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Middleton LYM, Nguyen VK, Dou J, Wang H, Patel C, Park SK, Colacino JA, Bakulski KM. Environmental chemical-wide associations with immune biomarkers in US adults: A cross-sectional analysis. Environ Res 2024:118956. [PMID: 38640990 DOI: 10.1016/j.envres.2024.118956] [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: 01/22/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 04/21/2024]
Abstract
Environmental chemical exposures influence immune system functions, and humans are exposed to a wide range of chemicals, termed the chemical "exposome". A comprehensive, discovery analysis of the associations of multiple chemical families with immune biomarkers is needed. In this study, we tested the associations between environmental chemical concentrations and immune biomarkers. We analyzed the United States cross-sectional National Health and Nutrition Examination Survey (NHANES 1999-2018). Chemical biomarker concentrations were measured in blood or urine (196 chemicals, 17 chemical families). Immune biomarkers included counts of lymphocytes, neutrophils, monocytes, basophils, eosinophils, red blood cells, white blood cells, and mean corpuscular volume. We conducted separate survey-weighted, multivariable linear regressions of each log2-transformed chemicals on immune measures, adjusted for relevant covariates. We accounted for multiple comparisons using a false discovery rate (FDR). Among 45,528 adult participants, the mean age was 45.7 years, 51.4% were female, and 69.3% were Non-Hispanic White. 71 (36.2%) chemicals were associated with at least one of the eight immune biomarkers. The most chemical associations (FDR<0.05) were observed with mean corpuscular volume (36 chemicals) and red blood cell counts (35 chemicals). For example, a doubling in the concentration of cotinine was associated with 0.16 fL (95% CI: 0.15, 0.17; FDR<0.001) increased mean corpuscular volume, and a doubling in the concentration of blood lead was associated with 61,736 increased red blood cells per μL (95% CI: 54,335, 69,138; FDR<0.001). A wide variety of chemicals, such as metals and smoking-related compounds, were highly associated with immune system biomarkers. This environmental chemical-wide association study identified chemicals from multiple families for further toxicological, immunologic, and epidemiological investigation.
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Affiliation(s)
- Lauren Y M Middleton
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Vy K Nguyen
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA; Department of Biomedical Informatics, Harvard Medical School, Harvard University, Boston, MA, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Herong Wang
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Chirag Patel
- Department of Biomedical Informatics, Harvard Medical School, Harvard University, Boston, MA, USA
| | - Sung Kyun Park
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Program in the Environment, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
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Wang K, Kim N, Bagherian M, Li K, Chou E, Colacino JA, Dolinoy DC, Sartor MA. Gene Target Prediction of Environmental Chemicals Using Coupled Matrix-Matrix Completion. Environ Sci Technol 2024; 58:5889-5898. [PMID: 38501580 DOI: 10.1021/acs.est.4c00458] [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] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Human exposure to toxic chemicals presents a huge health burden. Key to understanding chemical toxicity is knowledge of the molecular target(s) of the chemicals. Because a comprehensive safety assessment for all chemicals is infeasible due to limited resources, a robust computational method for discovering targets of environmental exposures is a promising direction for public health research. In this study, we implemented a novel matrix completion algorithm named coupled matrix-matrix completion (CMMC) for predicting direct and indirect exposome-target interactions, which exploits the vast amount of accumulated data regarding chemical exposures and their molecular targets. Our approach achieved an AUC of 0.89 on a benchmark data set generated using data from the Comparative Toxicogenomics Database. Our case studies with bisphenol A and its analogues, PFAS, dioxins, PCBs, and VOCs show that CMMC can be used to accurately predict molecular targets of novel chemicals without any prior bioactivity knowledge. Our results demonstrate the feasibility and promise of computationally predicting environmental chemical-target interactions to efficiently prioritize chemicals in hazard identification and risk assessment.
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Affiliation(s)
- Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Nicole Kim
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Maryam Bagherian
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Michigan Institute for Data Science (MIDAS), University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kai Li
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Elysia Chou
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan 48109, United States
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Sala-Hamrick KE, Tapaswi A, Polemi KM, Nguyen VK, Colacino JA. High-Throughput Transcriptomics of Nontumorigenic Breast Cells Exposed to Environmentally Relevant Chemicals. Environ Health Perspect 2024; 132:47002. [PMID: 38568856 PMCID: PMC10990114 DOI: 10.1289/ehp12886] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND There is a suite of chemicals, including metals, pesticides, and personal care product compounds, which are commonly detected at high levels in US Center for Disease Control's National Health and Nutrition Examination Survey (NHANES) chemical biomarker screens. Whether these chemicals influence development of breast cancer is not well understood. OBJECTIVES The objectives were to perform an unbiased concentration-dependent assessment of these chemicals, to quantify differences in cancer-specific genes and pathways, to describe if these differences occur at human population-relevant concentrations, and to specifically test for differences in markers of stemness and cellular plasticity. METHODS We treated nontumorigenic mammary epithelial cells, MCF10A, with 21 chemicals at four concentrations (25 nM , 250 nM , 2.5 μ M , and 25 μ M ) for 48 h. We conducted RNA-sequencing for these 408 samples, adapting the plexWell plate-based RNA-sequencing method to analyze differences in gene expression. We calculated gene and biological pathway-specific benchmark concentrations (BMCs) using BMDExpress3, identifying differentially expressed genes and generating the best fit benchmark concentration models for each chemical across all genes. We identified enriched biological processes and pathways for each chemical and tested whether chemical exposures change predicted cell type distributions. We contextualized benchmark concentrations relative to human population biomarker concentrations in NHANES. RESULTS We detected chemical concentration-dependent differences in gene expression for thousands of genes. Enrichment and cell type distribution analyses showed benchmark concentration responses correlated with differences in breast cancer-related pathways, including induction of basal-like characteristics for some chemicals, including arsenic, lead, copper, and methyl paraben. Comparison of benchmark data to NHANES chemical biomarker (urine or blood) concentrations indicated an overlap between exposure levels and levels sufficient to cause a gene expression response. DISCUSSION These analyses revealed that many of these 21 chemicals resulted in differences in genes and pathways involved in breast cancer in vitro at human exposure-relevant concentrations. https://doi.org/10.1289/EHP12886.
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Affiliation(s)
| | - Anagha Tapaswi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Katelyn M. Polemi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
| | - Vy K. Nguyen
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, Michigan, USA
- Program in the Environment, University of Michigan, Ann Arbor, Michigan, USA
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Niu J, Brown C, Law M, Colacino JA, Ritov Y. Longitudinal Position and Cancer Risk in the United States Revisited. Cancer Res Commun 2024; 4:328-336. [PMID: 38284880 PMCID: PMC10848893 DOI: 10.1158/2767-9764.crc-23-0503] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/12/2024] [Accepted: 01/17/2024] [Indexed: 01/30/2024]
Abstract
The debate over daylight saving time (DST) has surged, with interests in the effects of sunlight exposure on health. Prior studies simulated DST and standard time conditions by analyzing different locations within time zones and neighboring areas across time zone borders. We analyzed cancer incidence rates from various longitudinal positions within time zones and at time zone borders in the contiguous United States. Using data from State Cancer Profiles (2016-2020), we analyzed total cancer of 19 types and specific rates for eight cancers, adjusted for age and includes all demographics. log-linear regression is used to replicate a previous study, and spatial regression models are employed to explore discontinuities at borders. Cancer rate differences lack statistical significance within time zones and near borders for total cancer and most individual cancers. Exceptions included breast, prostate, and liver and bile duct cancers, which exhibited significant relationships with relative position at the 95% significance level. Breast and liver and bile duct cancers saw decreases, while prostate cancer incidence increased from west to east within time zones. Relative position does not have a significant impact on cancer incidence, hence cancer development in general. Isolated exceptions may warrant further investigation as more data become available. Our findings challenge prior research, revealing numerous inconsistencies. These disparities urge a reconsideration of the potential disparities in human health associated with DST and standard time. They offer insights contribute to the ongoing discussion surrounding the retention or abandonment of DST. SIGNIFICANCE In this article, we investigate the relation between the epidemiology of cancer incidence in the United States and time zone-related longitudinal positions. Our results differ from previous research, which were based on a subset of our data, and show that the time zone effect on cancer incidence rate is not significant. Our research provides implications on the implementation of DST by suggesting that there is no cancer-risk associated reason to prefer one time over the other. Our study also uses regression discontinuity design using natural splines, a more advanced statistical method, to increase robustness of our result. Our findings challenge prior research, revealing numerous inconsistencies. These disparities urge a reconsideration of the potential disparities in human health associated with DST and standard time. They offer insights contribute to the ongoing discussion surrounding the retention or abandonment of DST.
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Affiliation(s)
- Jin Niu
- Department of Economics, Brown University, Providence, Rhode Island
| | - Charlotte Brown
- Department of Statistics, University of Michigan, Ann Arbor, Michigan
| | - Michael Law
- Seminar für Statistik, ETH Zürich, Zürich, Switzerland
| | | | - Ya'acov Ritov
- Department of Statistics, University of Michigan, Ann Arbor, Michigan
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Radyk MD, Nelson BS, Halbrook CJ, Wood A, Lavoie B, Salvatore L, Corfas G, Colacino JA, Shah YM, Crawford HC, Lyssiotis CA. Glucose-6-phosphate dehydrogenase deficiency accelerates pancreatic acinar-to-ductal metaplasia. bioRxiv 2023:2023.11.06.565895. [PMID: 37986898 PMCID: PMC10659312 DOI: 10.1101/2023.11.06.565895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Activating mutations in KRAS extensively reprogram cellular metabolism to support the continuous growth, proliferation, and survival of pancreatic tumors. Targeting these metabolic dependencies are promising approaches for the treatment of established tumors. However, metabolic reprogramming is required early during tumorigenesis to provide transformed cells selective advantage towards malignancy. Acinar cells can give rise to pancreatic tumors through acinar-to-ductal metaplasia (ADM). Dysregulation of pathways that maintain acinar homeostasis accelerate tumorigenesis. During ADM, acinar cells transdifferentiate to duct-like cells, a process driven by oncogenic KRAS. The metabolic reprogramming that is required for the transdifferentiation in ADM is unclear. We performed transcriptomic analysis on mouse acinar cells undergoing ADM and found metabolic programs are globally enhanced, consistent with the transition of a specialized cell to a less differentiated phenotype with proliferative potential. Indeed, we and others have demonstrated how inhibiting metabolic pathways necessary for ADM can prevent transdifferentiation and tumorigenesis. Here, we also find NRF2-target genes are differentially expressed during ADM. Among these, we focused on the increase in the gene coding for NADPH-producing enzyme, Glucose-6-phosphate dehydrogenase (G6PD). Using established mouse models of KrasG12D-driven pancreatic tumorigenesis and G6PD-deficiency, we find that mutant G6pd accelerates ADM and pancreatic intraepithelial neoplasia. Acceleration of cancer initiation with G6PD-deficiency is dependent on its NADPH-generating function in reactive oxygen species (ROS) management, as opposed to other outputs of the pentose phosphate pathway. Together, this work provides new insights into the function of metabolic pathways during early tumorigenesis.
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Affiliation(s)
- Megan D. Radyk
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Barbara S. Nelson
- Doctoral Program in Cancer Biology, University of Michigan, Ann Arbor, USA
| | - Christopher J. Halbrook
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
- University of California Irvine Chao Family Comprehensive Cancer Center, Orange, CA, USA
| | - Alexander Wood
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Brooke Lavoie
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Lucie Salvatore
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
| | - Gabriel Corfas
- Kresge Hearing Research Institute and Dept. of Otolaryngology, Head and Neck Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Program in the Environment, College of Literature, Sciences, and the Arts, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Yatrik M. Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
| | - Howard C. Crawford
- Department of Surgery, Henry Ford Pancreatic Cancer Center, Henry Ford Health System, Detroit, MI, USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- University of Michigan Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, MI, USA
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Diedrich JD, Cole CE, Pianko MJ, Colacino JA, Bernard JJ. Non-Toxicological Role of Aryl Hydrocarbon Receptor in Obesity-Associated Multiple Myeloma Cell Growth and Survival. Cancers (Basel) 2023; 15:5255. [PMID: 37958428 PMCID: PMC10649826 DOI: 10.3390/cancers15215255] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Obesity is not only a risk factor for multiple myeloma (MM) incidence, but it is also associated with an increased risk of progression from myeloma precursors-monoclonal gammopathy of undetermined significance-and smoldering myeloma. Adipocytes in the bone marrow (BMAs) microenvironment have been shown to facilitate MM cell growth via secreted factors, but the nature of these secreted factors and their mechanism of action have not been fully elucidated. The elevated expression of aryl hydrocarbon receptor (AhR) is associated with a variety of different cancers, including MM; however, the role of AhR activity in obesity-associated MM cell growth and survival has not been explored. Indeed, this is of particular interest as it has been recently shown that bone marrow adipocytes are a source of endogenous AhR ligands. Using multiple in vitro models of tumor-adipocyte crosstalk to mimic the bone microenvironment, we identified a novel, non-toxicological role of the adipocyte-secreted factors in the suppression of AhR activity in MM cells. A panel of six MM cell lines were cultured in the presence of bone marrow adipocytes in (1) a direct co-culture, (2) a transwell co-culture, or (3) an adipocyte-conditioned media to interrogate the effects of the secreted factors on MM cell AhR activity. Nuclear localization and the transcriptional activity of the AhR, as measured by CYP1A1 and CYP1B1 gene induction, were suppressed by exposure to BMA-derived factors. Additionally, decreased AhR target gene expression was associated with worse clinical outcomes. The knockdown of AhR resulted in reduced CYP1B1 expression and increased cellular growth. This tumor-suppressing role of CYP1A1 and CYP1B1 was supported by patient data which demonstrated an association between reduced target gene expression and worse overall survival. These data demonstrated a novel mechanism by which bone marrow adipocytes promote MM progression.
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Affiliation(s)
- Jonathan D. Diedrich
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
| | - Craig E. Cole
- Department of Medicine, Division of Hematology/Oncology, Michigan State University, East Lansing, MI 48910, USA;
- Karmanos Cancer Institute, McLaren Greater Lansing, Lansing, MI 48910, USA
- Department of Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Matthew J. Pianko
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Justin A. Colacino
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI 48109, USA;
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamie J. Bernard
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA;
- Department of Medicine, Michigan State University, East Lansing, MI 48824, USA
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Morgan RK, Wang K, Svoboda LK, Rygiel CA, Lalancette C, Cavalcante R, Bartolomei MS, Prasasya R, Neier K, Perera BP, Jones TR, Colacino JA, Sartor MA, Dolinoy DC. Effects of Developmental Lead and Phthalate Exposures on DNA Methylation in Adult Mouse Blood, Brain, and Liver Identifies Tissue- and Sex-Specific Changes with Implications for Genomic Imprinting. bioRxiv 2023:2023.09.29.560131. [PMID: 37873115 PMCID: PMC10592650 DOI: 10.1101/2023.09.29.560131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Background Maternal exposure to environmental chemicals can cause adverse health effects in offspring. Mounting evidence supports that these effects are influenced, at least in part, by epigenetic modifications. Objective We examined tissue- and sex-specific changes in DNA methylation (DNAm) associated with human-relevant lead (Pb) and di(2-ethylhexyl) phthalate (DEHP) exposure during perinatal development in cerebral cortex, blood, and liver. Methods Female mice were exposed to human relevant doses of either Pb (32ppm) via drinking water or DEHP (5 mg/kg-day) via chow for two weeks prior to mating through offspring weaning. Whole genome bisulfite sequencing (WGBS) was utilized to examine DNAm changes in offspring cortex, blood, and liver at 5 months of age. Metilene and methylSig were used to identify differentially methylated regions (DMRs). Annotatr and Chipenrich were used for genomic annotations and geneset enrichment tests of DMRs, respectively. Results The cortex contained the majority of DMRs associated with Pb (69%) and DEHP (58%) exposure. The cortex also contained the greatest degree of overlap in DMR signatures between sexes (n = 17 and 14 DMRs with Pb and DEHP exposure, respectively) and exposure types (n = 79 and 47 DMRs in males and females, respectively). In all tissues, detected DMRs were preferentially found at genomic regions associated with gene expression regulation (e.g., CpG islands and shores, 5' UTRs, promoters, and exons). An analysis of GO terms associated with DMR-containing genes identified imprinted genes to be impacted by both Pb and DEHP exposure. Of these, Gnas and Grb10 contained DMRs across tissues, sexes, and exposures. DMRs were enriched in the imprinting control regions (ICRs) of Gnas and Grb10, with 15 and 17 ICR-located DMRs across cortex, blood, and liver in each gene, respectively. The ICRs were also the location of DMRs replicated across target and surrogate tissues, suggesting epigenetic changes these regions may be potentially viable biomarkers. Conclusions We observed Pb- and DEHP-specific DNAm changes in cortex, blood, and liver, and the greatest degree of overlap in DMR signatures was seen between exposures followed by sex and tissue type. DNAm at imprinted control regions was altered by both Pb and DEHP, highlighting the susceptibility of genomic imprinting to these exposures during the perinatal window of development.
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Affiliation(s)
- Rachel K. Morgan
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Claudia Lalancette
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Raymond Cavalcante
- Epigenomics Core, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Marisa S. Bartolomei
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi Prasasya
- Department of Cell and Developmental Biology, Center of Excellence in Environmental Toxicology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bambarendage P.U. Perera
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
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Cathey AL, Nguyen VK, Colacino JA, Woodruff TJ, Reynolds P, Aung MT. Exploratory profiles of phenols, parabens, and per- and poly-fluoroalkyl substances among NHANES study participants in association with previous cancer diagnoses. J Expo Sci Environ Epidemiol 2023; 33:687-698. [PMID: 37718377 PMCID: PMC10541322 DOI: 10.1038/s41370-023-00601-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/19/2023]
Abstract
BACKGROUND Some hormonally active cancers have low survival rates, but a large proportion of their incidence remains unexplained. Endocrine disrupting chemicals may affect hormone pathways in the pathology of these cancers. OBJECTIVE To evaluate cross-sectional associations between per- and polyfluoroalkyl substances (PFAS), phenols, and parabens and self-reported previous cancer diagnoses in the National Health and Nutrition Examination Survey (NHANES). METHODS We extracted concentrations of 7 PFAS and 12 phenols/parabens and self-reported diagnoses of melanoma and cancers of the thyroid, breast, ovary, uterus, and prostate in men and women (≥20 years). Associations between previous cancer diagnoses and an interquartile range increase in exposure biomarkers were evaluated using logistic regression models adjusted for key covariates. We conceptualized race as social construct proxy of structural social factors and examined associations in non-Hispanic Black, Mexican American, and other Hispanic participants separately compared to White participants. RESULTS Previous melanoma in women was associated with higher PFDE (OR:2.07, 95% CI: 1.25, 3.43), PFNA (OR:1.72, 95% CI: 1.09, 2.73), PFUA (OR:1.76, 95% CI: 1.07, 2.89), BP3 (OR: 1.81, 95% CI: 1.10, 2.96), DCP25 (OR: 2.41, 95% CI: 1.22, 4.76), and DCP24 (OR: 1.85, 95% CI: 1.05, 3.26). Previous ovarian cancer was associated with higher DCP25 (OR: 2.80, 95% CI: 1.08, 7.27), BPA (OR: 1.93, 95% CI: 1.11, 3.35) and BP3 (OR: 1.76, 95% CI: 1.00, 3.09). Previous uterine cancer was associated with increased PFNA (OR: 1.55, 95% CI: 1.03, 2.34), while higher ethyl paraben was inversely associated (OR: 0.31, 95% CI: 0.12, 0.85). Various PFAS were associated with previous ovarian and uterine cancers in White women, while MPAH or BPF was associated with previous breast cancer among non-White women. IMPACT STATEMENT Biomarkers across all exposure categories (phenols, parabens, and per- and poly- fluoroalkyl substances) were cross-sectionally associated with increased odds of previous melanoma diagnoses in women, and increased odds of previous ovarian cancer was associated with several phenols and parabens. Some associations differed by racial group, which is particularly impactful given the established racial disparities in distributions of exposure to these chemicals. This is the first epidemiological study to investigate exposure to phenols in relation to previous cancer diagnoses, and the first NHANES study to explore racial/ethnic disparities in associations between environmental phenol, paraben, and PFAS exposures and historical cancer diagnosis.
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Affiliation(s)
- Amber L Cathey
- Department of Environmental Health Sciences, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Vy K Nguyen
- Department of Environmental Health Sciences, University of Michigan, School of Public Health, Ann Arbor, MI, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Tracey J Woodruff
- Program on Reproductive Health and the Environment, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Peggy Reynolds
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Max T Aung
- Department of Population and Public Health Sciences, University of Southern California, Keck School of Medicine, Los Angeles, CA, USA.
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Lapehn S, Colacino JA, Harris C. Spatiotemporal protein dynamics during early organogenesis in mouse conceptuses treated with valproic acid. Neurotoxicol Teratol 2023; 99:107286. [PMID: 37442398 PMCID: PMC10697214 DOI: 10.1016/j.ntt.2023.107286] [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: 04/30/2022] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023]
Abstract
Valproic acid (VPA) is an anti-epileptic medication that increases the risk of neural tube defect (NTD) outcomes in infants exposed during gestation. Previous studies into VPA's mechanism of action have focused on alterations in gene expression and metabolism but have failed to consider how exposure changes the abundance of critical developmental proteins over time. This study evaluates the effects of VPA on protein abundance in the developmentally distinct tissues of the mouse visceral yolk sac (VYS) and embryo proper (EMB) using mouse whole embryo culture. Embryos were exposed to 600 μM VPA at 2 h intervals over 10 h during early organogenesis with the aim of identifying protein pathways relevant to VPA's mechanism of action in failed NTC. Protein abundance was measured through tandem mass tag (TMT) labeling followed by liquid chromatography and mass spectrometry. Overall, there were over 1500 proteins with altered abundance after VPA exposure in the EMB or VYS with 428 of these proteins showing previous gene expression associations with VPA exposure. Limited overlap of significant proteins between tissues supported the conclusion of independent roles for the VYS and EMB in response to VPA. Pathway analysis of proteins with increased or decreased abundance identified multiple pathways with mechanistic relevance to NTC and embryonic development including convergent extension, Wnt Signaling/planar cell polarity, cellular migration, cellular proliferation, cell death, and cytoskeletal organization processes as targets of VPA. Clustering of co-regulated proteins to identify shared patterns of protein abundance over time highlighted 4 h and 6/10 h as periods of divergent protein abundance between control and VPA-treated samples in the VYS and EMB, respectively. Overall, this study demonstrated that VPA temporally alters protein content in critical developmental pathways in the VYS and the EMB during early organogenesis in mice.
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Affiliation(s)
- Samantha Lapehn
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
| | - Craig Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, United States
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10
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Forté CA, Millar JA, Colacino JA. Integrating NHANES and toxicity forecaster data to compare pesticide exposure and bioactivity by farmwork history and US citizenship. J Expo Sci Environ Epidemiol 2023:10.1038/s41370-023-00583-5. [PMID: 37474644 PMCID: PMC10799167 DOI: 10.1038/s41370-023-00583-5] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Farmworkers in the United States, especially migrant workers, face unique barriers to healthcare and have documented disparities in health outcomes. Exposure to pesticides, especially those persistent in the environment, may contribute to these health disparities. OBJECTIVE Quantify differences in pesticide exposure bioactivity by farmworker category and US citizenship status. METHODS We queried the National Health and Nutrition Examination Study (NHANES) from 1999-2014 for pesticide exposure biomarker concentrations among farmworkers and non-farmworkers by citizenship status. We combined this with toxicity assay data from the US Environmental Protection Agency's (EPA's) Toxicity Forecaster (ToxCast). We estimated adverse biological effects that occur across a range of human population-relevant pesticide doses. RESULTS In total, there were 844 people with any farmwork history and 23,592 non-farmworkers. Of 12 commonly detectable pesticide biomarkers in NHANES, 2,4-dichlorophenoxyacetic acid (OR = 3.76, p = 1.33 × 10-6) was significantly higher in farmworkers than non-farmworkers. Farmworkers were 1.15 times more likely to have a bioactive pesticide biomarker measurement in comparison to non-farmworkers (adjusted OR = 1.15, 95% CI: 0.87, 1.51). Non-U.S. citizens were 1.39 times more likely to have bioactive pesticide biomarker concentrations compared to people with U.S. citizenship (adjusted OR 1.39, 95% CI: 1.17, 1.64). Additionally, non-citizens were significantly more exposed to bioactive levels of β-hexachlorocyclohexane (BHC) (OR = 8.10, p = 1.33 × 10-6), p,p-DDE (OR = 2.60, p = 0.02), and p,p'-DDT (OR = 7.75, p = 0.01). IMPACT STATEMENT Farmworkers are a vulnerable population due to social determinants of health and occupational exposures. Here, we integrate US population chemical biomonitoring data and toxicity outcome data to assess pesticide exposure by farmwork history and citizenship. We find that farmworkers and those without US citizenship are significantly more likely to be exposed to concentrations of pesticides which are bioactive in toxicological assays. Thus, farmworkers employed in the US but who are not citizens could be at increased risk of harm to their health due to pesticides. These findings are important to shape evidence-based policies in regulatory science to promote worker safety.
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Affiliation(s)
- Chanese A Forté
- The University of Michigan School of Public Health, Department of Environmental Health Sciences, Ann Arbor, MI, USA
- The University of Michigan, College of Engineering, Michigan Institute of Computational Discovery and Engineering, Ann Arbor, MI, USA
| | - Jess A Millar
- The University of Michigan School of Public Health, Department of Epidemiology, Ann Arbor, MI, USA
- The University of Michigan Medical School, Department of Computational Medicine and Bioinformatics, Ann Arbor, MI, USA
| | - Justin A Colacino
- The University of Michigan School of Public Health, Department of Environmental Health Sciences, Ann Arbor, MI, USA.
- The University of Michigan School of Public Health, Department of Nutritional Sciences, Ann Arbor, MI, USA.
- The University of Michigan College of Literature, Sciences, and the Arts, Program in the Environment, Ann Arbor, MI, USA.
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11
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Petroff RL, Cavalcante RG, Colacino JA, Goodrich JM, Jones TR, Lalancette C, Morgan RK, Neier K, Perera BPU, Rygiel CA, Svoboda LK, Wang K, Sartor MA, Dolinoy DC. Developmental exposures to common environmental contaminants, DEHP and lead, alter adult brain and blood hydroxymethylation in mice. Front Cell Dev Biol 2023; 11:1198148. [PMID: 37384255 PMCID: PMC10294071 DOI: 10.3389/fcell.2023.1198148] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 05/25/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction: The developing epigenome changes rapidly, potentially making it more sensitive to toxicant exposures. DNA modifications, including methylation and hydroxymethylation, are important parts of the epigenome that may be affected by environmental exposures. However, most studies do not differentiate between these two DNA modifications, possibly masking significant effects. Methods: To investigate the relationship between DNA hydroxymethylation and developmental exposure to common contaminants, a collaborative, NIEHS-sponsored consortium, TaRGET II, initiated longitudinal mouse studies of developmental exposure to human-relevant levels of the phthalate plasticizer di(2-ethylhexyl) phthalate (DEHP), and the metal lead (Pb). Exposures to 25 mg DEHP/kg of food (approximately 5 mg DEHP/kg body weight) or 32 ppm Pb-acetate in drinking water were administered to nulliparous adult female mice. Exposure began 2 weeks before breeding and continued throughout pregnancy and lactation, until offspring were 21 days old. At 5 months, perinatally exposed offspring blood and cortex tissue were collected, for a total of 25 male mice and 17 female mice (n = 5-7 per tissue and exposure). DNA was extracted and hydroxymethylation was measured using hydroxymethylated DNA immunoprecipitation sequencing (hMeDIP-seq). Differential peak and pathway analysis was conducted comparing across exposure groups, tissue types, and animal sex, using an FDR cutoff of 0.15. Results: DEHP-exposed females had two genomic regions with lower hydroxymethylation in blood and no differences in cortex hydroxymethylation. For DEHP-exposed males, ten regions in blood (six higher and four lower) and 246 regions (242 higher and four lower) and four pathways in cortex were identified. Pb-exposed females had no statistically significant differences in blood or cortex hydroxymethylation compared to controls. Pb-exposed males, however, had 385 regions (all higher) and six pathways altered in cortex, but no differential hydroxymethylation was identified in blood. Discussion: Overall, perinatal exposure to human-relevant levels of two common toxicants showed differences in adult DNA hydroxymethylation that was specific to sex, exposure type, and tissue, but male cortex was most susceptible to hydroxymethylation differences by exposure. Future assessments should focus on understanding if these findings indicate potential biomarkers of exposure or are related to functional long-term health effects.
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Affiliation(s)
- Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Raymond G. Cavalcante
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Tamara R. Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Claudia Lalancette
- Epigenomics Core, Biomedical Research Core Facilities, Michigan Medicine, Ann Arbor, MI, United States
| | - Rachel K. Morgan
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Kari Neier
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Bambarendage P. U. Perera
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Christine A. Rygiel
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K. Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, Michigan Medicine, Ann Arbor, MI, United States
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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12
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Kim H, Villareal LB, Liu Z, Haneef M, Falcon DM, Martin DR, Lee H, Dame MK, Attili D, Chen Y, Varani J, Spence JR, Kovbasnjuk O, Colacino JA, Lyssiotis CA, Lin HC, Shah YM, Xue X. Transferrin Receptor-Mediated Iron Uptake Promotes Colon Tumorigenesis. Adv Sci (Weinh) 2023; 10:e2207693. [PMID: 36703617 PMCID: PMC10074045 DOI: 10.1002/advs.202207693] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Indexed: 05/17/2023]
Abstract
Transferrin receptor (TFRC) is the major mediator for iron entry into a cell. Under excessive iron conditions, TFRC is expected to be reduced to lower iron uptake and toxicity. However, the mechanism whereby TFRC expression is maintained at high levels in iron-enriched cancer cells and the contribution of TFRC to cancer development are enigmatic. Here the work shows TFRC is induced by adenomatous polyposis coli (APC) gene loss-driven β-catenin activation in colorectal cancer, whereas TFRC-mediated intratumoral iron accumulation potentiates β-catenin signaling by directly enhancing the activity of tankyrase. Disruption of TFRC leads to a reduction of colonic iron levels and iron-dependent tankyrase activity, which caused stabilization of axis inhibition protein 2 (AXIN2) and subsequent repression of the β-catenin/c-Myc/E2F Transcription Factor 1/DNA polymerase delta1 (POLD1) axis. POLD1 knockdown, iron chelation, and TFRC disruption increase DNA replication stress, DNA damage response, apoptosis, and reduce colon tumor growth. Importantly, a combination of iron chelators and DNA damaging agents increases DNA damage response and reduces colon tumor cell growth. TFRC-mediated iron import is at the center of a novel feed-forward loop that facilitates colonic epithelial cell survival. This discovery may provide novel strategies for colorectal cancer therapy.
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Affiliation(s)
- Hyeoncheol Kim
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Luke B Villareal
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Zhaoli Liu
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Mohammad Haneef
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Daniel M Falcon
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - David R Martin
- Department of PathologyUniversity of New MexicoAlbuquerqueNM87131USA
| | - Ho‐Joon Lee
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Michael K Dame
- Department of Internal MedicineDivision of GastroenterologyUniversity of MichiganAnn ArborMI48109USA
| | - Durga Attili
- Department of PathologyThe University of Michigan Medical SchoolAnn ArborMI48109USA
| | - Ying Chen
- Center for clinical research and translational medicineYangpu hospitalTongji University School of MedicineShanghai200090China
| | - James Varani
- Department of PathologyThe University of Michigan Medical SchoolAnn ArborMI48109USA
| | - Jason R. Spence
- Department of Internal MedicineDivision of GastroenterologyUniversity of MichiganAnn ArborMI48109USA
| | - Olga Kovbasnjuk
- Division of Gastroenterology and HepatologyDepartment of Medicinethe University of New MexicoAlbuquerqueNM87131USA
| | - Justin A Colacino
- Department of Environmental Health SciencesUniversity of MichiganAnn ArborMI48109USA
| | - Costas A. Lyssiotis
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Henry C Lin
- Section of GastroenterologyMedicine ServiceNew Mexico VA Health Care SystemAlbuquerqueNM87108USA
| | - Yatrik M Shah
- Department of Molecular and Integrative PhysiologyUniversity of MichiganAnn ArborMI48109USA
| | - Xiang Xue
- Department of Biochemistry and Molecular BiologyUniversity of New MexicoAlbuquerqueNM87131USA
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13
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Campbell KA, Colacino JA, Puttabyatappa M, Dou JF, Elkin ER, Hammoud SS, Domino SE, Dolinoy DC, Goodrich JM, Loch-Caruso R, Padmanabhan V, Bakulski KM. Placental cell type deconvolution reveals that cell proportions drive preeclampsia gene expression differences. Commun Biol 2023; 6:264. [PMID: 36914823 PMCID: PMC10011423 DOI: 10.1038/s42003-023-04623-6] [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: 09/09/2021] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
The placenta mediates adverse pregnancy outcomes, including preeclampsia, which is characterized by gestational hypertension and proteinuria. Placental cell type heterogeneity in preeclampsia is not well-understood and limits mechanistic interpretation of bulk gene expression measures. We generated single-cell RNA-sequencing samples for integration with existing data to create the largest deconvolution reference of 19 fetal and 8 maternal cell types from placental villous tissue (n = 9 biological replicates) at term (n = 40,494 cells). We deconvoluted eight published microarray case-control studies of preeclampsia (n = 173 controls, 157 cases). Preeclampsia was associated with excess extravillous trophoblasts and fewer mesenchymal and Hofbauer cells. Adjustment for cellular composition reduced preeclampsia-associated differentially expressed genes (log2 fold-change cutoff = 0.1, FDR < 0.05) from 1154 to 0, whereas downregulation of mitochondrial biogenesis, aerobic respiration, and ribosome biogenesis were robust to cell type adjustment, suggesting direct changes to these pathways. Cellular composition mediated a substantial proportion of the association between preeclampsia and FLT1 (37.8%, 95% CI [27.5%, 48.8%]), LEP (34.5%, 95% CI [26.0%, 44.9%]), and ENG (34.5%, 95% CI [25.0%, 45.3%]) overexpression. Our findings indicate substantial placental cellular heterogeneity in preeclampsia contributes to previously observed bulk gene expression differences. This deconvolution reference lays the groundwork for cellular heterogeneity-aware investigation into placental dysfunction and adverse birth outcomes.
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Affiliation(s)
- Kyle A Campbell
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | | | - John F Dou
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Elana R Elkin
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Saher S Hammoud
- Human Genetics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Steven E Domino
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Rita Loch-Caruso
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Pediatrics, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
- Obstetrics and Gynecology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.
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14
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Svoboda LK, Wang K, Goodrich JM, Jones TR, Colacino JA, Peterson KE, Tellez-Rojo MM, Sartor MA, Dolinoy DC. Perinatal Lead Exposure Promotes Sex-Specific Epigenetic Programming of Disease-Relevant Pathways in Mouse Heart. Toxics 2023; 11:85. [PMID: 36668811 PMCID: PMC9860846 DOI: 10.3390/toxics11010085] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/21/2022] [Accepted: 12/25/2022] [Indexed: 06/17/2023]
Abstract
Environmental contaminants such as the metal lead (Pb) are associated with cardiovascular disease, but the underlying molecular mechanisms are poorly understood. In particular, little is known about how exposure to Pb during early development impacts the cardiac epigenome at any point across the life course and potential differences between sexes. In a mouse model of human-relevant perinatal exposures, we utilized RNA-seq and Enhanced Reduced Representation Bisulfite Sequencing (ERRBS) to investigate the effects of Pb exposure during gestation and lactation on gene expression and DNA methylation, respectively, in the hearts of male and female mice at weaning. For ERRBS, we identified differentially methylated CpGs (DMCs) or differentially methylated 1000 bp regions (DMRs) based on a minimum absolute change in methylation of 10% and an FDR < 0.05. For gene expression data, an FDR < 0.05 was considered significant. No individual genes met the FDR cutoff for gene expression; however, we found that Pb exposure leads to significant changes in the expression of gene pathways relevant to cardiovascular development and disease. We further found that Pb promotes sex-specific changes in DNA methylation at hundreds of gene loci (280 DMCs and 99 DMRs in males, 189 DMCs and 121 DMRs in females), and pathway analysis revealed that these CpGs and regions collectively function in embryonic development. In males, differential methylation also occurred at genes related to immune function and metabolism. We then investigated whether genes exhibiting differential methylation at weaning were also differentially methylated in hearts from a cohort of Pb-exposed mice at adulthood. We found that a single gene, Galnt2, showed differential methylation in both sexes and time points. In a human cohort investigating the influence of prenatal Pb exposure on the epigenome, we also observed an inverse association between first trimester Pb concentrations and adolescent blood leukocyte DNA methylation at a locus in GALNT2, suggesting that this gene may represent a biomarker of Pb exposure across species. Together, these data, across two time points in mice and in a human birth cohort study, collectively demonstrate that Pb exposure promotes sex-specific programming of the cardiac epigenome, and provide potential mechanistic insight into how Pb causes cardiovascular disease.
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Affiliation(s)
- Laurie K. Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Jaclyn M. Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Tamara R. Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Justin A. Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Karen E. Peterson
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Martha M. Tellez-Rojo
- Center for Research on Nutrition and Health, National Institute of Public Health, Cuernavaca 62100, Mexico
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dana C. Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
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15
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Elkin ER, Su AL, Dou JF, Colacino JA, Bridges D, Padmanabhan V, Harris SM, Boldenow E, Loch-Caruso R, Bakulski KM. Sexually concordant and dimorphic transcriptional responses to maternal trichloroethylene and/or N-acetyl cysteine exposure in Wistar rat placental tissue. Toxicology 2023; 483:153371. [PMID: 36396003 PMCID: PMC10078828 DOI: 10.1016/j.tox.2022.153371] [Citation(s) in RCA: 2] [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: 08/19/2022] [Revised: 10/20/2022] [Accepted: 11/02/2022] [Indexed: 11/16/2022]
Abstract
Numerous Superfund sites are contaminated with the volatile organic chemical trichloroethylene (TCE). In women, exposure to TCE in pregnancy is associated with reduced birth weight. Our previous study reported that TCE exposure in pregnant rats decreased fetal weight and elevated oxidative stress biomarkers in placentae, suggesting placental injury as a potential mechanism of TCE-induced adverse birth outcomes. In this study, we investigated if co-exposure with the antioxidant N-acetylcysteine (NAC) attenuates TCE exposure effects on RNA expression. Timed-pregnant Wistar rats were exposed orally to 480 mg TCE/kg/day on gestation days 6-16. Exposure of 200 mg NAC/kg/day alone or as a pre/co-exposure with TCE occurred on gestation days 5-16 to stimulate antioxidant genes prior to TCE exposure. Tissue was collected on gestation day 16. In male and female placentae, we evaluated TCE- and/or NAC-induced changes to gene expression and pathway enrichment analyses using false discovery rate (FDR) and fold-change criteria. In female placentae, exposure to TCE caused significant differential expression 129 genes while the TCE+NAC altered 125 genes, compared with controls (FDR< 0.05 + fold-change >1). In contrast, in male placentae TCE exposure differentially expressed 9 genes and TCE+NAC differentially expressed 35 genes, compared with controls (FDR< 0.05 + fold-change >1). NAC alone did not significantly alter gene expression in either sex. Differentially expressed genes observed with TCE exposure were enriched in mitochondrial biogenesis and oxidative phosphorylation pathways in females whereas immune system pathways and endoplasmic reticulum stress pathways were differentially expressed in both sexes (FDR<0.05). TCE treatment was differentially enriched for genes regulated by the transcription factors ATF6 (both sexes) and ATF4 (males only), indicating a cellular condition triggered by misfolded proteins during endoplasmic reticulum stress. This study demonstrates novel genes and pathways involved in TCE-induced placental injury and showed antioxidant co-treatment largely did not attenuate TCE exposure effects.
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Affiliation(s)
- Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA.
| | - Anthony L Su
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - John F Dou
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Dave Bridges
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Vasantha Padmanabhan
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Pediatrics, Michigan Medicine, Ann Arbor, MI, USA; Department of Obstetrics and Gynecology, Michigan Medicine, Ann Arbor, MI, USA
| | - Sean M Harris
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Erica Boldenow
- Department of Biology, Calvin University, Grand Rapids, MI, USA
| | - Rita Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
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16
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Delgado E, Keeley TM, Hibdon ES, McGowan KP, Gillilland MG, Colacino JA, Stoffel E, Samuelson LC. Distinct Wnt Signaling Thresholds Required for Polyposis in the Proximal and Distal Stomach. FASEB J 2022. [DOI: 10.1096/fasebj.2022.36.s1.r2025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Elizabeth Delgado
- Department of Molecular & Integrative PhysiologyUniversity of MichiganAnn ArborMI
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17
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Su AL, Harris SM, Elkin ER, Karnovsky A, Colacino JA, Loch-Caruso R. Trichloroethylene modifies energy metabolites in the amniotic fluid of Wistar rats. Reprod Toxicol 2022; 109:80-92. [PMID: 35301063 PMCID: PMC9000924 DOI: 10.1016/j.reprotox.2022.03.004] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 03/05/2022] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
Abstract
Exposure to trichloroethylene (TCE), an industrial solvent, is associated with several adverse pregnancy outcomes in humans and decreased fetal weight in rats. However, effects of TCE on energy metabolites in amniotic fluid, which have associations with pregnancy outcomes, has not been published previously. In the current exploratory study, timed-pregnant Wistar rats were exposed to 480 mg TCE/kg/day via vanilla wafer or to vehicle (wafer) alone from gestational day (GD) 6-16. Amniotic fluid collected on GD 16 was analyzed for metabolites important in energy metabolism using short chain fatty acid and tricarboxylic acid plus platforms (N = 4 samples/sex/treatment). TCE decreased concentrations of the following metabolites in amniotic fluid for both fetal sexes: 6-phosphogluconate, guanosine diphosphate, adenosine diphosphate, adenosine triphosphate, and flavin adenine dinucleotide. TCE decreased fructose 1,6-bisphosphate and guanosine triphosphate concentrations in amniotic fluid of male but not female fetuses. Moreover, TCE decreased uridine diphosphate-D-glucuronate concentrations, and increased arginine and phosphocreatine concentrations, in amniotic fluid of female fetuses only. No metabolites were increased in amniotic fluid of male fetuses. Pathway analysis suggested that TCE altered folate biosynthesis and pentose phosphate pathway in both sexes. Using metabolite ratios to investigate changes within specific pathways, some ratio alterations, including those in arginine metabolism and phenylalanine metabolism, were detected in females only. Ratio analysis also suggested enzymes, including gluconokinase, as potential TCE targets. Together, results from this exploratory study suggest that TCE differentially modified energy metabolites in amniotic fluid based on sex. These findings may inform future studies of TCE reproductive toxicity.
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Affiliation(s)
- Anthony L Su
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Sean M Harris
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Alla Karnovsky
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Palmer Commons, 100 Washtenaw Ave #2017, Ann Arbor, MI 48109, USA.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA; Department of Nutritional Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
| | - Rita Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109, USA.
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18
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Polemi KM, Nguyen VK, Heidt J, Kahana A, Jolliet O, Colacino JA. Identifying the link between chemical exposures and breast cancer in African American women via integrated in vitro and exposure biomarker data. Toxicology 2021; 463:152964. [PMID: 34600088 PMCID: PMC8593892 DOI: 10.1016/j.tox.2021.152964] [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: 08/24/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/27/2022]
Abstract
Among women, breast cancer is the most prevalent form of cancer worldwide and has the second highest mortality rate of any cancer in the United States. The breast cancer related death rate is 40 % higher in non-Hispanic Black women compared to non-Hispanic White women. The incidence of triple negative breast cancer (TNBC), an aggressive subtype of breast cancer for which there is no targeted therapy, is also approximately three times higher for Black, relative to, White women. The drivers of these differences are poorly understood. Here, we aimed to identify chemical exposures which play a role in breast cancer disparities. Using chemical biomonitoring data from the National Health and Nutrition Examination Survey (NHANES) and biological activity data from the EPA's ToxCast program, we assessed the toxicological profiles of chemicals to which US Black women are disproportionately exposed. We conducted a literature search to identify breast cancer targets in ToxCast to analyze the response of chemicals with exposure disparities in these assays. Forty-three chemical biomarkers are significantly higher in Black women. Investigation of these chemicals in ToxCast resulted in 32,683 assays for analysis, 5172 of which contained nonzero values for the concentration at which the dose-response fitted model reaches the cutoff considered "active". Of these chemicals BPA, PFOS, and thiram are most comprehensively assayed. 2,5-dichlorophenol, 1,4-dichlorobenzene, and methyl and propyl parabens had higher biomarker concentrations in Black women and moderate testing and activity in ToxCast. The distribution of active concentrations for these chemicals in ToxCast assays are comparable to biomarker concentrations in Black women NHANES participants. Through this integrated analysis, we identify that multiple chemicals, including thiram, propylparaben, and p,p' DDE, have disproportionate exposures in Black women and have breast cancer associated biological activity at human exposure relevant doses.
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Affiliation(s)
- Katelyn M Polemi
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Vy K Nguyen
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Julien Heidt
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Adam Kahana
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Olivier Jolliet
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA.
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19
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Elkin ER, Bakulski KM, Colacino JA, Bridges D, Kilburn BA, Armant DR, Loch-Caruso R. Transcriptional profiling of the response to the trichloroethylene metabolite S-(1,2-dichlorovinyl)-L-cysteine revealed activation of the eIF2α/ATF4 integrated stress response in two in vitro placental models. Arch Toxicol 2021; 95:1595-1619. [PMID: 33725128 PMCID: PMC7961173 DOI: 10.1007/s00204-021-03011-5] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
Trichloroethylene (TCE) is an industrial solvent and widespread environmental contaminant. Although TCE exposure is prevalent, epidemiological studies of TCE exposure associations with adverse birth outcomes are inconclusive. Prior studies show that the TCE metabolite S-(1,2-dichlorovinyl)-l-cysteine (DCVC) exhibits toxicity in a placental cell line. In the current study, genome-wide gene expression and gene set enrichment analyses were used to identify novel genes and pathway alterations in the HTR-8/SVneo human trophoblast cell line and human placental villous explants treated with DCVC at concentrations relevant to human exposures. In the cells, concentration- and time-dependent effects were observed, as evidenced by the magnitude of altered gene expression after treatment with 20 µM DCVC versus 10 µM, and 12-h versus 6-h of treatment. Comparing the two models for the transcriptional response to 12-h 20 µM DCVC treatment, no differentially expressed genes reached significance in villous explants, whereas 301 differentially expressed genes were detected in HTR-8/SVneo cells compared with non-treated controls (FDR < 0.05 + LogFC > 0.35 [FC > 1.3]). GSEA revealed five upregulated enriched pathways in common between explants and cells (FDR < 0.05). Moreover, all 12-h DCVC treatment groups from both models contained upregulated pathways enriched for genes regulated by the ATF4 transcription factor. The overrepresentation of ATF4 regulation of differentially expressed genes indicated activation of the integrated stress response (ISR), a condition triggered by multiple stress stimuli, including the unfolded protein response. DCVC-induced ISR activation was confirmed by elevated eIF2α phosphorylation, ATF4 protein concentrations, and decreased global protein synthesis in HTR-8/SVneo cells. This study identifies a mechanism of DCVC-induced cytotoxicity by revealing the involvement of a specific stress signaling pathway.
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Affiliation(s)
- Elana R Elkin
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA.
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA.,Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Dave Bridges
- Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Brian A Kilburn
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA
| | - D Randall Armant
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI, USA.,Department of Anatomy and Cell Biology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Rita Loch-Caruso
- Department of Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI, 48109-2029, USA
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20
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Middleton LYM, Dou J, Fisher J, Heiss JA, Nguyen VK, Just AC, Faul J, Ware EB, Mitchell C, Colacino JA, M Bakulski K. Saliva cell type DNA methylation reference panel for epidemiological studies in children. Epigenetics 2021; 17:161-177. [PMID: 33588693 DOI: 10.1080/15592294.2021.1890874] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Saliva is a widely used biological sample, especially in pediatric research, containing a heterogenous mixture of immune and epithelial cells. Associations of exposure or disease with saliva DNA methylation can be influenced by cell-type proportions. Here, we developed a saliva cell-type DNA methylation reference panel to estimate interindividual cell-type heterogeneity in whole saliva studies. Saliva was collected from 22 children (7-16 years) and sorted into immune and epithelial cells, using size exclusion filtration and magnetic bead sorting. DNA methylation was measured using the Illumina MethylationEPIC BeadChip. We assessed cell-type differences in DNA methylation profiles and tested for enriched biological pathways. Immune and epithelial cells differed at 181,577 (22.8%) DNA methylation sites (t-test p < 6.28 × 10-8). Immune cell hypomethylated sites are mapped to genes enriched for immune pathways (p < 3.2 × 10-5). Epithelial cell hypomethylated sites were enriched for cornification (p = 5.2 × 10-4), a key process for hard palette formation. Saliva immune and epithelial cells have distinct DNA methylation profiles which can drive whole-saliva DNA methylation measures. A primary saliva DNA methylation reference panel, easily implemented with an R package, will allow estimates of cell proportions from whole saliva samples and improve epigenetic epidemiology studies by accounting for measurement heterogeneity by cell-type proportions.
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Affiliation(s)
- Lauren Y M Middleton
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - John Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jonah Fisher
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Jonathan A Heiss
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Vy K Nguyen
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jessica Faul
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Erin B Ware
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA.,Population Studies Center, Institute for Social Research, University of Michigan
| | - Colter Mitchell
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA.,Population Studies Center, Institute for Social Research, University of Michigan
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Department of Nutritional Sciences, School of Public Health, University of Michigan.,Center for Computational Medicine and Bioinformatics, University of Michigan.,Program in the Environment, College of Literature, Sciences, and the Arts, University of Michigan
| | - Kelly M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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21
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Campbell KA, Colacino JA, Park SK, Bakulski KM. Cell Types in Environmental Epigenetic Studies: Biological and Epidemiological Frameworks. Curr Environ Health Rep 2021; 7:185-197. [PMID: 32794033 DOI: 10.1007/s40572-020-00287-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [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: 12/13/2022]
Abstract
PURPOSE OF REVIEW This article introduces the roles of perinatal DNA methylation in human health and disease, highlights the challenges of tissue and cellular heterogeneity to studying DNA methylation, summarizes approaches to overcome these challenges, and offers recommendations in conducting research in environmental epigenetics. RECENT FINDINGS Epigenetic modifications are essential for human development and are labile to environmental influences, especially during gestation. Epigenetic dysregulation is also a hallmark of multiple diseases. Environmental epigenetic studies routinely measure DNA methylation in readily available tissues. However, tissues and cell types exhibit specific epigenetic patterning and heterogeneity between samples complicates epigenetic studies. Failure to account for cell-type heterogeneity limits identification of biological mechanisms and biases study results. Tissue-level epigenetic measures represent a convolution of epigenetic signals from individual cell types. Tissue-specific epigenetics is an evolving field and the use of disease-affected target, surrogate, or multiple tissues has inherent trade-offs and affects inference. Likewise, experimental and bioinformatic approaches to accommodate cell-type heterogeneity have varying assumptions and inherent trade-offs that affect inference. The relationships between exposure, disease, tissue-level DNA methylation, cell type-specific DNA methylation, and cell-type heterogeneity must be carefully considered in study design and analysis. Causal diagrams can inform study design and analytic strategies. Properly addressing cell-type heterogeneity limits sources of potential bias, avoids misinterpretation of study results, and allows investigators to distinguish shifts in cell-type proportions from direct changes to cellular epigenetic programming, both of which provide insights into environmental disease etiology and aid development of novel methods for prevention and treatment.
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Affiliation(s)
- Kyle A Campbell
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Sung Kyun Park
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Department of Environmental Health Sciences, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan School of Public Health, University of Michigan, Ann Arbor, MI, USA
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22
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Liu S, Wang K, Svoboda LK, Rygiel CA, Neier K, Jones TR, Cavalcante RG, Colacino JA, Dolinoy DC, Sartor MA. Perinatal DEHP exposure induces sex- and tissue-specific DNA methylation changes in both juvenile and adult mice. Environ Epigenet 2021; 7:dvab004. [PMID: 33986952 PMCID: PMC8107644 DOI: 10.1093/eep/dvab004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 02/12/2021] [Accepted: 03/17/2021] [Indexed: 05/04/2023]
Abstract
Di(2-ethylhexyl) phthalate (DEHP) is a type of phthalate plasticizer found in a variety of consumer products and poses a public health concern due to its metabolic and endocrine disruption activities. Dysregulation of epigenetic modifications, including DNA methylation, has been shown to be an important mechanism for the pathogenic effects of prenatal exposures, including phthalates. In this study, we used an established mouse model to study the effect of perinatal DEHP exposure on the DNA methylation profile in liver (a primary target tissue of DEHP) and blood (a common surrogate tissue) of both juvenile and adult mice. Despite exposure ceasing at 3 weeks of age (PND21), we identified thousands of sex-specific differential DNA methylation events in 5-month old mice, more than identified at PND21, both in blood and liver. Only a small number of these differentially methylated cytosines (DMCs) overlapped between the time points, or between tissues (i.e. liver and blood), indicating blood may not be an appropriate surrogate tissue to estimate the effects of DEHP exposure on liver DNA methylation. We detected sex-specific DMCs common between 3-week and 5-month samples, pointing to specific DNA methylation alterations that are consistent between weanling and adult mice. In summary, this is the first study to assess the genome-wide DNA methylation profiles in liver and blood at two different aged cohorts in response to perinatal DEHP exposure. Our findings cast light on the implications of using surrogate tissue instead of target tissue in human population-based studies and identify epigenetic biomarkers for DEHP exposure.
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Affiliation(s)
- Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Laurie K Svoboda
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Christine A Rygiel
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Raymond G Cavalcante
- Epigenomics Core, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
- Nutritional Sciences, University of Michigan, 500 S State St., Ann Arbor, MI 48109, USA
| | - Dana C Dolinoy
- Correspondence address. Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA. Tel: +734-647-3155; Fax: +734-936-7283; E-mail: (D.C.D.); Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI 48109-2218, USA . Tel: +734-763-8013; Fax: +734-615-6553; E-mail: (M.A.S.)
| | - Maureen A Sartor
- Correspondence address. Environmental Health Sciences, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109-2029, USA. Tel: +734-647-3155; Fax: +734-936-7283; E-mail: (D.C.D.); Department of Computational Medicine and Bioinformatics, University of Michigan, 100 Washtenaw Ave., Ann Arbor, MI 48109-2218, USA . Tel: +734-763-8013; Fax: +734-615-6553; E-mail: (M.A.S.)
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23
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Bohm MS, Dame MK, Boyd J, Su K, Wu A, Attili D, Chu V, Colacino JA, Spence JR. Low-Level Mouse DNA in Conditioned Medium Generates False Positive Cross-Species Contamination Results in Human Organoid Cultures. Front Cell Dev Biol 2020; 8:587107. [PMID: 33240885 PMCID: PMC7677229 DOI: 10.3389/fcell.2020.587107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/24/2020] [Accepted: 10/20/2020] [Indexed: 12/15/2022] Open
Abstract
Cell line authentication is critical for preventing the use of mixed or misidentified cell lines in research. Current efforts include short tandem repeat (STR) analysis and PCR-based assays to detect mixed species cultures. Using PCR analysis with mouse-specific primers, we identified contaminating mouse DNA in growth factor conditioned medium (CM) derived from the L-WRN cell line (L-WRN CM), as well as in human organoid cultures maintained in the L-WRN CM. DNA isolated from L-WRN CM matched the L-WRN cell signature by STR analysis. Organoid lines that were positive for murine DNA by PCR were further analyzed via bulk RNA-sequencing and transcripts were aligned to the human and mouse genomes. RNA analysis failed to detect mouse-specific gene expression above background levels, suggesting no viable murine cells were present in the organoid cultures. We interpret our data to show conclusive evidence that mouse cell-derived CM can be a source of contaminating murine DNA detected in human organoid cultures, even though live, transcriptionally-active murine cells are not present. Together, our findings suggest that multiple methods may be required to authenticate human organoid or cell lines and urges cautious interpretation of DNA-based PCR cell line authentication results.
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Affiliation(s)
- Margaret S Bohm
- Division of Gastroenterology, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Michael K Dame
- Division of Gastroenterology, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Joseph Boyd
- Millipore-Sigma Corporation, Temecula, CA, United States
| | - Kevin Su
- Millipore-Sigma Corporation, Temecula, CA, United States
| | - Angeline Wu
- Division of Gastroenterology, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Durga Attili
- Department of Cell and Developmental Biology, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Vi Chu
- Millipore-Sigma Corporation, Temecula, CA, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, The University of Michigan School of Public Health, Ann Arbor, MI, United States.,Department of Nutritional Sciences, The University of Michigan School of Public Health, Ann Arbor, MI, United States.,Center for Computational Medicine and Bioinformatics, The University of Michigan Medical School, Ann Arbor, MI, United States
| | - Jason R Spence
- Division of Gastroenterology, Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Cell and Developmental Biology, The University of Michigan Medical School, Ann Arbor, MI, United States.,Department of Biomedical Engineering, The University of Michigan Medical School, Ann Arbor, MI, United States
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24
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Svoboda LK, Neier K, Wang K, Cavalcante RG, Rygiel CA, Tsai Z, Jones TR, Liu S, Goodrich JM, Lalancette C, Colacino JA, Sartor MA, Dolinoy DC. Tissue and sex-specific programming of DNA methylation by perinatal lead exposure: implications for environmental epigenetics studies. Epigenetics 2020; 16:1102-1122. [PMID: 33164632 DOI: 10.1080/15592294.2020.1841872] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Early developmental environment can influence long-term health through reprogramming of the epigenome. Human environmental epigenetics studies rely on surrogate tissues, such as blood, to assess the effects of environment on disease-relevant but inaccessible target tissues. However, the extent to which environment-induced epigenetic changes are conserved between these tissues is unclear. A better understanding of this conservation is imperative for effective design and interpretation of human environmental epigenetics studies. The Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET II) consortium was established by the National Institute of Environmental Health Sciences to address the utility of surrogate tissues as proxies for toxicant-induced epigenetic changes in target tissues. We and others have recently reported that perinatal exposure to lead (Pb) is associated with adverse metabolic outcomes. Here, we investigated the sex-specific effects of perinatal exposure to a human environmentally relevant level of Pb on DNA methylation in paired liver and blood samples from adult mice using enhanced reduced-representation bisulphite sequencing. Although Pb exposure ceased at 3 weeks of age, we observed thousands of sex-specific differentially methylated cytosines in the blood and liver of Pb-exposed animals at 5 months of age, including 44 genomically imprinted loci. We observed significant tissue overlap in the genes mapping to differentially methylated cytosines. A small but significant subset of Pb-altered genes exhibit basal sex differences in gene expression in the mouse liver. Collectively, these data identify potential molecular targets for Pb-induced metabolic diseases, and inform the design of more robust human environmental epigenomics studies.
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Affiliation(s)
- Laurie K Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | | | - Christine A Rygiel
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Zing Tsai
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Claudia Lalancette
- Epigenomics Core, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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25
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Wang K, Liu S, Svoboda LK, Rygiel CA, Neier K, Jones TR, Colacino JA, Dolinoy DC, Sartor MA. Tissue- and Sex-Specific DNA Methylation Changes in Mice Perinatally Exposed to Lead (Pb). Front Genet 2020; 11:840. [PMID: 32973866 PMCID: PMC7472839 DOI: 10.3389/fgene.2020.00840] [Citation(s) in RCA: 9] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/10/2020] [Indexed: 12/22/2022] Open
Abstract
Lead (Pb) is a well-known toxicant that interferes with the development of a child’s nervous and metabolic systems and increases the risk of developing diseases later in life. Although studies have investigated epigenetic effects associated with Pb exposure, knowledge of genome-wide changes with in vivo low dose perinatal Pb exposure in multiple tissues is limited. Within the Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET II) consortium, we utilized a mouse model to investigate tissue- and sex-specific DNA methylation. Dams were assigned to control or Pb-acetate water, respectively. Exposures started 2 weeks prior to mating and continued until weaning at post-natal day 21 (PND21). Liver and blood were collected from PND21 mice, and the DNA methylome was assessed using enhanced reduced representation bisulfite sequencing (ERRBS). We identified ∼1000 perinatal Pb exposure related differentially methylated cytosines (DMCs) for each tissue- and sex-specific comparison, and hundreds of tissue- and sex-specific differentially methylated regions (DMRs). Several mouse imprinted genes were differentially methylated across both tissues in males and females. Overall, our findings demonstrate that perinatal Pb exposure can induce tissue- and sex-specific DNA methylation changes and provide information for future Pb studies in humans.
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Affiliation(s)
- Kai Wang
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Siyu Liu
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Christine A Rygiel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Kari Neier
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Tamara R Jones
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, School of Medicine, University of Michigan, Ann Arbor, MI, United States.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
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Svoboda LK, Wang K, Cavalcante RG, Neier K, Colacino JA, Sartor MA, Dolinoy DC. Sex-Specific Programming of Cardiac DNA Methylation by Developmental Phthalate Exposure. Epigenet Insights 2020; 13:2516865720939971. [PMID: 32864567 PMCID: PMC7430087 DOI: 10.1177/2516865720939971] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 04/05/2020] [Accepted: 06/15/2020] [Indexed: 01/05/2023] Open
Abstract
Phthalate plasticizers are ubiquitous chemicals linked to several cardiovascular diseases in animal models and humans. Despite this, the mechanisms by which phthalate exposures cause adverse cardiac health outcomes are unclear. In particular, whether phthalate exposures during pregnancy interfere with normal developmental programming of the cardiovascular system, and the resulting implications this may have for long-term disease risk, are unknown. Recent studies suggest that the effects of phthalates on metabolic and neurobehavioral outcomes are sex-specific. However, the influence of sex on cardiac susceptibility to phthalate exposures has not been investigated. One mechanism by which developmental exposures may influence long-term health is through altered programming of DNA methylation. In this work, we utilized an established mouse model of human-relevant perinatal exposure and enhanced reduced representation bisulfite sequencing to investigate the long-term effects of diethylhexyl phthalate (DEHP) exposure on DNA methylation in the hearts of adult male and female offspring at 5 months of age (n = 5-7 mice per sex and exposure). Perinatal DEHP exposure led to hundreds of sex-specific, differentially methylated cytosines (DMCs) and differentially methylated regions (DMRs) in the heart. Pathway analysis of DMCs revealed enrichment for several pathways in females, including insulin signaling, regulation of histone methylation, and tyrosine phosphatase activity. In males, DMCs were enriched for glucose transport, energy generation, and developmental programs. Notably, many sex-specific genes differentially methylated with DEHP exposure in our mouse model were also differentially methylated in published data of heart tissues collected from human heart failure patients. Together, these data highlight the potential role for DNA methylation in DEHP-induced cardiac effects and emphasize the importance of sex as a biological variable in environmental health studies.
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Affiliation(s)
- Laurie K Svoboda
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Raymond G Cavalcante
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Kari Neier
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA.,Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
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27
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Bakulski KM, Dou JF, Thompson RC, Lee C, Middleton LY, Perera BPU, Ferris SP, Jones TR, Neier K, Zhou X, Sartor MA, Hammoud SS, Dolinoy DC, Colacino JA. Single-Cell Analysis of the Gene Expression Effects of Developmental Lead (Pb) Exposure on the Mouse Hippocampus. Toxicol Sci 2020; 176:396-409. [PMID: 32458983 PMCID: PMC7416319 DOI: 10.1093/toxsci/kfaa069] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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] [Indexed: 12/12/2022] Open
Abstract
Lead (Pb) exposure is ubiquitous with permanent neurodevelopmental effects. The hippocampus brain region is involved in learning and memory with heterogeneous cellular composition. The hippocampus cell type-specific responses to Pb are unknown. The objective of this study is to examine perinatal Pb treatment effects on adult hippocampus gene expression, at the level of individual cells. In mice perinatally exposed to control water or a human physiologically relevant level (32 ppm in maternal drinking water) of Pb, 2 weeks prior to mating through weaning, we tested for hippocampus gene expression and cellular differences at 5 months of age. We sequenced RNA from 5258 hippocampal cells to (1) test for treatment gene expression differences averaged across all cells, (2) compare cell cluster composition by treatment, and (3) test for treatment gene expression and pathway differences within cell clusters. Gene expression patterns revealed 12 hippocampus cell clusters, mapping to major expected cell types (eg, microglia, astrocytes, neurons, and oligodendrocytes). Perinatal Pb treatment was associated with 12.4% more oligodendrocytes (p = 4.4 × 10-21) in adult mice. Across all cells, Pb treatment was associated with expression of cell cluster marker genes. Within cell clusters, Pb treatment (q < 0.05) caused differential gene expression in endothelial, microglial, pericyte, and astrocyte cells. Pb treatment upregulated protein folding pathways in microglia (p = 3.4 × 10-9) and stress response in oligodendrocytes (p = 3.2 × 10-5). Bulk tissue analysis may be influenced by changes in cell type composition, obscuring effects within vulnerable cell types. This study serves as a biological reference for future single-cell toxicant studies, to ultimately characterize molecular effects on cognition and behavior.
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Affiliation(s)
| | | | | | | | | | | | - Sean P Ferris
- Medical School, University of Michigan, Ann Arbor, Michigan 48109
| | | | | | | | - Maureen A Sartor
- School of Public Health
- Medical School, University of Michigan, Ann Arbor, Michigan 48109
| | - Saher S Hammoud
- Medical School, University of Michigan, Ann Arbor, Michigan 48109
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Thong T, Wang Y, Brooks MD, Lee CT, Scott C, Balzano L, Wicha MS, Colacino JA. Hybrid Stem Cell States: Insights Into the Relationship Between Mammary Development and Breast Cancer Using Single-Cell Transcriptomics. Front Cell Dev Biol 2020; 8:288. [PMID: 32457901 PMCID: PMC7227401 DOI: 10.3389/fcell.2020.00288] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 12/13/2019] [Accepted: 04/02/2020] [Indexed: 12/15/2022] Open
Abstract
Similarities between stem cells and cancer cells have implicated mammary stem cells in breast carcinogenesis. Recent evidence suggests that normal breast stem cells exist in multiple phenotypic states: epithelial, mesenchymal, and hybrid epithelial/mesenchymal (E/M). Hybrid E/M cells in particular have been implicated in breast cancer metastasis and poor prognosis. Mounting evidence also suggests that stem cell phenotypes change throughout the life course, for example, through embryonic development and pregnancy. The goal of this study was to use single cell RNA-sequencing to quantify cell state distributions of the normal mammary (NM) gland throughout developmental stages and when perturbed into a stem-like state in vitro using conditional reprogramming (CR). Using machine learning based dataset alignment, we integrate multiple mammary gland single cell RNA-seq datasets from human and mouse, along with bulk RNA-seq data from breast tumors in the Cancer Genome Atlas (TCGA), to interrogate hybrid stem cell states in the normal mammary gland and cancer. CR of human mammary cells induces an expanded stem cell state, characterized by increased expression of embryonic stem cell associated genes. Alignment to a mouse single-cell transcriptome atlas spanning mammary gland development from in utero to adulthood revealed that NM cells align to adult mouse cells and CR cells align across the pseudotime trajectory with a stem-like population aligning to the embryonic mouse cells. Three hybrid populations emerge after CR that are rare in NM: KRT18+/KRT14+ (hybrid luminal/basal), EPCAM+/VIM+ (hybrid E/M), and a quadruple positive population, expressing all four markers. Pseudotime analysis and alignment to the mouse developmental trajectory revealed that E/M hybrids are the most developmentally immature. Analyses of single cell mouse mammary RNA-seq throughout pregnancy show that during gestation, there is an enrichment of hybrid E/M cells, suggesting that these cells play an important role in mammary morphogenesis during lactation. Finally, pseudotime analysis and alignment of TCGA breast cancer expression data revealed that breast cancer subtypes express distinct developmental signatures, with basal tumors representing the most “developmentally immature” phenotype. These results highlight phenotypic plasticity of normal mammary stem cells and provide insight into the relationship between hybrid cell populations, stemness, and cancer.
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Affiliation(s)
- Tasha Thong
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Yutong Wang
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, United States
| | - Michael D Brooks
- Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Christopher T Lee
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, United States
| | - Clayton Scott
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, United States.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Laura Balzano
- Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI, United States
| | - Max S Wicha
- Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States.,Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, United States.,Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, United States
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29
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Nguyen VK, Kahana A, Heidt J, Polemi K, Kvasnicka J, Jolliet O, Colacino JA. A comprehensive analysis of racial disparities in chemical biomarker concentrations in United States women, 1999-2014. Environ Int 2020; 137:105496. [PMID: 32113086 PMCID: PMC7137529 DOI: 10.1016/j.envint.2020.105496] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [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: 09/24/2019] [Revised: 01/09/2020] [Accepted: 01/14/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Stark racial disparities in disease incidence among American women remain a persistent public health challenge. These disparities likely result from complex interactions between genetic, social, lifestyle, and environmental risk factors. The influence of environmental risk factors, such as chemical exposure, however, may be substantial and is poorly understood. OBJECTIVES We quantitatively evaluated chemical-exposure disparities by race/ethnicity, life stage, and time in United States (US) women (n = 38,080) by using biomarker data for 143 chemicals from the National Health and Nutrition Examination Survey (NHANES) 1999-2014. METHODS We applied a series of survey-weighted, generalized linear models using data from the entire NHANES women population along with cycle and age-group stratified subpopulations. The outcome was chemical biomarker concentration, and the main predictor was race/ethnicity with adjustment for age, socioeconomic status, smoking habits, and NHANES cycle. RESULTS Compared to non-Hispanic White women, the highest disparities were observed for non-Hispanic Black, Mexican American, Other Hispanic, and Other Race/Multi-Racial women with higher levels of pesticides and their metabolites, including 2,5-dichlorophenol, o,p'-DDE, beta-hexachlorocyclohexane, and 2,4-dichlorophenol, along with personal care and consumer product compounds, including parabens and monoethyl phthalate, as well as several metals, such as mercury and arsenic. Moreover, for Mexican American, Other Hispanic, and non-Hispanic black women, there were several exposure disparities that persisted across age groups, such as higher 2,4- and 2,5-dichlorophenol concentrations. Exposure levels for methyl and propyl parabens, however, were the highest in non-Hispanic black compared to non-Hispanic white children with average differences exceeding 4-fold. Exposure disparities for methyl and propyl parabens are increasing over time in Other Race/Multi-Racial women while fluctuating for non-Hispanic Black, Mexican American, and Other Hispanic. Cotinine levels are among the highest in Non-Hispanic White women compared to Mexican American and Other Hispanic women with disparities plateauing and increasing, respectively. DISCUSSION We systematically evaluated differences in chemical exposures across women of various race/ethnic groups and across age groups and time. Our findings could help inform chemical prioritization in designing epidemiological and toxicological studies. In addition, they could help guide public health interventions to reduce environmental and health disparities across populations.
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Affiliation(s)
- Vy Kim Nguyen
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
| | - Adam Kahana
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Julien Heidt
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Katelyn Polemi
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jacob Kvasnicka
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Olivier Jolliet
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.
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30
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Abstract
An estimated 70-90% of all cancers are linked to exposure to environmental risk factors. In parallel, the number of stem cells in a tissue has been shown to be a strong predictor of risk of developing cancer in that tissue. Tumors themselves are characterized by an acquisition of "stem cell" characteristics, and a growing body of evidence points to tumors themselves being sustained and propagated by a stem cell-like population. Here, we review our understanding of the interplay between environmental exposures, stem cell biology, and cancer. We provide an overview of the role of stem cells in development, tissue homeostasis, and wound repair. We discuss the pathways and mechanisms governing stem cell plasticity and regulation of the stem cell state, and describe experimental methods for assessment of stem cells. We then review the current understanding of how environmental exposures impact stem cell function relevant to carcinogenesis and cancer prevention, with a focus on environmental and occupational exposures to chemical, physical, and biological hazards. We also highlight key areas for future research in this area, including defining whether the biological basis for cancer disparities is related to effects of complex exposure mixtures on stem cell biology.
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Affiliation(s)
- Tasha Thong
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Chanese A Forté
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Michigan Institute for Computational Discovery and Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Evan M Hill
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
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31
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Malloy MA, Kochmanski JJ, Jones TR, Colacino JA, Goodrich JM, Dolinoy DC, Svoboda LK. Perinatal Bisphenol A Exposure and Reprogramming of Imprinted Gene Expression in the Adult Mouse Brain. Front Genet 2019; 10:951. [PMID: 31649729 PMCID: PMC6796247 DOI: 10.3389/fgene.2019.00951] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/05/2019] [Indexed: 12/11/2022] Open
Abstract
Genomic imprinting, a phenomenon by which genes are expressed in a monoallelic, parent-of-origin-dependent fashion, is critical for normal brain development. Expression of imprinted genes is regulated via epigenetic mechanisms, including DNA methylation (5-methylcytosine, 5mC), and disruptions in imprinting can lead to disease. Early-life exposure to the endocrine disrupting chemical bisphenol A (BPA) is associated with abnormalities in brain development and behavior, as well as with disruptions in epigenetic patterning, including 5mC and DNA hydroxymethylation (5-hydroxymethylcytosine, 5hmC). Using an established mouse model of perinatal environmental exposure, the objective of this study was to examine the effects of perinatal BPA exposure on epigenetic regulation of imprinted gene expression in adult mice. Two weeks prior to mating, dams were assigned to control chow or chow containing an environmentally relevant dose (50 µg/kg) of BPA. Exposure continued until offspring were weaned at post-natal day 21, and animals were followed until 10 months of age. Expression of three imprinted genes—Pde10a, Ppp1r9a, and Kcnq1, as well as three genes encoding proteins critical for regulation of 5mC and 5hmC—Dnmt1, Tet1, and Tet2, were evaluated in the right cortex and midbrain using qRT-PCR. Perinatal BPA exposure was associated with a significant increase in adult Kcnq1 (p = 0.04) and Dnmt1 (p = 0.02) expression in the right cortex, as well as increased expression of Tet2 in the midbrain (p = 0.03). Expression of Tet2 and Kcnq1 were positively correlated in the midbrain. Analysis of 5mC and 5hmC at the Kcnq1 locus was conducted in parallel samples using standard and oxidative bisulfite conversion followed by pyrosequencing. This analysis revealed enrichment of both 5mC and 5hmC at this locus in both brain regions. No significant changes in 5mC and 5hmC at Kcnq1 were observed with perinatal BPA exposure. Together, these data suggest that perinatal BPA exposure results in altered expression of Kcnq1, Dnmt1, and Tet2 in the adult mouse brain. Further studies with larger sample sizes are necessary to understand the mechanistic basis for these changes, as well as to determine the implications they have for brain development and function.
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Affiliation(s)
- Maureen A Malloy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Joseph J Kochmanski
- Department of Translational Science & Molecular Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Tamara R Jones
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Jaclyn M Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Dana C Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
| | - Laurie K Svoboda
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, United States
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32
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Rocco SA, Koneva L, Middleton LYM, Thong T, Solanki S, Karram S, Nambunmee K, Harris C, Rozek LS, Sartor MA, Shah YM, Colacino JA. Cadmium Exposure Inhibits Branching Morphogenesis and Causes Alterations Consistent With HIF-1α Inhibition in Human Primary Breast Organoids. Toxicol Sci 2019; 164:592-602. [PMID: 29741670 DOI: 10.1093/toxsci/kfy112] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Developmental cadmium exposure in vivo disrupts mammary gland differentiation, while exposure of breast cell lines to cadmium causes invasion consistent with the epithelial-mesenchymal transition (EMT). The effects of cadmium on normal human breast stem cells have not been measured. Here, we quantified the effects of cadmium exposure on reduction mammoplasty patient-derived breast stem cell proliferation and differentiation. Using the mammosphere assay and organoid formation in 3D hydrogels, we tested 2 physiologically relevant doses of cadmium, 0.25 and 2.5 µM, and tested for molecular alterations using RNA-seq. We functionally validated our RNA-seq findings with a hypoxia-inducible factor (HIF)-1α activity reporter line and pharmaceutical inhibition of HIF-1α in organoid formation assays. 2.5 µM cadmium reduced primary mammosphere formation and branching structure organoid formation rates by 33% and 87%, respectively. Despite no changes in mammosphere formation, 0.25 µM cadmium inhibited branching organoid formation in hydrogels by 73%. RNA-seq revealed cadmium downregulated genes associated with extracellular matrix formation and EMT, while upregulating genes associated with metal response including metallothioneins and zinc transporters. In the RNA-seq data, cadmium downregulated HIF-1α target genes including LOXL2, ZEB1, and VIM. Cadmium significantly inhibited HIF-1α activity in a luciferase assay, and the HIF-1α inhibitor acriflavine ablated mammosphere and organoid formation. These findings show that cadmium, at doses relevant to human exposure, inhibited human mammary stem cell proliferation and differentiation, potentially through disruption of HIF-1α activity.
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Affiliation(s)
- Sabrina A Rocco
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Lada Koneva
- Department of Computational Medicine and Bioinformatics
| | - Lauren Y M Middleton
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Tasha Thong
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Sumeet Solanki
- Molecular and Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Sarah Karram
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Kowit Nambunmee
- Department of Occupational Health and Safety, Mae Fah Luong University, Chiang Rai, Thailand, 57100
| | - Craig Harris
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029
| | | | - Yatrik M Shah
- Molecular and Integrative Physiology and Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan 48109
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan 48109-2029.,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, 48109
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33
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Hill EM, Esper RM, Sen A, Simon BR, Aslam MN, Jiang Y, Dame MK, McClintock SD, Colacino JA, Djuric Z, Wicha MS, Smith WL, Brenner DE. Dietary polyunsaturated fatty acids modulate adipose secretome and is associated with changes in mammary epithelial stem cell self-renewal. J Nutr Biochem 2019; 71:45-53. [PMID: 31272031 DOI: 10.1016/j.jnutbio.2019.05.007] [Citation(s) in RCA: 3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 05/09/2019] [Accepted: 05/10/2019] [Indexed: 02/07/2023]
Abstract
Chronic low-grade adipose inflammation, characterized by aberrant adipokine production and pro-inflammatory macrophage activation/polarization is associated with increased risk of breast cancer. Adipocyte fatty acid composition is influenced by dietary availability and may regulate adipokine secretion and adipose inflammation. After feeding F344 rats for 20 weeks with a Western diet or a fish oil-supplemented diet, we cultured primary rat adipose tissue in a three-dimensional explant culture and collected the conditioned medium. The rat adipose tissue secretome was assayed using the Proteome Profiler Cytokine XL Array, and adipose tissue macrophage polarization (M1/M2 ratio) was assessed using the iNOS/ARG1 ratio. We then assessed the adipokine's effects upon stem cell self-renewal using primary human mammospheres from normal breast mammoplasty tissue. Adipose from rats fed the fish oil diet had an ω-3:ω-6 fatty acid ratio of 0.28 compared to 0.04 in Western diet rats. The adipokine profile from the fish oil-fed rats was shifted toward adipokines associated with reduced inflammation compared to the rats fed the Western diet. The M1/M2 macrophage ratio decreased by 50% in adipose of fish oil-fed rats compared to that from rats fed the Western diet. Conditioned media from rats fed the high ω-6 Western diet increased stem cell self-renewal by 62%±9% (X¯%±SD) above baseline compared to only an 11%±11% increase with the fish oil rat adipose. Modulating the adipokine secretome with dietary interventions therefore may alter stromal-epithelial signaling that plays a role in controlling mammary stem cell self-renewal.
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Affiliation(s)
- Evan M Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Raymond M Esper
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ananda Sen
- Department of Family Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Becky R Simon
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Muhammad N Aslam
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yan Jiang
- MD Anderson Cancer Center, Houston, TX, USA
| | - Michael K Dame
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shannon D McClintock
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Zora Djuric
- Department of Family Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Max S Wicha
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - William L Smith
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Dean E Brenner
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, USA.
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34
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Gonzalez TL, Rae JM, Colacino JA, Richardson RJ. Homology models of mouse and rat estrogen receptor- α ligand-binding domain created by in silico mutagenesis of a human template: molecular docking with 17ß-estradiol, diethylstilbestrol, and paraben analogs. Comput Toxicol 2019; 10:1-16. [PMID: 30740556 PMCID: PMC6363358 DOI: 10.1016/j.comtox.2018.11.003] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Crystal structures exist for human, but not rodent, estrogen receptor-α ligand-binding domain (ERα-LBD). Consequently, rodent studies involving binding of compounds to ERα-LBD are limited in their molecular-level interpretation and extrapolation to humans. Because the sequences of rodent and human ERα-LBDs are > 95% identical, we expected their 3D structures and ligand binding to be highly similar. To test this hypothesis, we used the human ERα-LBD structure (PDB 3UUD) as a template to produce rat and mouse homology models. Employing the rodent models and human structure, we generated docking poses of 23 Group A ligands (17ß-estradiol, diethylstilbestrol, and 21 paraben analogs) in AutoDock Vina for interspecies comparisons. Ligand RMSDs (Å) (median, 95% CI) were 0.49 (0.21-1.82) (human-mouse) and 1.19 (0.22-1.82) (human-rat), well below the 2.0-2.5 Å range for equivalent docking poses. Numbers of interspecies ligand-receptor residue contacts were highly similar, with Sorensen Sc (%) = 96.8 (90.0-100) (human-mouse) and 97.7 (89.5-100) (human-rat). Likewise, numbers of interspecies ligand-receptor residue contacts were highly correlated: Pearson r = 0.913 (human-mouse) and 0.925 (human-rat). Numbers of interspecies ligand-receptor atom contacts were even more tightly correlated: r = 0.979 (human-mouse) and 0.986 (human-rat). Pyramid plots of numbers of ligand-receptor atom contacts by residue exhibited high interspecies symmetry and had Spearman r s = 0.977 (human-mouse) and 0.966 (human-rat). Group B ligands included 15 ring-substituted parabens recently shown experimentally to exhibit decreased binding to human ERα and to exert increased antimicrobial activity. Ligand efficiencies calculated from docking ligands into human ERα-LBD were well correlated with those derived from published experimental data (Pearson partial r p = 0.894 and 0.918; Groups A and B, respectively). Overall, the results indicate that our constructed rodent ERα-LBDs interact with ligands in like manner to the human receptor, thus providing a high level of confidence in extrapolations of rodent to human ligand-receptor interactions.
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Affiliation(s)
- Thomas L. Gonzalez
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - James M. Rae
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109 USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
| | - Rudy J. Richardson
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Neurology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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35
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Triner D, Devenport SN, Ramakrishnan SK, Ma X, Frieler RA, Greenson JK, Inohara N, Nunez G, Colacino JA, Mortensen RM, Shah YM. Neutrophils Restrict Tumor-Associated Microbiota to Reduce Growth and Invasion of Colon Tumors in Mice. Gastroenterology 2019; 156:1467-1482. [PMID: 30550822 PMCID: PMC6441634 DOI: 10.1053/j.gastro.2018.12.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/26/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Neutrophils are among the most prevalent immune cells in the microenvironment of colon tumors; they are believed to promote growth of colon tumors, and their numbers correlate with outcomes of patients with colon cancer. Trials of inhibitors of neutrophil trafficking are underway in patients with cancer, but it is not clear how neutrophils contribute to colon tumorigenesis. METHODS Colitis-associated colon cancer was induced in mice with conditional deletion of neutrophils (LysMCre;Mcl1fl/fl) and wild-type littermates (LysMCre;Mcl1wt/wt, control mice) by administration of azoxythmethane and/or dextran sulfate sodium. Sporadic colon tumorigenesis was assessed in neutrophil-deficient and neutrophil-replete mice with conditional deletion of colon epithelial Apc (Cdx2-CreERT2;Apcfl/fl). Primary colon tumor tissues from these mice were assessed by histology, RNA sequencing, quantitative polymerase chain reaction, and fluorescence in situ hybridization analyses. Fecal and tumor-associated microbiota were assessed by 16s ribosomal RNA sequencing. RESULTS In mice with inflammation-induced and sporadic colon tumors, depletion of neutrophils increased the growth, proliferation, and invasiveness of the tumors. RNA sequencing analysis identified genes that regulate antimicrobial and inflammatory processes that were dysregulated in neutrophil-deficient colon tumors compared with colon tumors from control mice. Neutrophil depletion correlated with increased numbers of bacteria in tumors and proliferation of tumor cells, tumor-cell DNA damage, and an inflammatory response mediated by interleukin 17 (IL17). The 16s ribosomal RNA sequencing identified significant differences in the composition of the microbiota between colon tumors from neutrophil-deficient vs control mice. Administration of antibiotics or a neutralizing antibody against IL17 to neutrophil-deficient mice resulted in development of less-invasive tumors compared with mice given vehicle. We found bacteria in tumors to induce production of IL17, which promotes influx of intratumor B cells that promote tumor growth and progression. CONCLUSIONS In comparisons of mice with vs without neutrophils, we found neutrophils to slow colon tumor growth and progression by restricting numbers of bacteria and tumor-associated inflammatory responses.
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Affiliation(s)
- Daniel Triner
- Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor MI
| | - Samantha N. Devenport
- Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor MI
| | | | - Xiaoya Ma
- Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor MI
| | - Ryan A. Frieler
- Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor MI
| | - Joel K. Greenson
- Department of Pathology, University of Michigan Medical School, Ann Arbor MI
| | - Naohiro Inohara
- Department of Pathology, University of Michigan Medical School, Ann Arbor MI
| | - Gabriel Nunez
- Department of Pathology, University of Michigan Medical School, Ann Arbor MI,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor MI
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor MI,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor MI
| | - Richard M. Mortensen
- Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor MI,Internal Medicine Division of Metabolism, Endocrinology, and Diabetes, University of Michigan Medical School, Ann Arbor MI
| | - Yatrik M. Shah
- Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor MI,Internal Medicine Division of Gastroenterology, University of Michigan Medical School, Ann Arbor MI,Rogel Cancer Center, University of Michigan Medical School, Ann Arbor MI
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36
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Gonzalez TL, Rae JM, Colacino JA. Implication of environmental estrogens on breast cancer treatment and progression. Toxicology 2019; 421:41-48. [PMID: 30940549 DOI: 10.1016/j.tox.2019.03.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 10/01/2018] [Revised: 03/05/2019] [Accepted: 03/28/2019] [Indexed: 12/22/2022]
Abstract
Breast cancer is the most diagnosed malignancy among women in the United States. Approximately 70% of breast tumors express estrogen receptor alpha and are deemed ER-positive. ER-positive breast tumors depend upon endogenous estrogens to promote ER-mediated cellular proliferation. Decades of research have led to a fundamental understanding of the role ER signaling in this disease and this knowledge has led to significant advancements in the clinical use of antiestrogens for breast cancer treatment. However, adjuvant breast cancer recurrence and metastatic disease progression due to endocrine therapy resistance are prominent and unresolved issues. The established role that estrogens play in breast cancer pathogenesis explains why some patients initially respond to endocrine therapy but also why a significant number of patients become refractory to antiestrogen treatment. It is been hypothesized that exposure to environmental steroid hormone mimics and/or acquired mechanisms of resistance may explain why endocrine therapy fails in a subset of breast cancer patients. This review will highlight: 1) the relationship between ER signaling and breast cancer pathogenesis, 2) the implication of environmental exposures on steroid hormone regulated processes including breast cancer, and 3) the unresolved issue of endocrine therapy resistance.
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Affiliation(s)
- Thomas L Gonzalez
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA.
| | - James M Rae
- Division of Hematology/ Oncology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109, USA; Department of Pharmacology, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA; Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, 48109, USA; Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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37
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Ben-Yosef O, Burns JS, Colacino JA, Kota DJ, Péault B. Ask the experts: current obstacles and future developments in cell culture. Regen Med 2019; 14:145-150. [PMID: 30887896 DOI: 10.2217/rme-2019-0029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Oren Ben-Yosef
- Biological Industries Israel Beit Haemek Ltd, BeitHaemek, 25115, Israel
| | - Jorge S Burns
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania.,Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena and Reggio Emilia, Modena, Italy
| | - Justin A Colacino
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA.,Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Daniel J Kota
- Emory Personalized Immunotherapy Core Labs, Emory University, School of Medicine, Atlanta, GA 30322, USA
| | - Bruno Péault
- MRC Center for Regenerative Medicine, University of Edinburgh, Edinburgh, UK.,UCLA and Orthopaedic Hospital Department of Orthopaedic Surgery, Orthopaedic Hospital Research Center, Los Angeles, CA 90095, USA
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38
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Bakulski KM, Dou J, Lin N, London SJ, Colacino JA. DNA methylation signature of smoking in lung cancer is enriched for exposure signatures in newborn and adult blood. Sci Rep 2019; 9:4576. [PMID: 30872662 PMCID: PMC6418160 DOI: 10.1038/s41598-019-40963-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 09/21/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
Smoking impacts DNA methylation genome-wide in blood of newborns from maternal smoking during pregnancy and adults from personal smoking. We compared smoking-related DNA methylation in lung adenocarcinoma (61 never smokers, 91 current smokers, and 238 former smokers) quantified with the Illumina450k BeadArray in The Cancer Genome Atlas with published large consortium meta-analyses of newborn and adult blood. We assessed whether CpG sites related to smoking in blood from newborns and adults were enriched in the lung adenocarcinoma methylation signal. Testing CpGs differentially methylated by smoke exposure, we identified 296 in lung adenocarcinoma meeting a P < 10-4 cutoff, while previous meta-analyses identified 3,042 in newborn blood, and 8,898 in adult blood meeting the same P < 10-4 cutoff. Lung signals were highly enriched for those seen in newborn (24 overlapping CpGs, Penrichment = 1.2 × 10-18) and adult blood (66 overlapping CpGs, Penrichment = 1.2 × 10-48). The 105 genes annotated to CpGs differentially methylated in lung tumors, but not blood, were enriched for RNA processing ontologies. Some epigenetic alterations associated with cigarette smoke exposure are tissue specific, but others are common across tissues. These findings support the value of blood-based methylation biomarkers for assessing exposure effects in target tissues.
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Affiliation(s)
- K M Bakulski
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA.
| | - J Dou
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - N Lin
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - S J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina, USA
| | - J A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
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Ramakrishnan SK, Zhang H, Ma X, Jung I, Schwartz AJ, Triner D, Devenport SN, Das NK, Xue X, Zeng MY, Hu Y, Mortensen RM, Greenson JK, Cascalho M, Wobus CE, Colacino JA, Nunez G, Rui L, Shah YM. Intestinal non-canonical NFκB signaling shapes the local and systemic immune response. Nat Commun 2019; 10:660. [PMID: 30737385 PMCID: PMC6368617 DOI: 10.1038/s41467-019-08581-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 01/21/2019] [Indexed: 12/13/2022] Open
Abstract
Microfold cells (M-cells) are specialized cells of the intestine that sample luminal microbiota and dietary antigens to educate the immune cells of the intestinal lymphoid follicles. The function of M-cells in systemic inflammatory responses are still unclear. Here we show that epithelial non-canonical NFkB signaling mediated by NFkB-inducing kinase (NIK) is highly active in intestinal lymphoid follicles, and is required for M-cell maintenance. Intestinal NIK signaling modulates M-cell differentiation and elicits both local and systemic IL-17A and IgA production. Importantly, intestinal NIK signaling is active in mouse models of colitis and patients with inflammatory bowel diseases; meanwhile, constitutive NIK signaling increases the susceptibility to inflammatory injury by inducing ectopic M-cell differentiation and a chronic increase of IL-17A. Our work thus defines an important function of non-canonical NFkB and M-cells in immune homeostasis, inflammation and polymicrobial sepsis. Microfold cells (M-cell) are specialized cells of the intestine that sample luminal microbiota and dietary antigens. Here the authors show that epithelial non-canonical NFκB signalling, as induced by NIK, is important for M-cells maintenance, yet constitutive NIK activation is associated with gut inflammation and inflammatory bowel disease.
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Affiliation(s)
| | - Huabing Zhang
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Xiaoya Ma
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Inkyung Jung
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Andrew J Schwartz
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Daniel Triner
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Samantha N Devenport
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Nupur K Das
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Xiang Xue
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Melody Y Zeng
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.,Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yinling Hu
- Cancer and Inflammation Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, 21702, USA
| | - Richard M Mortensen
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA
| | - Joel K Greenson
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Marilia Cascalho
- Transplantation Biology, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Surgery, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Nutritional Sciences, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Gabriel Nunez
- Department of Pathology, University of Michigan, Ann Arbor, MI, 48109, USA.,Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Liangyou Rui
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA.,Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Michigan, MI, 48109, USA. .,Internal Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.
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40
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Nguyen VK, Colacino JA, Arnot JA, Kvasnicka J, Jolliet O. Characterization of age-based trends to identify chemical biomarkers of higher levels in children. Environ Int 2019; 122:117-129. [PMID: 30528102 PMCID: PMC6903703 DOI: 10.1016/j.envint.2018.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 05/30/2018] [Revised: 10/01/2018] [Accepted: 10/21/2018] [Indexed: 05/25/2023]
Abstract
BACKGROUND Chemical biomarker concentrations are driven by complex interactions between chemical use patterns, exposure pathways, and toxicokinetic parameters such as biological half-lives. Criteria to differentiate legacy from current exposures are helpful for interpreting variation in age-based and time trends of chemical exposure and identifying chemicals to which children are highly exposed. A systematic approach is needed to study temporal trends for a wide range of chemicals in the US population. OBJECTIVES Using National Health and Nutrition Examination Survey (NHANES) data on measured biomarker concentrations for 141 chemicals from 1999 to 2014, we aim to 1) understand the influence of temporal determinants, in particular time trends, biological half-lives, and restriction dates on age-based trends, 2) systematically define an age-based pattern to identify chemicals with ongoing and high exposure in children, and 3) characterize how age-based trends for six Per- and Polyfluoroalkyl Substances (PFASs) are changing over time. METHODS We performed an integrated analysis of biological half-lives and restriction dates, compared distributions of chemical biomarker concentrations by age group, and then applied a series of regression models to evaluate the linear (βage) and nonlinear (βage2) relationships between age and chemical biomarker levels. RESULTS For restricted chemicals, a minimum persistence of 1 year in the human body is needed to observe substantial differences between the less exposed young population and historically exposed adults. We define a metric ( [Formula: see text] ) that identifies several phthalates, brominated flame retardants, pesticides, and metals such as lead and tungsten as elevated and ongoing exposures in children. While a substantial reduction in children's exposures was reflected in PFOS and PFOA, levels of PFNA and PFHxS in children were higher in 2013-2014 compared to those in 1999-2000. CONCLUSIONS Integrating a series of regression models with systemized stratified analyses by age group enabled us to define an age-based pattern to identify chemicals that are of higher levels in children.
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Affiliation(s)
- Vy Kim Nguyen
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA.
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA; Department of Nutritional Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jon A Arnot
- ARC Arnot Research & Consulting Inc, Toronto, Ontario, Canada
| | - Jacob Kvasnicka
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Olivier Jolliet
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, Medical School, University of Michigan, Ann Arbor, MI, USA
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41
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Wang T, Pehrsson EC, Purushotham D, Li D, Zhuo X, Zhang B, Lawson HA, Province MA, Krapp C, Lan Y, Coarfa C, Katz TA, Tang WY, Wang Z, Biswal S, Rajagopalan S, Colacino JA, Tsai ZTY, Sartor MA, Neier K, Dolinoy DC, Pinto J, Hamanaka RB, Mutlu GM, Patisaul HB, Aylor DL, Crawford GE, Wiltshire T, Chadwick LH, Duncan CG, Garton AE, McAllister KA, Bartolomei MS, Walker CL, Tyson FL. The NIEHS TaRGET II Consortium and environmental epigenomics. Nat Biotechnol 2018; 36:225-227. [PMID: 29509741 DOI: 10.1038/nbt.4099] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ting Wang
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erica C Pehrsson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Deepak Purushotham
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Daofeng Li
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Xiaoyu Zhuo
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA.,The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Bo Zhang
- Center for Regenerative Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Heather A Lawson
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael A Province
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Christopher Krapp
- Epigenetics Institute, Center for Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yemin Lan
- Epigenetics Institute, Center for Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Tiffany A Katz
- Center for Precision Environmental Health, Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Wan Yee Tang
- Department of Environmental Health Sciences, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Zhibin Wang
- Department of Environmental Health Sciences, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Shyam Biswal
- Department of Environmental Health Sciences, Johns Hopkins School of Public Health, Baltimore, Maryland, USA
| | - Sanjay Rajagopalan
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Zing Tsung-Yeh Tsai
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Maureen A Sartor
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Kari Neier
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Dana C Dolinoy
- Department of Environmental Health Sciences and Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Jayant Pinto
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Robert B Hamanaka
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Gokhan M Mutlu
- Department of Medicine, The University of Chicago, Chicago, Illinois, USA
| | - Heather B Patisaul
- Department of Biological Sciences, Center for Human Health and the Environment, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - David L Aylor
- Department of Biological Sciences, Center for Human Health and the Environment, Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina, USA
| | - Gregory E Crawford
- Center for Genomic & Computational Biology, Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, North Carolina, USA
| | - Tim Wiltshire
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, Chapel Hill, North Carolina, USA
| | - Lisa H Chadwick
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Christopher G Duncan
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Amanda E Garton
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Kimberly A McAllister
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | | | - Marisa S Bartolomei
- Epigenetics Institute, Center for Excellence in Environmental Toxicology, Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Departments of Molecular & Cellular Biology and Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Frederick L Tyson
- Genes Environment and Health Branch, Division of Extramural Research and Training, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
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Schwartz AJ, Das NK, Ramakrishnan SK, Jain C, Jurkovic MT, Wu J, Nemeth E, Lakhal-Littleton S, Colacino JA, Shah YM. Hepatic hepcidin/intestinal HIF-2α axis maintains iron absorption during iron deficiency and overload. J Clin Invest 2018; 129:336-348. [PMID: 30352047 DOI: 10.1172/jci122359] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 10/16/2018] [Indexed: 01/22/2023] Open
Abstract
Iron-related disorders are among the most prevalent diseases worldwide. Systemic iron homeostasis requires hepcidin, a liver-derived hormone that controls iron mobilization through its molecular target ferroportin (FPN), the only known mammalian iron exporter. This pathway is perturbed in diseases that cause iron overload. Additionally, intestinal HIF-2α is essential for the local absorptive response to systemic iron deficiency and iron overload. Our data demonstrate a hetero-tissue crosstalk mechanism, whereby hepatic hepcidin regulated intestinal HIF-2α in iron deficiency, anemia, and iron overload. We show that FPN controlled cell-autonomous iron efflux to stabilize and activate HIF-2α by regulating the activity of iron-dependent intestinal prolyl hydroxylase domain enzymes. Pharmacological blockade of HIF-2α using a clinically relevant and highly specific inhibitor successfully treated iron overload in a mouse model. These findings demonstrate a molecular link between hepatic hepcidin and intestinal HIF-2α that controls physiological iron uptake and drives iron hyperabsorption during iron overload.
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Affiliation(s)
| | - Nupur K Das
- Department of Molecular and Integrative Physiology, and
| | | | - Chesta Jain
- Department of Molecular and Integrative Physiology, and
| | | | - Jun Wu
- Department of Molecular and Integrative Physiology, and.,Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Elizabeta Nemeth
- Department of Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
| | - Samira Lakhal-Littleton
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, and.,Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, Michigan, USA
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43
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Muñoz I, Colacino JA, Lewis RC, Arthur AE, Meeker JD, Ferguson KK. Associations between school lunch consumption and urinary phthalate metabolite concentrations in US children and adolescents: Results from NHANES 2003-2014. Environ Int 2018; 121:287-295. [PMID: 30223205 PMCID: PMC6221921 DOI: 10.1016/j.envint.2018.09.009] [Citation(s) in RCA: 4] [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] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 09/04/2018] [Accepted: 09/06/2018] [Indexed: 05/05/2023]
Abstract
Diet is a major route of phthalate exposure in humans due to use in food packaging materials. School lunches may be an important contributor to phthalate exposure in children and adolescents in the US because of the large amount of packaging necessary for mass-produced foods. We used 2003-2014 National Health and Nutrition Examination Survey data to study the association between school lunch consumption and urinary phthalate metabolite concentrations in children (ages 6-11 years, N = 2196) and adolescents (ages 12-19 years, N = 2314). After adjustment for other covariates, children who Always consumed school lunch had significantly elevated urinary concentrations of the following phthalate metabolites compared to levels in children who Never ate school lunch: sum of di(2‑ethylhexyl) phthalate metabolites, (28% higher, 95% confidence interval, CI: 10, 49%); mono‑(carboxy‑octyl) phthalate (MCOP; 43% higher, 95% CI: 17, 76%) and mono‑n‑butyl phthalate (18% higher, 95% CI: 3.5, 34%). We did not find statistically significant associations in adolescents, but the trend for MCOP concentrations was similar to that of children. In sensitivity analyses, associations between 24-hour recall of cafeteria food and urinary phthalate metabolites were not statistically significant, which could indicate that associations observed with Always consuming school lunch are due to residual confounding. Our findings show that children who Always eat school lunch had higher levels of exposure to some phthalates, but the source of differences in exposure need to be evaluated in additional studies.
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Affiliation(s)
- Isabel Muñoz
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Division of Epidemiology, School of Public Health, University of California, Berkeley, CA, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Ryan C Lewis
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Anna E Arthur
- Department of Food Science and Human Nutrition, Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA; Carle Cancer Center, Carle Foundation Hospital, Urbana, IL, USA
| | - John D Meeker
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kelly K Ferguson
- Epidemiology Branch, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA; Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.
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44
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Defever K, Rentschler KM, Khazan A, Pinkerton E, Virani S, Sriplung H, Pang J, Kleer CG, Leon CFMD, Colacino JA, Rozek LS. Abstract 4219: Breast cancer distribution and survival among Buddhist and Muslim women in southern Thailand. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4219] [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
Objective: Thailand is undergoing a period of rapid economic growth, which has led to an epidemiologic transition from infectious to chronic diseases such as cancer. Preliminary research shows a difference in rates of breast cancer incidence and mortality between Buddhist and Muslim women in southern Thailand. This study examines differences in breast cancer and potential explanations for this disparity. Methods: Demographic, diagnostic, and outcome data from breast cancer patients diagnosed from 2001-2015 were collected from a population-based cancer registry in southern Thailand and matched with formalin-fixed paraffin-embedded blocks from Songklanagarind Hospital. This region was selected due to the relatively high proportion of Muslim women. Of 424 cases selected, 369 were Buddhist and 55 were Muslim. Formalin-fixed paraffin-embedded blocks were sent to Michigan Medicine and histological and subtype analyses were performed by two pathologists. Statistical analysis was performed in RStudio using chi-square tests of independence, logistic regression, and Cox proportional hazards models. Results: Muslim women were generally diagnosed at a younger age than Buddhist women (Muslim mean: 46.6 years, Buddhist mean: 52.7 years) and with later stage cancers (Muslim: 36% stage 3 and 14% stage 4, Buddhist: 20% stage 3 and 8% stage 4). Buddhist and Muslim women had similar distributions of Luminal A and B subtypes, but Muslim women were more likely to be diagnosed with Triple Negative breast cancer (Muslim: 30%, Buddhist: 18%), the histological subtype with the worst prognosis. Invasive ductal carcinoma was most common in both groups, but Buddhists had more heterogeneity in subtypes. There were no significant differences in tumor histology or subtype by religion. Conclusions: These analyses show differences in the distribution of breast cancer between Buddhist and Muslim women. Muslim women are diagnosed younger with later stage breast cancers, and with histological differences, which generally lead to lower survival rates. Lack of statistical significance may be due to small sample size, necessitating further studies.
Citation Format: Kali Defever, Katie M. Rentschler, Ana Khazan, Elizabeth Pinkerton, Shama Virani, Hutcha Sriplung, Judy Pang, Celina G. Kleer, Carlos F. Mendes de Leon, Justin A. Colacino, Laura S. Rozek. Breast cancer distribution and survival among Buddhist and Muslim women in southern Thailand [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4219.
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Affiliation(s)
| | | | | | | | - Shama Virani
- 2Prince of Songkla University, Hat Yai, Thailand
| | | | - Judy Pang
- 1University of Michigan, Ann Arbor, MI
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45
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McClintock SD, Colacino JA, Attili D, Dame MK, Rizvi AH, Richter A, Reddy AR, Basrur V, Turgeon DK, Varani J, Aslam MN. Abstract 1276: Differentiation of human colon adenomas in an enteroid culture: A treatment comparison. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-1276] [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
Introduction: Previous murine studies have demonstrated that dietary Aquamin®, a calcium-rich, multi-mineral natural product, suppressed colon polyp formation and transition to invasive tumors more effectively than calcium alone when provided over the lifespan of the animals.
Methods: In the present study, we compared Aquamin® to calcium for modulation of growth and differentiation in human colon adenomas in enteroid culture. Adenoma growth and differentiation were assessed at the light and electron microscopic levels and by immunostaining. Image quantitation of immunohistochemical markers was performed using Aperio Imagescope to compare these interventions. A proteomic assessment was done to compare protein expression patterns in treated cultures as compared to cultures maintained under control conditions (calcium 0.15 mM). Enteroids established from normal colonic tissue were examined in parallel.
Results: Both calcium and Aquamin® provided at 1.5 mM calcium fostered differentiation in the adenoma enteroid cultures as compared to control, but Aquamin® was more effective. Even at a concentration providing only 0.15 mM calcium, Aquamin® induced differentiation in some individual enteroids. Aquamin® was more effective than calcium in inducing upregulation of proteins. There were 35 proteins upregulated with Aquamin as compared to 20 with calcium 1.5mM at 1.8-fold change or above (in 3 colonic adenomas) with less than 2% FDR. Both calcium and Aquamin® induced differences in the expression pattern of proteins known to be involved in differentiation (table). In addition, several keratins and histones, as well as merlin and Olfactomedin-4 were upregulated.
Conclusion: These findings support that i) calcium (1.5 mM) has the capacity to modulate growth and differentiation in large human colon adenomas and ii) the additional trace elements provided along with calcium in Aquamin® can have effects on proliferation and differentiation at lower levels than observed with calcium at 1.5mM.
Expression of Immunohistochemical Markers in enteroid cultures of Human Adenomas (Fold-Changes)IHC MarkersCalcium 0.15mMAquamin 0.15mMCalcium 1.5mMAquamin 1.5mMKi6710.750.59*0.49*CK2012.13*2.36*2.35*E-Cadherin11.051.57*1.57*NF2 (Merlin)12.44*#1.012.56*#Occludin11.23*1.25*1.29**reflects significance as compared to Ca 0.15mM. #reflects significance as compared to Ca 1.5mM
Citation Format: Shannon D. McClintock, Justin A. Colacino, Durga Attili, Michael K. Dame, Areeba H. Rizvi, Aliah Richter, Anusha R. Reddy, Venkatesha Basrur, D. Kim Turgeon, James Varani, Muhammad N. Aslam. Differentiation of human colon adenomas in an enteroid culture: A treatment comparison [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1276.
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46
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Tsai YH, Czerwinski M, Wu A, Dame MK, Attili D, Hill E, Colacino JA, Nowacki LM, Shroyer NF, Higgins PD, Kao JY, Spence JR. A Method for Cryogenic Preservation of Human Biopsy Specimens and Subsequent Organoid Culture. Cell Mol Gastroenterol Hepatol 2018; 6:218-222.e7. [PMID: 30105282 PMCID: PMC6085494 DOI: 10.1016/j.jcmgh.2018.04.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 04/23/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Yu-Hwai Tsai
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Michael Czerwinski
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Angeline Wu
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Michael K. Dame
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Durga Attili
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Evan Hill
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Lauren Marie Nowacki
- Division of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas
| | - Noah F. Shroyer
- Division of Medicine, Section of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas,Department of Medicine and Dan L. Duncan Cancer, Baylor College of Medicine, Houston, Texas,Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, Texas
| | - Peter D.R. Higgins
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan
| | - John Y. Kao
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Jason R. Spence
- Department of Internal Medicine, Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan,Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, Michigan,Center for Organogenesis, University of Michigan Medical School, Ann Arbor, Michigan,Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, Michigan,Corresponding author:
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47
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Virani S, Wetzel EC, Laohawiriyakamol S, Boonyaphiphat P, Geater A, Kleer CG, Pang J, Rentschler KM, Colacino JA, de Leon CFM, Rozek LS, Sriplung H. Ethnic disparity in breast cancer survival in southern Thai women. Cancer Epidemiol 2018; 54:82-89. [PMID: 29684800 DOI: 10.1016/j.canep.2018.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 10/31/2017] [Revised: 02/18/2018] [Accepted: 02/21/2018] [Indexed: 11/17/2022]
Abstract
BACKGROUND Breast cancer has the highest incidence in women of all cancers and its burden is expected to continue to increase worldwide, especially in middle-income countries such as Thailand. The southern region of Thailand is unique in that it is comprised of 30% Muslims, whereas the rest of Thailand is 95% Buddhist. Breast cancer incidence and survival differ between these religious groups, but the association between clinical subtype of breast cancer and survival has not yet been assessed. METHODS Here we characterized differences in breast cancer survival with consideration to clinical subtype by religious group (Muslim Thai and Buddhist Thai women). We compared distributions of age, stage and clinical subtype and assessed overall survival by religion. RESULTS Our findings show that Muslim Thai women with breast cancer are diagnosed at a younger age, at later stages and have shorter overall survival times compared to Buddhist Thai women with breast cancer. We also observe a higher proportion of triple negative tumors characterized in Muslim Thai women. CONCLUSIONS Our findings confirm previous studies that have shown lower survival rates in Muslim Thai women compared to Buddhist women with breast cancer and offer novel information on subtype distribution. To date, this is the first study assessing clinical subtypes in southern Thailand by religious status. IMPACT Our findings are critical in providing information on the role of clinical subtype in cancer disparities and provide evidence from the Southeast Asian region for global studies on breast cancer survival.
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Affiliation(s)
- Shama Virani
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Elizabeth C Wetzel
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | | | - Pleumjit Boonyaphiphat
- Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Alan Geater
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Celina G Kleer
- Department of Pathology University of Michigan, Ann Arbor, MI USA
| | - Judy Pang
- Department of Pathology University of Michigan, Ann Arbor, MI USA
| | - Katie M Rentschler
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI USA
| | - Carlos F Mendes de Leon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, School of Public Health, University of Michigan, Ann Arbor, MI USA.
| | - Hutcha Sriplung
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
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48
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McClintock SD, Colacino JA, Attili D, Dame MK, Richter A, Reddy AR, Basrur V, Rizvi AH, Turgeon DK, Varani J, Aslam MN. Calcium-Induced Differentiation of Human Colon Adenomas in Colonoid Culture: Calcium Alone versus Calcium with Additional Trace Elements. Cancer Prev Res (Phila) 2018; 11:413-428. [PMID: 29636350 DOI: 10.1158/1940-6207.capr-17-0308] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 12/27/2017] [Accepted: 04/06/2018] [Indexed: 01/02/2023]
Abstract
Previous murine studies have demonstrated that dietary Aquamin, a calcium-rich, multi-mineral natural product, suppressed colon polyp formation and transition to invasive tumors more effectively than calcium alone when provided over the lifespan of the animals. In the current study, we compared calcium alone to Aquamin for modulation of growth and differentiation in human colon adenomas in colonoid culture. Colonoids established from normal colonic tissue were examined in parallel. Both calcium alone at 1.5 mmol/L and Aquamin (provided at 1.5 mmol/L calcium) fostered differentiation in the adenoma colonoid cultures as compared with control (calcium at 0.15 mmol/L). When Aquamin was provided at an amount delivering 0.15 mmol/L calcium, adenoma differentiation also occurred, but was not as complete. Characteristic of colonoids undergoing differentiation was a reduction in the number of small, highly proliferative buds and their replacement by fewer but larger buds with smoother surface. Proliferation marker (Ki67) expression was reduced and markers of differentiation (CK20 and occludin) were increased along with E-cadherin translocalization to the cell surface. Additional proteins associated with differentiation/growth control [including histone-1 family members, certain keratins, NF2 (merlin), olfactomedin-4 and metallothioneins] were altered as assessed by proteomics. Immunohistologic expression of NF2 was higher with Aquamin as compared with calcium at either concentration. These findings support the conclusions that (i) calcium (1.5 mmol/L) has the capacity to modulate growth and differentiation in large human colon adenomas and (ii) Aquamin delivering 0.15 mmol/L calcium has effects on proliferation and differentiation not observed when calcium is used alone at this concentration. Cancer Prev Res; 11(7); 413-28. ©2018 AACR.
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Affiliation(s)
- Shannon D McClintock
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - Justin A Colacino
- Department of Environmental Health Sciences and Nutritional Sciences, The University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Durga Attili
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - Michael K Dame
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - Aliah Richter
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - Anusha R Reddy
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - Venkatesha Basrur
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - Areeba H Rizvi
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - D Kim Turgeon
- Department of Internal Medicine, The University of Michigan Medical School, Ann Arbor, Michigan
| | - James Varani
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan
| | - Muhammad N Aslam
- Department of Pathology, The University of Michigan Medical School, Ann Arbor, Michigan.
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49
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Colacino JA, Azizi E, Brooks MD, Harouaka R, Fouladdel S, McDermott SP, Lee M, Hill D, Madden J, Boerner J, Cote ML, Sartor MA, Rozek LS, Wicha MS. Heterogeneity of Human Breast Stem and Progenitor Cells as Revealed by Transcriptional Profiling. Stem Cell Reports 2018; 10:1596-1609. [PMID: 29606612 PMCID: PMC5995162 DOI: 10.1016/j.stemcr.2018.03.001] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [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: 03/13/2017] [Revised: 02/28/2018] [Accepted: 03/01/2018] [Indexed: 01/10/2023] Open
Abstract
During development, the mammary gland undergoes extensive remodeling driven by stem cells. Breast cancers are also hierarchically organized and driven by cancer stem cells characterized by CD44+CD24low/− or aldehyde dehydrogenase (ALDH) expression. These markers identify mesenchymal and epithelial populations both capable of tumor initiation. Less is known about these populations in non-cancerous mammary glands. From RNA sequencing, ALDH+ and ALDH−CD44+CD24− human mammary cells have epithelial-like and mesenchymal-like characteristics, respectively, with some co-expressing ALDH+ and CD44+CD24− by flow cytometry. At the single-cell level, these cells have the greatest mammosphere-forming capacity and express high levels of stemness and epithelial-to-mesenchymal transition-associated genes including ID1, SOX2, TWIST1, and ZEB2. We further identify single ALDH+ cells with a hybrid epithelial/mesenchymal phenotype that express genes associated with aggressive triple-negative breast cancers. These results highlight single-cell analyses to characterize tissue heterogeneity, even in marker-enriched populations, and identify genes and pathways that define this heterogeneity. Isolation and RNA-seq of ALDH+ and CD44+CD24− breast cells Unlike in cancer, there is substantial overlap in ALDH+ and CD44+CD24− populations Single-cell analysis of ALDH+ cells identifies unexpected subpopulation structure Hybrid epithelial/mesenchymal ALDH+ cells have a cancer-like expression signature
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Affiliation(s)
- Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA.
| | - Ebrahim Azizi
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael D Brooks
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Ramdane Harouaka
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shamileh Fouladdel
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Sean P McDermott
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Michael Lee
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - David Hill
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Julie Madden
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Julie Boerner
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Michele L Cote
- Department of Oncology, Wayne State University School of Medicine, Detroit, MI, USA; Population Sciences and Health Disparities Program, Karmanos Cancer Institute, Detroit, MI, USA
| | - Maureen A Sartor
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Laura S Rozek
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Max S Wicha
- Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA.
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50
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Dame MK, Attili D, McClintock SD, Dedhia PH, Ouillette P, Hardt O, Chin AM, Xue X, Laliberte J, Katz EL, Newsome GM, Hill DR, Miller AJ, Tsai YH, Agorku D, Altheim CH, Bosio A, Simon B, Samuelson LC, Stoerker JA, Appelman HD, Varani J, Wicha MS, Brenner DE, Shah YM, Spence JR, Colacino JA. Identification, isolation and characterization of human LGR5-positive colon adenoma cells. Development 2018; 145:dev.153049. [PMID: 29467240 DOI: 10.1242/dev.153049] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [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: 04/04/2017] [Accepted: 02/06/2018] [Indexed: 01/02/2023]
Abstract
The intestine is maintained by stem cells located at the base of crypts and distinguished by the expression of LGR5. Genetically engineered mouse models have provided a wealth of information about intestinal stem cells, whereas less is known about human intestinal stem cells owing to difficulty detecting and isolating these cells. We established an organoid repository from patient-derived adenomas, adenocarcinomas and normal colon, which we analyzed for variants in 71 colorectal cancer (CRC)-associated genes. Normal and neoplastic colon tissue organoids were analyzed by immunohistochemistry and fluorescent-activated cell sorting for LGR5. LGR5-positive cells were isolated from four adenoma organoid lines and were subjected to RNA sequencing. We found that LGR5 expression in the epithelium and stroma was associated with tumor stage, and by integrating functional experiments with LGR5-sorted cell RNA sequencing data from adenoma and normal organoids, we found correlations between LGR5 and CRC-specific genes, including dickkopf WNT signaling pathway inhibitor 4 (DKK4) and SPARC-related modular calcium binding 2 (SMOC2). Collectively, this work provides resources, methods and new markers to isolate and study stem cells in human tissue homeostasis and carcinogenesis.
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Affiliation(s)
- Michael K Dame
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Durga Attili
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | | | - Priya H Dedhia
- Department of Surgery, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter Ouillette
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olaf Hardt
- Miltenyi Biotec GmbH, Bergisch Gladbach, 51429, Germany
| | - Alana M Chin
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiang Xue
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Julie Laliberte
- Department of Research and Development, Progenity, Inc., Ann Arbor, MI 48109, USA
| | - Erica L Katz
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Gina M Newsome
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Alyssa J Miller
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yu-Hwai Tsai
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - David Agorku
- Miltenyi Biotec GmbH, Bergisch Gladbach, 51429, Germany
| | - Christopher H Altheim
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andreas Bosio
- Miltenyi Biotec GmbH, Bergisch Gladbach, 51429, Germany
| | - Becky Simon
- BioCentury Publications, Redwood City, CA 94065, USA
| | - Linda C Samuelson
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jay A Stoerker
- Department of Research and Development, Progenity, Inc., Ann Arbor, MI 48109, USA
| | - Henry D Appelman
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - James Varani
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Max S Wicha
- Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Dean E Brenner
- Department of Internal Medicine, Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yatrik M Shah
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Justin A Colacino
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA .,Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
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