRNA levels in AD cerebellum.
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Affiliation(s)
- Tathyane C Faria
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Héctor L Maldonado
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Leonardo C Santos
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Roger DeLabio
- Faculdade de Medicina de Marília (FAMEMA), Marília, SP, Brazil
| | | | - Gustavo Turecki
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, Canada
| | - Naguib Mechawar
- Department of Psychiatry, Douglas Hospital Research Center, McGill University, Montreal, QC, Canada
| | - Dalileia A Santana
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Carolina O Gigek
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Bernardo Lemos
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Marilia A C Smith
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil
| | - Elizabeth S Chen
- Departamento de Morfologia e Genética, Programa de Pós-Graduação em Biologia Estrutural e Funcional da UNIFESP/EPM, Disciplina de Genética, Universidade Federal de São Paulo (UNIFESP/EPM), São Paulo, SP, Brazil.
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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Barbosa RH, dos Santos MLB, Silva TP, Rosa-Fernandes L, Pinto AMV, Spínola PS, Bonvicino CR, Fernandes PV, Lucena E, Palmisano G, Melo RCN, Cardoso CAA, Lemos B. Impression Cytology Is a Non-invasive and Effective Method for Ocular Cell Retrieval of Zika Infected Babies: Perspectives in OMIC Studies. Front Mol Neurosci 2019; 12:279. [PMID: 31866819 PMCID: PMC6907025 DOI: 10.3389/fnmol.2019.00279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 11/01/2019] [Indexed: 01/08/2023] Open
Abstract
IMPORTANCE Non-invasive techniques for retrieving ocular surface cells from babies infected by zika virus (ZIKV) during the gestational period remain to be determined. OBJECTIVES The aim of this study was to describe an optimized impression cytology method for the isolation of viable cells from Zika infected babies with and without Congenital Zika Syndrome (CZS) in satisfactory amount and quality to enable easy adoption in the field and application in the context of genomic and molecular approaches. DESIGN SETTINGS AND PARTICIPANTS Ocular surface samples were obtained with a hydrophilic nitrocellulose membrane (through optimized impression cytology method) from twelve babies referred to the Pediatric Service of the Antonio Pedro Hospital, Universidade Federal Fluminense (UFF), Niteroi, Rio de Janeiro, Brazil. After an authorized written informed consent from the parents, samples were collected from both eyes of 12 babies (4 babies with maternal ZIKV exposure during gestation and presence of clinical signs which included ocular abnormalities and microcephaly; 4 babies with maternal ZIKV exposure during gestation but no clinical signs; and 4 unaffected control babies with negative PCR for Zika virus and without clinical signs). Cells were used for microscopy analyses and evaluated for their suitability for downstream molecular applications in transcriptomic and proteomic experiments. RESULTS Our optimized impression cytology protocol enabled the capture of a considerable number of viable cells. The microscopic features of the conjunctival epithelial cells were described by both direct analysis of the membrane-attached cells and analysis of cytospinned captured cells using several staining procedures. Epithelial basal, polyhedral and goblet cells were clearly identified in all groups. All cases of ZIKV infected babies showed potential morphological alterations (cell keratinization, pyknosis, karyolysis, anucleation, and vacuolization). Molecular approaches were also performed in parallel. Genomic DNA and RNA were successfully isolated from all samples to enable the establishment of transcriptomic and proteomic studies. CONCLUSIONS AND RELEVANCE Our method proved to be a suitable, fast, and non-invasive tool to obtain ocular cell preparations from babies with and without Zika infection. The method yielded sufficient cells for detailed morphological and molecular analyses of samples. We discuss perspectives for the application of impression cytology in the context of ZIKV studies in basic and clinical research.
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Affiliation(s)
- Raquel Hora Barbosa
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
- Department of Maternal and Child, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil
- Genetics Program, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Maria Luiza B. dos Santos
- Department of Maternal and Child, School of Medicine, Universidade Federal Fluminense, Niterói, Brazil
| | - Thiago P. Silva
- Laboratory of Cellular Biology, Department of Biology, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | - Liva Rosa-Fernandes
- Glycoproteomics Laboratory, Department of Parasitology, ICB, Universidade de São Paulo, São Paulo, Brazil
| | - Ana M. V. Pinto
- Biomedical Institute, Universidade Federal Fluminense, Niterói, Brazil
| | - Pricila S. Spínola
- Genetics Department – Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | | | - Evandro Lucena
- Division of Clinical Research, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Giuseppe Palmisano
- Glycoproteomics Laboratory, Department of Parasitology, ICB, Universidade de São Paulo, São Paulo, Brazil
| | - Rossana C. N. Melo
- Laboratory of Cellular Biology, Department of Biology, Universidade Federal de Juiz de Fora, Juiz de Fora, Brazil
| | | | - Bernardo Lemos
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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27
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Drinnenberg IA, Berger F, Elsässer SJ, Andersen PR, Ausió J, Bickmore WA, Blackwell AR, Erwin DH, Gahan JM, Gaut BS, Harvey ZH, Henikoff S, Kao JY, Kurdistani SK, Lemos B, Levine MT, Luger K, Malik HS, Martín-Durán JM, Peichel CL, Renfree MB, Rutowicz K, Sarkies P, Schmitz RJ, Technau U, Thornton JW, Warnecke T, Wolfe KH. EvoChromo: towards a synthesis of chromatin biology and evolution. Development 2019; 146:146/19/dev178962. [PMID: 31558570 DOI: 10.1242/dev.178962] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Over the past few years, interest in chromatin and its evolution has grown. To further advance these interests, we organized a workshop with the support of The Company of Biologists to debate the current state of knowledge regarding the origin and evolution of chromatin. This workshop led to prospective views on the development of a new field of research that we term 'EvoChromo'. In this short Spotlight article, we define the breadth and expected impact of this new area of scientific inquiry on our understanding of both chromatin and evolution.
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Affiliation(s)
- Ines A Drinnenberg
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique UMR 3664, Paris 75005, France
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Simon J Elsässer
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Peter R Andersen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohrgasse 3, 1030 Vienna, Austria
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Wendy A Bickmore
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | | | - Douglas H Erwin
- Department of Paleobiology, MRC-121, National Museum of Natural History, Washington, DC 20013-7012, USA
| | - James M Gahan
- Sars Centre for Marine Molecular Biology, University of Bergen, Thormøhlensgt. 55, 5008 Bergen, Norway
| | - Brandon S Gaut
- Department of Ecology and Evolutionary Biology, University of California, Irvine, Irvine, CA 92697, USA
| | - Zachary H Harvey
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Steven Henikoff
- Division of Basic Sciences and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Joyce Y Kao
- Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA.,Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, Otto-Stern-Weg 3, 8093 Zürich, Switzerland
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Mia T Levine
- Department of Biology, Epigenetics Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Karolin Luger
- Howard Hughes Medical Institute and Department of Biochemistry, CU Boulder, Boulder, CO 80303, USA
| | - Harmit S Malik
- Division of Basic Sciences and Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - José M Martín-Durán
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, UK
| | - Catherine L Peichel
- Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Marilyn B Renfree
- School of BioSciences, The University of Melbourne, Melbourne, 3010 VIC, Australia
| | - Kinga Rutowicz
- Institute of Plant and Microbial Biology, Zurich-Basel Plant Science Center, University of Zurich, 8092 Zürich, Switzerland
| | - Peter Sarkies
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, IMperial College London, Du Cane Road, London W12 0NN, UK
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Ulrich Technau
- Department for Molecular Evolution and Development, Centre of Organismal Systems Biology, University of Vienna, Vienna A-1090, Austria
| | - Joseph W Thornton
- Department of Human Genetics, and Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Tobias Warnecke
- MRC London Institute of Medical Sciences and Institute of Clinical Sciences, IMperial College London, Du Cane Road, London W12 0NN, UK
| | - Kenneth H Wolfe
- Conway Institute and School of Medicine, University College Dublin, Dublin 4, Ireland
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Cerqueira AV, Lemos B. Ribosomal DNA and the Nucleolus as Keystones of Nuclear Architecture, Organization, and Function. Trends Genet 2019; 35:710-723. [PMID: 31447250 DOI: 10.1016/j.tig.2019.07.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 12/12/2022]
Abstract
The multicopy ribosomal DNA (rDNA) array gives origin to the nucleolus, a large nonmembrane-bound organelle that occupies a substantial volume within the cell nucleus. The rDNA/nucleolus has emerged as a coordinating hub in which seemingly disparate cellular functions converge, and from which a variety of cellular and organismal phenotypes emerge. However, the role of the nucleolus as a determinant and organizer of nuclear architecture and other epigenetic states of the genome is not well understood. We discuss the role of rDNA and the nucleolus in nuclear organization and function - from nucleolus-associated domains (NADs) to the regulation of imprinted loci and X chromosome inactivation, as well as rDNA contact maps that anchor and position the rDNA relative to the rest of the genome. The influence of the nucleolus on nuclear organization undoubtedly modulates diverse biological processes from metabolism to cell proliferation, genome-wide gene expression, maintenance of epigenetic states, and aging.
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Affiliation(s)
- Amanda V Cerqueira
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Bernardo Lemos
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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Qiao R, Sheng C, Lu Y, Zhang Y, Ren H, Lemos B. Microplastics induce intestinal inflammation, oxidative stress, and disorders of metabolome and microbiome in zebrafish. Sci Total Environ 2019; 662:246-253. [PMID: 30690359 DOI: 10.1016/j.scitotenv.2019.01.245] [Citation(s) in RCA: 418] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/16/2019] [Accepted: 01/20/2019] [Indexed: 05/20/2023]
Abstract
Microplastics (MPs) can be ingested by a variety of species and mainly accumulate in the gut. However, the consequences of MPs exposure in the gut are largely unknown. Here we evaluated the impacts of MPs exposure in zebrafish gut. Animals were experimentally exposed to polystyrene MPs (5-μm beads; 50 μg/L and 500 μg/L) for 21 days and monitored for alterations in tissue histology, enzymatic biomarkers, gut microbiome and metabolomic responses. Inflammation and oxidative stress were observed in the zebrafish gut after exposed to MPs. Furthermore, significant alterations in the gut microbiome and tissue metabolic profiles were observed, with most of these were associated with oxidative stress, inflammation and lipid metabolism. This study provides evidence that MPs exposure causes gut damage as well as alterations in gut metabolome and microbiome, yielding novel insights into the consequences of MPs exposure.
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Affiliation(s)
- Ruxia Qiao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Cheng Sheng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yifeng Lu
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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30
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Abstract
The ribosomal DNA (rDNA) is the most evolutionarily conserved segment of the genome and gives origin to the nucleolus, an energy intensive nuclear organelle and major hub influencing myriad molecular processes from cellular metabolism to epigenetic states of the genome. The rDNA/nucleolus has been directly and mechanistically implicated in aging and longevity in organisms as diverse as yeasts, Drosophila, and humans. The rDNA is also a significant target of DNA methylation that silences supernumerary rDNA units and regulates nucleolar activity. Here, we introduce an age clock built exclusively with CpG methylation within the rDNA. The ribosomal clock is sufficient to accurately estimate individual age within species, is responsive to genetic and environmental interventions that modulate life-span, and operates across species as distant as humans, mice, and dogs. Further analyses revealed a significant excess of age-associated hypermethylation in the rDNA relative to other segments of the genome, and which forms the basis of the rDNA clock. Our observations identified an evolutionarily conserved marker of aging that is easily ascertained, grounded on nucleolar biology, and could serve as a universal marker to gauge individual age and response to interventions in humans as well as laboratory and wild organisms across a wide diversity of species.
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Affiliation(s)
- Meng Wang
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA
| | - Bernardo Lemos
- Department of Environmental Health, Program in Molecular and Integrative Physiological Sciences, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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Abstract
Hexavalent chromium [Cr (VI)] contributes a significant health risk and causes a number of chronic diseases and cancers. While the genotoxic and carcinogenic effects of hexavalent chromium exposure are explicit and better-characterized, the exact mechanism underlying the carcinogenic process of Cr (VI) is still a matter of debate. In recent years, studies have shown that epigenetic modifications, especially DNA methylation, may play a significant role in Cr (VI)-induced carcinogenesis. The aim of this review is to summarize our understanding regarding the effects of Cr (VI) on global and gene-specific DNA methylation.
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Affiliation(s)
- Xinnian Guo
- Institute of Occupation Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, Zhejiang, P.R.China
| | - Lingfang Feng
- Institute of Occupation Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, Zhejiang, P.R.China
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Jianlin Lou
- Institute of Occupation Diseases, Zhejiang Academy of Medical Sciences, Hangzhou, 310013, Zhejiang, P.R.China
- Corresponding author at: Institute of Occupation Diseases, Zhejiang Academy of Medical Sciences, 182 Tianmushan Road, Hangzhou, 310013, P.R.C. Telephone: +86-571-88215566. Fax: +86-571-88215576.
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32
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Barbosa FB, Simioni M, Wiezel CEV, Torres FR, Molck MC, Bonilla MM, de Araujo TK, Donadi EA, Gil-da-Silva-Lopes VL, Lemos B, Simões AL. Copy number variation in the susceptibility to systemic lupus erythematosus. PLoS One 2018; 13:e0206683. [PMID: 30485348 PMCID: PMC6261406 DOI: 10.1371/journal.pone.0206683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 05/30/2018] [Indexed: 11/23/2022] Open
Abstract
Systemic lupus erythematosus (SLE) is an autoimmune disease with a strong genetic component and etiology characterized by chronic inflammation and autoantibody production. The purpose of this study was to ascertain copy number variation (CNV) in SLE using a case-control design in an admixed Brazilian population. The whole-genome detection of CNV was performed using Cytoscan HD array in SLE patients and healthy controls. The best CNV candidates were then evaluated by quantitative real-time PCR in a larger cohort or validated using droplet digital PCR. Logistic regression models adjusted for sex and ancestry covariates was applied to evaluate the association between CNV with SLE susceptibility. The data showed a synergistic effect between the FCGR3B and ADAM3A loci with the presence of deletions in both loci significantly increasing the risk to SLE (5.9-fold) compared to the deletion in the single FCGR3B locus (3.6-fold). In addition, duplications in these genes were indeed more frequent in healthy subjects, suggesting that high FCGR3B/ADAM3A gene copy numbers are protective factors against to disease development. Overall, 21 rare CNVs were identified in SLE patients using a four-step pipeline created for identification of rare variants. Furthermore, heterozygous deletions overlapping the CFHR4, CFHR5 and HLA-DPB2 genes were described for the first time in SLE patients. Here we present the first genome-wide CNV study of SLE patients in a tri-hybrid population. The results show that novel susceptibility loci to SLE can be found once the distribution of structural variants is analyzed throughout the whole genome.
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Affiliation(s)
| | - Milena Simioni
- Department of Medical Genetics, Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil
| | | | - Fábio Rossi Torres
- Department of Medical Genetics, Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil
| | - Miriam Coelho Molck
- Department of Medical Genetics, Faculty of Medical Sciences, UNICAMP, Campinas, SP, Brazil
| | - Melvin M. Bonilla
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | | | - Eduardo Antônio Donadi
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, USP, Ribeirão Preto, SP, Brazil
| | | | - Bernardo Lemos
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, United States of America
| | - Aguinaldo Luiz Simões
- Department of Genetics, Ribeirão Preto Medical School, USP, Ribeirão Preto, SP, Brazil
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Chang CH, MacIntosh D, Lemos B, Zhang Q, Lu C. Characterization of Daily Dietary Intake and the Health Risk of Neonicotinoid Insecticides for the U.S. Population. J Agric Food Chem 2018; 66:10097-10105. [PMID: 30192531 DOI: 10.1021/acs.jafc.8b02982] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Although neonicotinoids have been the most commonly used insecticides globally, very limited data related to their dietary intake and health risks are available. In this study, we used the relative potency factor approach to aggregate individual neonicotinoids into a single metric (IMIRPF) representing the intakes of total neonicotinoids in relation to imidacloprid for each food item. We then estimated the average daily intake (ADI) of neonicotinoids using residue data collected from U.S. Congressional Cafeteria study (USCC) and USDA/PDP and food consumption data from NHANES 2011-2012. Among the USCC and USDA/PDP samples, squash (427.2 ng/g) and spinach (569.2 ng/g), had the highest average IMIRPF, respectively. The estimated ADIs were below the current chronic reference dose (cRfD) for imidacloprid. However, due to their wide use, it is logical to expect the ubiquity of neonicotinoids in foods. Therefore, the importance of conducting routine dietary intake assessment for neonicotinoids should not be ignored.
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Affiliation(s)
- Chi-Hsuan Chang
- Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , Massachusetts 02115 , United States
| | - David MacIntosh
- Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , Massachusetts 02115 , United States
| | - Bernardo Lemos
- Department of Environmental Health , Harvard T.H. Chan School of Public Health , Boston , Massachusetts 02115 , United States
| | - Quan Zhang
- College of Environment , Zhejiang University of Technology , Hangzhou , Zhejiang 310032 , People's Republic of China
| | - Chensheng Lu
- College of Resources and Environment , Southwest University , Chongqing 400715 , People's Republic of China
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Palacios-Gimenez OM, Bardella VB, Lemos B, Cabral-de-Mello DC. Satellite DNAs are conserved and differentially transcribed among Gryllus cricket species. DNA Res 2018; 25:137-147. [PMID: 29096008 PMCID: PMC5909420 DOI: 10.1093/dnares/dsx044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/19/2017] [Indexed: 11/21/2022] Open
Abstract
Satellite DNA (satDNA) is an abundant class of non-coding repetitive DNA that is preferentially found as tandemly repeated arrays in gene-poor heterochromatin but is also present in gene-rich euchromatin. Here, we used DNA- and RNA-seq from Gryllus assimilis to address the content and transcriptional patterns of satDNAs. We also mapped RNA-seq libraries for other Gryllus species against the satDNAs found in G. assimilis and G. bimaculatus genomes to investigate their evolutionary conservation and transcriptional profiles in Gryllus. Through DNA-seq read clustering analysis using RepeatExplorer, dotplots analysis and fluorescence in situ hybridization mapping, we found that ∼4% of the G. assimilis genome is represented by 11 well-defined A + T-rich satDNA families. These are mainly located in heterochromatic areas, with some repeats able to form high-order repeat structures. By in silico transcriptional analysis we identified satDNAs that are conserved in Gryllus but differentially transcribed. The data regarding satDNA presence in G. assimilis genome were discussed in an evolutionary context, with transcriptional data enabling comparisons between sexes and across tissues when possible. We discuss hypotheses for the conservation and transcription of satDNAs in Gryllus, which might result from their role in sexual differentiation at the chromatin level, heterochromatin formation and centromeric function.
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Affiliation(s)
- Octavio Manuel Palacios-Gimenez
- Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, Brazil.,Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Vanessa Bellini Bardella
- Departamento de Biologia, Instituto de Biociências/IB, UNESP-Univ Estadual Paulista, Rio Claro, São Paulo, Brazil
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, MA 02115, USA
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35
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Deng Y, Zhang Y, Qiao R, Bonilla MM, Yang X, Ren H, Lemos B. Evidence that microplastics aggravate the toxicity of organophosphorus flame retardants in mice (Mus musculus). J Hazard Mater 2018; 357:348-354. [PMID: 29908513 DOI: 10.1016/j.jhazmat.2018.06.017] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 06/05/2018] [Accepted: 06/06/2018] [Indexed: 05/24/2023]
Abstract
This study was performed to reveal the health risks of co-exposure to organophosphorus flame retardants (OPFRs) and microplastics (MPs). We exposed mice to polyethylene (PE) and polystyrene (PS) MPs and OPFRs [tris (2-chloroethy) phosphate (TCEP) and tris (1,3-dichloro-2-propyl) phosphate (TDCPP)] for 90 days. Biochemical markers and metabolomics were used to determine whether MPs could enhance the toxicity of OPFRs. Superoxide dismutase (SOD) and catalase (CAT) increased (p < 0.05) by 21% and 26% respectively in 10 μg/L TDCPP + PE group compared to TDCPP group. Lactate dehydrogenase (LDH) in TDCPP + MPs groups were higher (18%-30%) than that in TDCPP groups (p < 0.05). Acetylcholinesterase (AChE) in TCEP + PE groups were lower (10%-19%) than those in TCEP groups (p < 0.05). These results suggested that OPFR co-exposure with MPs induced more toxicity than OPFR exposure alone. Finally, in comparison to controls we observed that 29, 41, 41, 26, 40 and 37 metabolites changed significantly (p < 0.05; fold-change > 1.2) in TCEP, TCEP + PS, TCEP + PE, TDCPP, TDCPP + PS and TDCPP + PE groups, respectively. Most of these metabolites are related to pathways of amino acid and energy metabolism. Our results indicate that MPs aggravate the toxicity of OPFRs and highlight the health risks of MP co-exposure with other pollutants.
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Affiliation(s)
- Yongfeng Deng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China.
| | - Ruxia Qiao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Melvin M Bonilla
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Xiaoliang Yang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Collaborative Innovation Center of Chemistry for Life Sciences, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
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Branco AT, Brito RM, Lemos B. Sex-specific adaptation and genomic responses to Y chromosome presence in female reproductive and neural tissues. Proc Biol Sci 2018; 284:rspb.2017.2062. [PMID: 29237855 DOI: 10.1098/rspb.2017.2062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/06/2017] [Indexed: 12/21/2022] Open
Abstract
Y chromosomes typically harbour a small number of genes and an abundance of repetitive sequences. In Drosophila, the Y chromosome comprises multimegabase long segments of repetitive DNA and a handful of protein-coding genes. In mammals, the Y chromosome also harbours a disproportionally high abundance of repeats. Here, we built on a Drosophila melanogaster model in which the Y chromosome is decoupled from sexual determination. Genotypes were genetically identical for the autosomes, X chromosome, and mitochondria, but differ by the presence or dose of the Y chromosome. Addition of an extra Y chromosome had limited impact in males. However, the presence of a Y chromosome in females induced a disproportionate response in genes expressed in the ovaries as well as genes encoded by the mitochondrial genome. Furthermore, the data revealed significant consequences of Y chromosome presence in larvae neuronal tissue. This included the repression of genes implicated in reproductive behaviour, courtship, mating and synaptic function. Our findings exhibit the Y chromosome as a hotspot for sex-specific adaptation. They suggest roles for natural selection on Y-linked genetic elements exerting impact on sex-specific tissues as well as somatic tissues shared by males and females.
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Affiliation(s)
- Alan T Branco
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, 02115, Boston, MA, USA
| | - Rute M Brito
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, 02115, Boston, MA, USA
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, 665 Huntington Avenue, 02115, Boston, MA, USA
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Abstract
The repeated rDNA array gives rise to the nucleolus, an organelle that is central to cellular processes as varied as stress response, cell cycle regulation, RNA modification, cell metabolism, and genome stability. The rDNA array is also responsible for the production of more than 70% of all cellular RNAs (the ribosomal RNAs). The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1 while the 45S rDNA arrays reside on the short arm of five human acrocentric chromosomes. These critical genome elements have remained unassembled and have been excluded from all Hi-C analyses to date. Here we built the first high resolution map of 5S and 45S rDNA array contacts with the rest of the genome combining over 15 billion Hi-C reads from several experiments. The data enabled sufficiently high coverage to map rDNA-genome interactions with 1MB resolution and identify rDNA-gene contacts. The map showed that the 5S and 45S arrays display preferential contact at common sites along the genome but are not themselves sufficiently close to yield 5S-45S Hi-C contacts. Ribosomal DNA contacts are enriched in segments of closed, repressed, and late replicating chromatin, as well as CTCF binding sites. Finally, we identified functional categories whose dispersed genes coalesced in proximity to the rDNA arrays or instead avoided proximity with the rDNA arrays. The observations further our understanding of the spatial localization of rDNA arrays and their contribution to the architecture of the cell nucleus.
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Affiliation(s)
- Shoukai Yu
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States of America
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences & Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, United States of America
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Palacios Gimenez OM, Bardella VB, Lemos B, Cabral de Mello DC. High-throughput sequencing data reveals evolutionary conservation and differential transcription of satellites DNA among crickets species (Orthoptera; Gryllinae). Semin Cienc Biol Saude 2018. [DOI: 10.5433/1679-0367.2017v38n1suplp184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Satellite DNA (satDNA) is a class of non-coding repetitive DNA abundant in most eukaryotic genomes. Mostly satDNAs constitute clustered arrays of tandemly repeated sequences located in the gene-poor heterochromatin of centromeres and telomeres. Moreover in some cases, they are also dispersed in eu/heterochromatin of sex chromosomes and as single or short arrays nearby protein-coding genes within euchromatin. Here we take advantages of DNA- and RNA-seq data from cricket’s species in order to perform a comparative analysis of content and expression of satDNAs. By graph-based clustering analysis of DNA-seq reads using RepeatExplorer software, dotplots analysis and FISH mapping we found that ~ 4% of the G. assimilis genome is represented by 13 A+T-rich satDNAs consisting of 11 well-defined families mainly located in the heterochromatic areas of chromosomes, and some of them able to form high-order repeats (HORs). In order to determine transcription profiles the raw RNA-seq reads from different tissues library of Gryllus species were mapped to each of the G. assimilis satDNAs using Bowtie2 and the method FPKM (fragments per kilo-base of transcript per million mapped reads) was used. The in silico transcriptional analysis of RNA-seq reads in G. assimilis, G. bimaculatus, G, firmus and G. rubens showed that some satDNAs are conserved in Gryllus species but differentially expressed in distinct tissues, sexes and besides tissue- and species-specific. In concordances with the transcriptional activity we found that G. assimilis satDNAs are also capable to adopt RNA secondary structures with well-defined helices ranging from 2 bp to 7 bp lengths. The folding possibility forming secondary structure helps to the satDNA dispersion along the genome by rolling-circle replication mechanism, in which circular monomer result from secondary structure RNA processing into linear monomers and subsequently circularization by a host-specific RNA ligase. The conservation of expression for different satDNAs in Gryllus species suggests a functional role for these sequences, as observed in other insects. Our data suggests functional roles of satDNAs for sexual differentiation at the chromatin levels, heterochromatin formation and centromeric function.
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Palacios-Gimenez OM, Milani D, Lemos B, Castillo ER, Martí DA, Ramos E, Martins C, Cabral-de-Mello DC. Uncovering the evolutionary history of neo-XY sex chromosomes in the grasshopper Ronderosia bergii (Orthoptera, Melanoplinae) through satellite DNA analysis. BMC Evol Biol 2018; 18:2. [PMID: 29329524 PMCID: PMC5767042 DOI: 10.1186/s12862-017-1113-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/08/2017] [Indexed: 03/26/2023] Open
Abstract
BACKGROUND Neo-sex chromosome systems arose independently multiple times in evolution, presenting the remarkable characteristic of repetitive DNAs accumulation. Among grasshoppers, occurrence of neo-XY was repeatedly noticed in Melanoplinae. Here we analyzed the most abundant tandem repeats of R. bergii (2n = 22, neo-XY♂) using deep Illumina sequencing and graph-based clustering in order to address the neo-sex chromosomes evolution. RESULTS The analyses revealed ten families of satDNAs comprising about ~1% of the male genome, which occupied mainly C-positive regions of autosomes. Regarding the sex chromosomes, satDNAs were recorded within centromeric or interstitial regions of the neo-X chromosome and four satDNAs occurred in the neo-Y, two of them being exclusive (Rber248 and Rber299). Using a combination of probes we uncovered five well-defined cytological variants for neo-Y, originated by multiple paracentric inversions and satDNA amplification, besides fragmented neo-Y. These neo-Y variants were distinct in frequency between embryos and adult males. CONCLUSIONS The genomic data together with cytogenetic mapping enabled us to better understand the neo-sex chromosome dynamics in grasshoppers, reinforcing differentiation of neo-X and neo-Y and revealing the occurrence of multiple additional rearrangements involved in the neo-Y evolution of R. bergii. We discussed the possible causes that led to differences in frequency for the neo-Y variants between embryos and adults. Finally we hypothesize about the role of DNA satellites in R. bergii as well as putative historical events involved in the evolution of the R. bergii neo-XY.
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Affiliation(s)
- Octavio M. Palacios-Gimenez
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
| | - Diogo Milani
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard University T. H. Chan School of Public Health, Boston, Massachusetts 02115 USA
| | | | | | - Erica Ramos
- Departamento de Morfologia, UNESP – Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Cesar Martins
- Departamento de Morfologia, UNESP – Univ Estadual Paulista, Instituto de Biociências/IB, Botucatu, São Paulo Brazil
| | - Diogo C. Cabral-de-Mello
- Departamento de Biologia, UNESP - Univ Estadual Paulista, Instituto de Biociências/IB, Rio Claro, São Paulo 13506-900 Brazil
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Nwanaji-Enwerem JC, Colicino E, Dai L, Di Q, Just AC, Hou L, Vokonas P, De Vivo I, Lemos B, Lu Q, Weisskopf MG, Baccarelli AA, Schwartz JD. miRNA processing gene polymorphisms, blood DNA methylation age and long-term ambient PM 2.5 exposure in elderly men. Epigenomics 2017; 9:1529-1542. [PMID: 29106301 PMCID: PMC5704092 DOI: 10.2217/epi-2017-0094] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 09/06/2017] [Indexed: 01/26/2023] Open
Abstract
AIM We tested whether genetic variation in miRNA processing genes modified the association of PM2.5 with DNA methylation (DNAm) age. PATIENTS & METHODS We conducted a repeated measures study based on 552 participants from the Normative Aging Study with multiple visits between 2000 and 2011 (n = 940 visits). Address-level 1-year PM2.5 exposures were estimated using the GEOS-chem model. DNAm-age and a panel of 14 SNPs in miRNA processing genes were measured from participant blood samples. RESULTS & CONCLUSION In fully adjusted linear mixed-effects models, having at least one copy of the minor rs4961280 [AGO2] allele was associated with a lower DNAm-age (β = -1.13; 95% CI: -2.26 to -0.002). However, the association of PM2.5 with DNAm-age was significantly (Pinteraction = 0.01) weaker in homozygous carriers of the major rs4961280 [AGO2] allele (β = 0.38; 95% CI: -0.20 to 0.96) when compared with all other participants (β = 1.58; 95% CI: 0.76 to 2.39). Our results suggest that miRNA processing impacts DNAm-age relationships. Graphical abstract: miRNA processing AGO2 polymorphism (rs4961280) modifies the association of long-term ambient fine particle exposure with blood DNA methylation age [Formula: see text] The graph depicts lines from a fully adjusted linear regression model with fine particle exposure levels ranging from the tenth to the ninetieth percentile, all other continuous variables held constant at their means, and all other categorical variables held at their most frequent level.
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Affiliation(s)
| | - Elena Colicino
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Lingzhen Dai
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qian Di
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Allan C Just
- Department of Environmental Medicine & Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lifang Hou
- Center for Population Epigenetics, Department of Preventive Medicine, Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pantel Vokonas
- VA Normative Aging Study, Veterans Affairs Boston Healthcare System & the Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Immaculata De Vivo
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bernardo Lemos
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Quan Lu
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Marc G Weisskopf
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Joel D Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Wang M, Lemos B. Ribosomal DNA copy number amplification and loss in human cancers is linked to tumor genetic context, nucleolus activity, and proliferation. PLoS Genet 2017; 13:e1006994. [PMID: 28880866 PMCID: PMC5605086 DOI: 10.1371/journal.pgen.1006994] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/19/2017] [Accepted: 08/21/2017] [Indexed: 12/21/2022] Open
Abstract
Ribosomal RNAs (rRNAs) are transcribed from two multicopy DNA arrays: the 5S ribosomal DNA (rDNA) array residing in a single human autosome and the 45S rDNA array residing in five human autosomes. The arrays are among the most variable segments of the genome, exhibit concerted copy number variation (cCNV), encode essential components of the ribosome, and modulate global gene expression. Here we combined whole genome data from >700 tumors and paired normal tissues to provide a portrait of rDNA variation in human tissues and cancers of diverse mutational signatures, including stomach and lung adenocarcinomas, ovarian cancers, and others of the TCGA panel. We show that cancers undergo coupled 5S rDNA array expansion and 45S rDNA loss that is accompanied by increased estimates of proliferation rate and nucleolar activity. These somatic changes in rDNA CN occur in a background of over 10-fold naturally occurring rDNA CN variation across individuals and cCNV of 5S-45S arrays in some but not all tissues. Analysis of genetic context revealed associations between cancer rDNA CN amplification or loss and the presence of specific somatic alterations, including somatic SNPs and copy number gain/losses in protein coding genes across the cancer genome. For instance, somatic inactivation of the tumor suppressor gene TP53 emerged with a strong association with coupled 5S expansion / 45S loss in several cancers. Our results uncover frequent and contrasting changes in the 5S and 45S rDNA along rapidly proliferating cell lineages with high nucleolar activity. We suggest that 5S rDNA amplification facilitates increased proliferation, nucleolar activity, and ribosomal synthesis in cancer, whereas 45S rDNA loss emerges as a byproduct of transcription-replication conflict in rapidly replicating tumor cells. The observations raise the prospects of using the rDNA arrays as re-emerging targets for the design of novel strategies in cancer therapy. The 45S and 5S ribosomal DNA (rDNA) arrays contain hundreds of rDNA copies, with substantial variability across individuals in human populations. Although physically unlinked, the arrays also exhibit joint variation across individual genotypes. However, whether this co-variation in copy number (CN) is universally observed across all tissues is unknown. It also remains unknown if rDNA CN might vary across tissues and in cancer lineages. Here we showed that most cancers undergo coupled 5S rDNA array amplification and 45S rDNA loss, and concerted 5S-45S CN variation in some but not all tissues. The coupled 5S amplification and 45S loss is associated with the presence of certain somatic genetic alterations, as well as increased estimates of cancerous cell proliferation rate and nucleolar activity. Our research uncovers frequent and contrasting changes in rDNA CN in cancers of diverse tissue origin and associated with diverse mutational contexts of tumor suppressors and oncogenes. The observations raise the prospects of using the rDNA arrays as re-emerging targets in novel strategies for cancer therapy.
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Affiliation(s)
- Meng Wang
- Department of Environmental Health & Molecular and Integrative Physiological Sciences program, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Bernardo Lemos
- Department of Environmental Health & Molecular and Integrative Physiological Sciences program, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
- * E-mail:
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42
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Deng Y, Zhang Y, Lemos B, Ren H. Tissue accumulation of microplastics in mice and biomarker responses suggest widespread health risks of exposure. Sci Rep 2017; 7:46687. [PMID: 28436478 PMCID: PMC5402289 DOI: 10.1038/srep46687] [Citation(s) in RCA: 457] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 03/27/2017] [Indexed: 02/08/2023] Open
Abstract
Microplastics (MPs) are a significant environmental health issue and increasingly greater source of concern. MPs have been detected in oceans, rivers, sediments, sewages, soil and even table salts. MPs exposure on marine organisms and humans has been documented, but information about the toxicity of MPs in mammal is limited. Here we used fluorescent and pristine polystyrene microplastics (PS-MPs) particles with two diameters (5 μm and 20 μm) to investigate the tissue distribution, accumulation, and tissue-specific health risk of MPs in mice. Results indicated that MPs accumulated in liver, kidney and gut, with a tissue-accumulation kinetics and distribution pattern that was strongly depended on the MPs particle size. In addition, analyses of multiple biochemical biomarkers and metabolomic profiles suggested that MPs exposure induced disturbance of energy and lipid metabolism as well as oxidative stress. Interestingly, blood biomarkers of neurotoxicity were also altered. Our results uncovered the distribution and accumulation of MPs across mice tissues and revealed significant alteration in several biomarkers that indicate potential toxicity from MPs exposure. Collectively, our data provided new evidence for the adverse consequences of MPs.
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Affiliation(s)
- Yongfeng Deng
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Yan Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Hongqiang Ren
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing, Jiangsu 210023, China
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Abstract
Ribosomal RNAs (rRNAs) account for >60% of all RNAs in eukaryotic cells and are encoded in the ribosomal DNA (rDNA) arrays. The rRNAs are produced from two sets of loci: the 5S rDNA array resides exclusively on human chromosome 1, whereas the 45S rDNA array resides on the short arm of five human acrocentric chromosomes. The 45S rDNA gives origin to the nucleolus, the nuclear organelle that is the site of ribosome biogenesis. Intriguingly, 5S and 45S rDNA arrays exhibit correlated copy number variation in lymphoblastoid cells (LCLs). Here we examined the genomic architecture and repeat content of the 5S and 45S rDNA arrays in multiple human genome assemblies (including PacBio MHAP assembly) and ascertained contacts between the rDNA arrays and the rest of the genome using Hi-C datasets from two human cell lines (erythroleukemia K562 and lymphoblastoid cells). Our analyses revealed that 5S and 45S arrays each have thousands of contacts in the folded genome, with rDNA-associated regions and genes dispersed across all chromosomes. The rDNA contact map displayed conserved and disparate features between two cell lines, and pointed to specific chromosomes, genomic regions, and genes with evidence of spatial proximity to the rDNA arrays; the data also showed a lack of direct physical interaction between the 5S and 45S rDNA arrays. Finally, the analysis identified an intriguing organization in the 5S array with Alu and 5S elements adjacent to one another and organized in opposite orientation along the array. Portraits of genome folding centered on the ribosomal DNA array could help understand the emergence of concerted variation, the control of 5S and 45S expression, as well as provide insights into an organelle that contributes to the spatial localization of human chromosomes during interphase.
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Affiliation(s)
- Shoukai Yu
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Bernardo Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
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44
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Branco AT, Schilling L, Silkaitis K, Dowling DK, Lemos B. Reproductive activity triggers accelerated male mortality and decreases lifespan: genetic and gene expression determinants in Drosophila. Heredity (Edinb) 2016; 118:221-228. [PMID: 27731328 DOI: 10.1038/hdy.2016.89] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 06/01/2016] [Accepted: 07/15/2016] [Indexed: 02/07/2023] Open
Abstract
Reproduction and aging evolved to be intimately associated. Experimental selection for early-life reproduction drives the evolution of decreased longevity in Drosophila whereas experimental selection for increased longevity leads to changes in reproduction. Although life history theory offers hypotheses to explain these relationships, the genetic architecture and molecular mechanisms underlying reproduction-longevity associations remain a matter of debate. Here we show that mating triggers accelerated mortality in males and identify hundreds of genes that are modulated upon mating in the fruit fly Drosophila melanogaster. Interrogation of genome-wide gene expression in virgin and recently mated males revealed coherent responses, with biological processes that are upregulated (testis-specific gene expression) or downregulated (metabolism and mitochondria-related functions) upon mating. Furthermore, using a panel of genotypes from the Drosophila Synthetic Population Resource (DSPR) as a source of naturally occurring genetic perturbation, we uncover abundant variation in longevity and reproduction-induced mortality among genotypes. Genotypes displayed more than fourfold variation in longevity and reproduction-induced mortality that can be traced to variation in specific segments of the genome. The data reveal individual variation in sensitivity to reproduction and physiological processes that are enhanced and suppressed upon mating. These results raise the prospect that variation in longevity and age-related traits could be traced to processes that coordinate germline and somatic function.
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Affiliation(s)
- A T Branco
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - L Schilling
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - K Silkaitis
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - D K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - B Lemos
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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45
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Laarits T, Bordalo P, Lemos B. Genes under weaker stabilizing selection increase network evolvability and rapid regulatory adaptation to an environmental shift. J Evol Biol 2016; 29:1602-16. [DOI: 10.1111/jeb.12897] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 05/03/2016] [Accepted: 05/13/2016] [Indexed: 11/28/2022]
Affiliation(s)
| | - P. Bordalo
- Department of Systems Biology; Harvard Medical School; Boston MA USA
| | - B. Lemos
- Program in Molecular and Integrative Physiological Sciences; Department of Environmental Health; Harvard T. H. Chan School of Public Health; Boston MA USA
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46
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Araripe LO, Tao Y, Lemos B. Interspecific Y chromosome variation is sufficient to rescue hybrid male sterility and is influenced by the grandparental origin of the chromosomes. Heredity (Edinb) 2016; 116:516-22. [PMID: 26980343 DOI: 10.1038/hdy.2016.11] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/25/2015] [Accepted: 12/29/2015] [Indexed: 12/15/2022] Open
Abstract
Y chromosomes display population variation within and between species. Co-evolution within populations is expected to produce adaptive interactions between Y chromosomes and the rest of the genome. One consequence is that Y chromosomes from disparate populations could disrupt harmonious interactions between co-evolved genetic elements and result in reduced male fertility, sterility or inviability. Here we address the contribution of 'heterospecific Y chromosomes' to fertility in hybrid males carrying a homozygous region of Drosophila mauritiana introgressed in the Drosophila simulans background. In order to detect Y chromosome-autosome interactions, which may go unnoticed in a single-species background of autosomes, we constructed hybrid genotypes involving three sister species: Drosophila simulans, D. mauritiana, and D. sechellia. These engineered strains varied due to: (i) species origin of the Y chromosome (D. simulans or D. sechellia); (ii) location of the introgressed D. mauritiana segment on the D. simulans third chromosome, and (iii) grandparental genomic background (three genotypes of D. simulans). We find complex interactions between the species origin of the Y chromosome, the identity of the D. mauritiana segment and the grandparental genetic background donating the chromosomes. Unexpectedly, the interaction of the Y chromosome and one segment of D. mauritiana drastically reduced fertility in the presence of Ysim, whereas the fertility is partially rescued by the Y chromosome of D. sechellia when it descends from a specific grandparental genotype. The restoration of fertility occurs in spite of an autosomal and X-linked genome that is mostly of D. simulans origin. These results illustrate the multifactorial basis of genetic interactions involving the Y chromosome. Our study supports the hypothesis that the Y chromosome can contribute significantly to the evolution of reproductive isolation and highlights the conditional manifestation of infertility in specific genotypic combinations.
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Affiliation(s)
- L O Araripe
- Laboratório de Biologia Molecular de Insetos, Fundação Oswaldo Cruz, IOC, Rio de Janeiro, Brasil
| | - Y Tao
- Department of Mathematics and Statistics, Georgia State University, Atlanta, GA, USA
| | - B Lemos
- Program in Molecular and Integrative Physiological Sciences, Department of Environmental Health, Harvard T. H. Chan School of Public Health, Boston, MA, USA
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47
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Yee WKW, Rogell B, Lemos B, Dowling DK. Intergenomic interactions between mitochondrial and Y-linked genes shape male mating patterns and fertility in Drosophila melanogaster. Evolution 2015; 69:2876-90. [PMID: 26419212 DOI: 10.1111/evo.12788] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/26/2015] [Accepted: 09/21/2015] [Indexed: 12/17/2022]
Abstract
Under maternal inheritance, mitochondrial genomes are prone to accumulate mutations that exhibit male-biased effects. Such mutations should, however, place selection on the nuclear genome for modifier adaptations that mitigate mitochondrial-incurred male harm. One gene region that might harbor such modifiers is the Y-chromosome, given the abundance of Y-linked variation for male fertility, and because Y-linked modifiers would not exert antagonistic effects in females because they would be found only in males. Recent studies in Drosophila revealed a set of nuclear genes whose expression is sensitive to allelic variation among mtDNA- and Y-haplotypes, suggesting these genes might be entwined in evolutionary conflict between mtDNA and Y. Here, we test whether genetic variation across mtDNA and Y haplotypes, sourced from three disjunct populations, interacts to affect male mating patterns and fertility across 10 days of early life in D. melanogaster. We also investigate whether coevolved mito-Y combinations outperform their evolutionarily novel counterparts, as predicted if the interacting Y-linked variance is comprised of modifier adaptations. Although we found no evidence that coevolved mito-Y combinations outperformed their novel counterparts, interactions between mtDNA and Y-chromosomes affected male mating patterns. These interactions were dependent on male age; thus male reproductive success was shaped by G × G × E interactions.
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Affiliation(s)
- Winston K W Yee
- School of Biological Sciences, Monash University, Clayton, 3800, Victoria, Australia.
| | - Björn Rogell
- School of Biological Sciences, Monash University, Clayton, 3800, Victoria, Australia.,Department of Zoology/Ecology, Stockholm University, 10691, Stockholm, Sweden
| | - Bernardo Lemos
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, 02115
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, 3800, Victoria, Australia
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48
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Dean R, Lemos B, Dowling DK. Context-dependent effects of Y chromosome and mitochondrial haplotype on male locomotive activity in Drosophila melanogaster. J Evol Biol 2015. [DOI: 10.1111/jeb.12702] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- R. Dean
- School of Biological Sciences; Monash University; Clayton Vic. Australia
- Department of Genetics, Environment and Evolution; University College London; London UK
| | - B. Lemos
- Molecular and Integrative Physiological Sciences Program; Department of Environmental Health; Harvard School of Public Health; Boston MA USA
| | - D. K. Dowling
- School of Biological Sciences; Monash University; Clayton Vic. Australia
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Case LK, Wall EH, Osmanski EE, Dragon JA, Saligrama N, Zachary JF, Lemos B, Blankenhorn EP, Teuscher C. Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring. Genome Biol 2015; 16:28. [PMID: 25886764 PMCID: PMC4396973 DOI: 10.1186/s13059-015-0591-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 01/20/2015] [Indexed: 12/11/2022] Open
Abstract
Background The prevalence of some autoimmune diseases is greater in females compared with males, although disease severity is often greater in males. The reason for this sexual dimorphism is unknown, but it may reflect negative selection of Y chromosome-bearing sperm during spermatogenesis or male fetuses early in the course of conception/pregnancy. Previously, we showed that the sexual dimorphism in experimental autoimmune encephalomyelitis (EAE) is associated with copy number variation (CNV) in Y chromosome multicopy genes. Here, we test the hypothesis that CNV in Y chromosome multicopy genes influences the paternal parent-of-origin effect on EAE susceptibility in female mice. Results We show that C57BL/6 J consomic strains of mice possessing an identical X chromosome and CNV in Y chromosome multicopy genes exhibit sperm head abnormalities and female-biased sex ratio. This is consistent with X-Y intragenomic conflict arising from an imbalance in CNV between homologous X:Y chromosome multicopy genes. These males also display paternal transmission of EAE to female offspring and differential loading of microRNAs within the sperm nucleus. Furthermore, in humans, families of probands with multiple sclerosis similarly exhibit a female-biased sex ratio, whereas families of probands affected with non-sexually dimorphic autoimmune diseases exhibit unbiased sex ratios. Conclusions These findings provide evidence for a mechanism at the level of the male gamete that contributes to the sexual dimorphism in EAE and paternal parent-of-origin effects in female mice, raising the possibility that a similar mechanism may contribute to the sexual dimorphism in multiple sclerosis. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0591-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Laure K Case
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Emma H Wall
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Erin E Osmanski
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA.
| | - Julie A Dragon
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, 05405, USA.
| | - Naresha Saligrama
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Current address: Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - James F Zachary
- Department of Pathobiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA.
| | - Bernardo Lemos
- Department of Environmental Health, Harvard School of Public Health, Boston, MA, 02115, USA.
| | - Elizabeth P Blankenhorn
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, 19129, USA.
| | - Cory Teuscher
- Department of Medicine, University of Vermont, Given Medical Building C317, Burlington, VT, 05405, USA. .,Department of Pathology, University of Vermont, Burlington, VT, 05405, USA.
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Branco AT, Lemos B. Interaction between bisphenol A and dietary sugar affects global gene transcription in Drosophila melanogaster. Genom Data 2014; 2:308-11. [PMID: 26484116 PMCID: PMC4535756 DOI: 10.1016/j.gdata.2014.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 09/14/2014] [Accepted: 09/17/2014] [Indexed: 11/23/2022]
Abstract
Human exposure to environmental toxins is a public health issue. The microarray data available in the Gene Expression Omnibus database under accession number GSE55655 and GSE55670GSE55655GSE55670 show the isolated and combined effects of dietary sugar and two organic compounds present in a variety of plastics [bisphenol A (BPA) and Bis(2-ethylhexyl) phthalate (DEHP)] on global gene expression in Drosophila melanogaster. The study was carried out with samples collected from flies exposed to these compounds for a limited period of time (48 h) in the adult stage, or throughout the entire development of the insect. The arrays were normalized using the limma/Bioconductor package. Differential expression was inferred using linear models in limma and BAGEL. The data show that each compound had its unique consequences to gene expression, and that the individual effect of each organic compound is maximized with the joint ingestion of dietary sugar.
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Affiliation(s)
- Alan T Branco
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard School of Public Health, 665 Huntington Avenue, Bldg. 2, Boston, MA 02115-6021, United States
| | - Bernardo Lemos
- Molecular and Integrative Physiological Sciences Program, Department of Environmental Health, Harvard School of Public Health, 665 Huntington Avenue, Bldg. 2, Boston, MA 02115-6021, United States
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