1
|
Arian C, Mahony EO, MacDonald JW, Bammler TK, Donowitz M, Kelly EJ, Thummel KE. Human Enteroid Monolayers: A Novel, Functionally-Stable Model for Investigating Oral Drug Disposition. Drug Metab Dispos 2024:DMD-AR-2023-001551. [PMID: 38744527 DOI: 10.1124/dmd.124.001551] [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: 01/25/2024] [Revised: 04/03/2024] [Accepted: 04/18/2024] [Indexed: 05/16/2024] Open
Abstract
To further the development of an in vitro model which faithfully recapitulates drug disposition of orally administered drugs, we investigated the utility of human enteroid monolayers to simultaneously assess intestinal drug absorption and first-pass metabolism processes. We cultured human enteroid monolayers from three donors, derived via biopsies containing duodenal stem cells that were propagated and then differentiated atop permeable Transwell® inserts, and confirmed transformation into a largely enterocyte population via RNA-seq analysis and immunocytochemical (ICC) assays. Proper cell morphology was assessed and confirmed via bright field microscopy and ICC imaging of tight junction proteins and other apically and basolaterally localized proteins. Enteroid monolayer barrier integrity was demonstrated by elevated transepithelial electrical resistance (TEER) that stabilized after 10 days in culture and persisted for 42 days. These results were corroborated by low paracellular transport probe permeability at 7 and 21 days in culture. The activity of a prominent drug metabolizing enzyme, CYP3A, was confirmed at 7, 21, and 42 days culture under basal, 1α,25(OH)2 vitamin D3-induced, and 6',7'-dihydroxybergamottin-inhibited conditions. The duration of these experiments is particularly noteworthy, as this is the first study assessing drug metabolizing enzymes and transporters (DMET) expression/function for enteroids cultured for greater than 12 days. The sum of these results suggests enteroid monolayers are a promising ex vivo model to investigate and quantitatively predict an orally administered drug's intestinal absorption and/or metabolism. Significance Statement This study presents a novel ex vivo model of the human intestine, human intestinal organoid (enteroid) monolayers, that maintain barrier function and metabolic functionality for up to 42-days in culture. The incorporation of both barrier integrity and metabolic function over an extended period within the same model is an advancement over historically used in vitro systems, which either lack one or both of these attributes or have limited viability.
Collapse
Affiliation(s)
- Christopher Arian
- Department of Pharmaceutics, University of Washington, United States
| | | | | | | | | | | | - Kenneth E Thummel
- Department of Pharmaceutics, University of Washington, United States
| |
Collapse
|
2
|
Barrett ES, Sullivan A, Workman T, Zhang Y, Loftus CT, Szpiro AA, Paquette A, MacDonald JW, Coccia M, Smith R, Bowman M, Smith A, Derefinko K, Nguyen RHN, Zhao Q, Sathyanarayana S, Karr C, LeWinn KZ, Bush NR. Sex-specific associations between placental corticotropin releasing hormone and problem behaviors in childhood. Psychoneuroendocrinology 2024; 163:106994. [PMID: 38387218 DOI: 10.1016/j.psyneuen.2024.106994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024]
Abstract
Placental corticotropin-releasing hormone (pCRH) is a neuroactive peptide produced in high concentrations in mid-late pregnancy, during key periods of fetal brain development. Some evidence suggests that higher pCRH exposure during gestation is associated with adverse neurodevelopment, particularly in female offspring. In 858 mother-child dyads from the sociodemographically diverse CANDLE cohort (Memphis, TN), we examined: (1) the slope of pCRH rise in mid-late pregnancy and (2) estimated pCRH at delivery as a measure of cumulative prenatal exposure. When children were 4 years-old, mothers reported on problem behaviors using the Child Behavior Checklist (CBCL) and cognitive performance was assessed by trained psychologists using the Stanford-Binet Intelligence Scales. We fitted linear regression models examining pCRH in relation to behavioral and cognitive performance measures, adjusting for covariates. Using interaction models, we evaluated whether associations differed by fetal sex, breastfeeding, and postnatal neighborhood opportunity. In the full cohort, log-transformed pCRH measures were not associated with outcomes; however, we observed sex differences in some models (interaction p-values≤0.01). In male offspring, an interquartile (IQR) increase in pCRH slope (but not estimated pCRH at delivery), was positively associated with raw Total (β=3.06, 95%CI: 0.40, 5.72), Internalizing (β=0.89, 95%CI: 0.03, 1.76), and Externalizing (β=1.25, 95%CI: 0.27, 2.22) Problem scores, whereas, in females, all associations were negative (Total Problems: β=-1.99, 95%CI: -3.89, -0.09; Internalizing: β=-0.82, 95%CI: -1.42, -0.23; Externalizing: β=-0.56, 95%CI: -1.34, 0.22). No associations with cognitive performance were observed nor did we observe moderation by breastfeeding or postnatal neighborhood opportunity. Our results provide further evidence that prenatal pCRH exposure may impact subsequent child behavior in sex-specific ways, however in contrast to prior studies suggesting adverse impacts in females, steeper mid-gestation pCRH rise was associated with more problem behaviors in males, but fewer in females.
Collapse
Affiliation(s)
- Emily S Barrett
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA; Environmental and Occupational Health Sciences Institute, Rutgers University, Piscataway, NJ, USA.
| | - Alexandra Sullivan
- Center for Health and Community, University of California, San Francisco, CA, USA; Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Tomomi Workman
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Yuhong Zhang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Christine T Loftus
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Adam A Szpiro
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Alison Paquette
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Michael Coccia
- Center for Health and Community, University of California, San Francisco, CA, USA
| | - Roger Smith
- Mothers and Babies Research Centre, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
| | - Maria Bowman
- Mothers and Babies Research Centre, Hunter Medical Research Institute, University of Newcastle, Newcastle, Australia
| | - Alicia Smith
- Department of Gynecology and Obstetrics, Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, USA
| | - Karen Derefinko
- Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Ruby H N Nguyen
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN, USA
| | - Qi Zhao
- Department of Preventive Medicine, University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Sheela Sathyanarayana
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Catherine Karr
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Kaja Z LeWinn
- Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Nicole R Bush
- Center for Health and Community, University of California, San Francisco, CA, USA; Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA; Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| |
Collapse
|
3
|
Wander PL, Bammler TK, MacDonald JW, Srinouanprachanh S, Boyko EJ, Enquobahrie DA. Plasma miRNAs and Treatment Failure in Participants in the Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) Study. Diabetes Care 2024; 47:471-475. [PMID: 38153877 PMCID: PMC10909680 DOI: 10.2337/dc23-1540] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/15/2023] [Indexed: 12/30/2023]
Abstract
OBJECTIVE To identify plasma miRNAs related to treatment failure in youth with type 2 diabetes (T2D). RESEARCH DESIGN AND METHODS We examined whether a panel of miRNAs could predict treatment failure in training/test data sets among participants in the Treatment Options for Type 2 Diabetes in Adolescents and Youth (TODAY) study (N = 209). We also examined whether individual miRNAs were associated with treatment failure. RESULTS Participants were age 14.5 years, and 62% were female. A panel of miRNAs did not predict treatment failure. However, for each doubling, miR-4306 was associated with a 12% decrease (P = 0.040) and miR-483-3p was marginally associated with a 12% increase (P = 0.080) in failure independently of sex, race/ethnicity, BMI, Tanner stage, HbA1c, maternal diabetes, oral disposition index, and treatment arm. The addition of both miRNAs improved model fit (log likelihood without vs. with miRNAs -360.3 vs. -363.5; P = 0.040). CONCLUSIONS miR-483-3p and miR-4306 may be associated with treatment failure in youth with T2D.
Collapse
Affiliation(s)
- Pandora L. Wander
- Veterans Affairs Puget Sound Health Care System, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA
| | - Sengeo Srinouanprachanh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA
| | - Edward J. Boyko
- Veterans Affairs Puget Sound Health Care System, Seattle, WA
- Department of Medicine, University of Washington, Seattle, WA
| | - Daniel A. Enquobahrie
- Department of Epidemiology, University of Washington, Seattle, WA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA
| |
Collapse
|
4
|
Hart A, Cesar F, Zelnick LR, O'Connor N, Bailey Z, Lo J, Van Ness K, Stanaway IB, Bammler TK, MacDonald JW, Thau MR, Himmelfarb J, Goss CH, Aitken M, Kelly EJ, Bhatraju PK. Identification of prognostic biomarkers for antibiotic associated nephrotoxicity in cystic fibrosis. J Cyst Fibros 2024; 23:293-299. [PMID: 37949747 PMCID: PMC11076417 DOI: 10.1016/j.jcf.2023.10.021] [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: 02/13/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Our objective was to discover novel urinary biomarkers of antibiotic-associated nephrotoxicity using an ex-vivo human microphysiological system (MPS) and to translate these findings to a prospectively enrolled cystic fibrosis (CF) population receiving aminoglycosides and/or polymyxin E (colistin) for a pulmonary exacerbation. METHODS We populated the MPS with primary human kidney proximal tubule epithelial cells (PTECs) from three donors and modeled nephrotoxin injury through exposure to 50 µg/mL polymyxin E for 72 h. We analyzed gene transcriptional responses by RNAseq and tested MPS effluents. We translated candidate biomarkers to a CF cohort via analysis of urine collected prior to, during and two weeks after antibiotics and patients were followed for a median of 3 years after antibiotic use. RESULTS Polymyxin E treatment resulted in a statistically significant increase in the pro-apoptotic Fas gene relative to control in RNAseq of MPS: fold-change = 1.63, FDR q-value = 7.29 × 10-5. Effluent analysis demonstrated an acute rise of soluble Fas (sFas) concentrations that correlated with cellular injury. In 16 patients with CF, urinary sFas concentrations were significantly elevated during antibiotic treatment, regardless of development of AKI. Over a median of three years of follow up, we identified seven cases of incident chronic kidney disease (CKD). Urinary sFas concentrations during antibiotic treatment were significantly associated with subsequent development of incident CKD (unadjusted relative risk = 2.02 per doubling of urinary sFas, 95 % CI = 1.40, 2.90, p < 0.001). CONCLUSIONS Using an ex-vivo MPS, we identified a novel biomarker of proximal tubule epithelial cell injury, sFas, and translated these findings to a clinical cohort of patients with CF.
Collapse
Affiliation(s)
- Andrew Hart
- University of Washington School of Medicine, Seattle, USA
| | - Francine Cesar
- Department of Pharmaceutics, University of Washington, Seattle, USA
| | - Leila R Zelnick
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA
| | - Nick O'Connor
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Zoie Bailey
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Jordan Lo
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Kirk Van Ness
- Department of Pharmaceutics, University of Washington, Seattle, USA
| | - Ian B Stanaway
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA
| | - Theo K Bammler
- Division of Pediatric Pulmonary Medicine, University of Washington, Seattle, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, USA
| | - Matthew R Thau
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Jonathan Himmelfarb
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA
| | - Christopher H Goss
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA; Division of Pediatric Pulmonary Medicine, University of Washington, Seattle, USA
| | - Moira Aitken
- Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA
| | - Edward J Kelly
- Department of Pharmaceutics, University of Washington, Seattle, USA
| | - Pavan K Bhatraju
- Kidney Research Institute and Division of Nephrology, Department of Medicine, University of Washington, Seattle, USA; Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle, USA.
| |
Collapse
|
5
|
Baker BH, Freije S, MacDonald JW, Bammler TK, Benson C, Carroll KN, Enquobahrie DA, Karr CJ, LeWinn KZ, Zhao Q, Bush NR, Sathyanarayana S, Paquette AG. Placental transcriptomic signatures of prenatal and preconceptional maternal stress. Mol Psychiatry 2024:10.1038/s41380-023-02403-6. [PMID: 38212375 DOI: 10.1038/s41380-023-02403-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024]
Abstract
Prenatal exposure to maternal psychological stress is associated with increased risk for adverse birth and child health outcomes. Accumulating evidence suggests that preconceptional maternal stress may also be transmitted intergenerationally to negatively impact offspring. However, understanding of mechanisms linking these exposures to offspring outcomes, particularly those related to placenta, is limited. Using RNA sequencing, we identified placental transcriptomic signatures associated with maternal prenatal stressful life events (SLEs) and childhood traumatic events (CTEs) in 1 029 mother-child pairs in two birth cohorts from Washington state and Memphis, Tennessee. We evaluated individual gene-SLE/CTE associations and performed an ensemble of gene set enrichment analyses combing across 11 popular enrichment methods. Higher number of prenatal SLEs was significantly (FDR < 0.05) associated with increased expression of ADGRG6, a placental tissue-specific gene critical in placental remodeling, and decreased expression of RAB11FIP3, an endocytosis and endocytic recycling gene, and SMYD5, a histone methyltransferase. Prenatal SLEs and maternal CTEs were associated with gene sets related to several biological pathways, including upregulation of protein processing in the endoplasmic reticulum, protein secretion, and ubiquitin mediated proteolysis, and down regulation of ribosome, epithelial mesenchymal transition, DNA repair, MYC targets, and amino acid-related pathways. The directional associations in these pathways corroborate prior non-transcriptomic mechanistic studies of psychological stress and mental health disorders, and have previously been implicated in pregnancy complications and adverse birth outcomes. Accordingly, our findings suggest that maternal exposure to psychosocial stressors during pregnancy as well as the mother's childhood may disrupt placental function, which may ultimately contribute to adverse pregnancy, birth, and child health outcomes.
Collapse
Affiliation(s)
- Brennan H Baker
- University of Washington, Seattle, WA, USA.
- Seattle Children's Research Institute, Seattle, WA, USA.
| | | | | | | | - Ciara Benson
- Global Alliance to Prevent Preterm Birth and Stillbirth (GAPPS), Lynnwood, WA, USA
| | | | | | | | - Kaja Z LeWinn
- University of California San Francisco, San Francisco, CA, USA
| | - Qi Zhao
- University of Tennessee Health Sciences Center, Memphis, TN, USA
| | - Nicole R Bush
- University of California San Francisco, San Francisco, CA, USA
| | - Sheela Sathyanarayana
- University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| | - Alison G Paquette
- University of Washington, Seattle, WA, USA
- Seattle Children's Research Institute, Seattle, WA, USA
| |
Collapse
|
6
|
Smith KD, Prince DK, MacDonald JW, Bammler TK, Akilesh S. Challenges and Opportunities for the Clinical Translation of Spatial Transcriptomics Technologies. Glomerular Dis 2024; 4:49-63. [PMID: 38600956 PMCID: PMC11006413 DOI: 10.1159/000538344] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024]
Abstract
Background The first spatially resolved transcriptomics platforms, GeoMx (Nanostring) and Visium (10x Genomics) were launched in 2019 and were recognized as the method of the year by Nature Methods in 2020. The subsequent refinement and expansion of these and other technologies to increase -plex, work with formalin-fixed paraffin-embedded tissue, and analyze protein in addition to gene expression have only added to their significance and impact on the biomedical sciences. In this perspective, we focus on two platforms for spatial transcriptomics, GeoMx and Visium, and how these platforms have been used to provide novel insight into kidney disease. The choice of platform will depend largely on experimental questions and design. The application of these technologies to clinically sourced biopsies presents the opportunity to identify specific tissue biomarkers that help define disease etiology and more precisely target therapeutic interventions in the future. Summary In this review, we provide a description of the existing and emerging technologies that can be used to capture spatially resolved gene and protein expression data from tissue. These technologies have provided new insight into the spatial heterogeneity of diseases, how reactions to disease are distributed within a tissue, which cells are affected, and molecular pathways that predict disease and response to therapy. Key Message The upcoming years will see intense use of spatial transcriptomics technologies to better define the pathophysiology of kidney diseases and develop novel diagnostic tests to guide personalized treatments for patients.
Collapse
Affiliation(s)
- Kelly D. Smith
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | | | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Shreeram Akilesh
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
- Kidney Research Institute, Seattle, WA, USA
| |
Collapse
|
7
|
Hussey MR, Enquobahrie DA, Loftus CT, MacDonald JW, Bammler TK, Paquette AG, Marsit CJ, Szpiro AA, Kaufman JD, LeWinn KZ, Bush NR, Tylavsky F, Zhao Q, Karr CJ, Sathyanarayana S. Associations of prenatal exposure to NO 2 and near roadway residence with placental gene expression. Placenta 2023; 138:75-82. [PMID: 37216796 DOI: 10.1016/j.placenta.2023.05.004] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 04/03/2023] [Accepted: 05/03/2023] [Indexed: 05/24/2023]
Abstract
INTRODUCTION Traffic-related air pollution (TRAP), a common exposure, potentially impacts pregnancy through altered placental function. We investigated associations between prenatal TRAP exposure and placental gene expression. METHODS Whole transcriptome sequencing was performed on placental samples from CANDLE (Memphis, TN) (n = 776) and GAPPS (Seattle and Yakima, WA) (n = 205), cohorts of the ECHO-PATHWAYS Consortium. Residential NO2 exposures were computed via spatiotemporal models for full-pregnancy, each trimester, and the first/last months of pregnancy. Individual cohort-specific, covariate-adjusted linear models were fit for 10,855 genes and respective exposures (NO2 or roadway proximity [≤150 m]). Infant-sex/exposure interactions on placental gene expression were tested with interaction terms in separate models. Significance was based on false discovery rate (FDR<0.10). RESULTS In GAPPS, final-month NO2 exposure was positively associated with MAP1LC3C expression (FDR p-value = 0.094). Infant-sex interacted with second-trimester NO2 on STRIP2 expression (FDR interaction p-value = 0.011, inverse and positive associations among male and female infants, respectively) and roadway proximity on CEBPA expression (FDR interaction p-value = 0.045, inverse among females). In CANDLE, infant-sex interacted with first-trimester and full-pregnancy NO2 on RASSF7 expression (FDR interaction p-values = 0.067 and 0.013, respectively, positive among male infants and inverse among female infants). DISCUSSION Overall, pregnancy NO2 exposure and placental gene expression associations were primarily null, with exception of final month NO2 exposure and placental MAP1LC3C association. We found several interactions of infant sex and TRAP exposures on placental expression of STRIP2, CEBPA, and RASSF7. These highlighted genes suggest influence of TRAP on placental cell proliferation, autophagy, and growth, though additional replication and functional studies are required for validation.
Collapse
Affiliation(s)
- Michael R Hussey
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA.
| | - Daniel A Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Health Systems and Population Health, School of Public Health, University of Washington, Seattle, WA, USA
| | - Christine T Loftus
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Alison G Paquette
- Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| | - Carmen J Marsit
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Adam A Szpiro
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Joel D Kaufman
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Kaja Z LeWinn
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nicole R Bush
- Department of Psychiatry and Behavioral Sciences, School of Medicine, University of California, San Francisco, San Francisco, CA, USA; Department of Pediatrics, School of Medicine, University of California, San Francisco, San, Francisco, CA, USA
| | - Frances Tylavsky
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Qi Zhao
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Catherine J Karr
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA; Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA
| | - Sheela Sathyanarayana
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA; Department of Pediatrics, School of Medicine, University of Washington, Seattle, WA, USA; Seattle Children's Research Institute, Seattle, WA, USA
| |
Collapse
|
8
|
Lapehn S, Houghtaling S, Ahuna K, Kadam L, MacDonald JW, Bammler TK, LeWinn KZ, Myatt L, Sathyanarayana S, Paquette AG. Mono(2-ethylhexyl) phthalate induces transcriptomic changes in placental cells based on concentration, fetal sex, and trophoblast cell type. Arch Toxicol 2023; 97:831-847. [PMID: 36695872 PMCID: PMC9968694 DOI: 10.1007/s00204-023-03444-0] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/17/2023] [Indexed: 01/26/2023]
Abstract
Phthalates are ubiquitous plasticizer chemicals found in consumer products. Exposure to phthalates during pregnancy has been associated with adverse pregnancy and birth outcomes and differences in placental gene expression in human studies. The objective of this research was to evaluate global changes in placental gene expression via RNA sequencing in two placental cell models following exposure to the phthalate metabolite mono(2-ethylhexyl) phthalate (MEHP). HTR-8/SVneo and primary syncytiotrophoblast cells were exposed to three concentrations (1, 90, 180 µM) of MEHP for 24 h with DMSO (0.1%) as a vehicle control. mRNA and lncRNAs were quantified using paired-end RNA sequencing, followed by identification of differentially expressed genes (DEGs), significant KEGG pathways, and enriched transcription factors (TFs). MEHP caused gene expression changes across all concentrations for HTR-8/SVneo and primary syncytiotrophoblast cells. Sex-stratified analysis of primary cells identified different patterns of sensitivity in response to MEHP dose by sex, with male placentas being more responsive to MEHP exposure. Pathway analysis identified 11 KEGG pathways significantly associated with at least one concentration in both cell types. Four ligand-inducible nuclear hormone TFs (PPARG, PPARD, ESR1, AR) were enriched in at least three treatment groups. Overall, we demonstrated that MEHP differentially affects placental gene expression based on concentration, fetal sex, and trophoblast cell type. This study confirms prior studies, as enrichment of nuclear hormone receptor TFs were concordant with previously published mechanisms of phthalate disruption, and generates new hypotheses, as we identified many pathways and genes not previously linked to phthalate exposure.
Collapse
Affiliation(s)
- Samantha Lapehn
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, 1900 9th Ave, Jack R. MacDonald Building, Seattle, WA 98101 USA
| | - Scott Houghtaling
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, 1900 9th Ave, Jack R. MacDonald Building, Seattle, WA 98101 USA
| | - Kylia Ahuna
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239 USA
| | - Leena Kadam
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239 USA
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195 USA
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA 98195 USA
| | - Kaja Z. LeWinn
- Department of Psychiatry, University of California-San Francisco, San Francisco, CA 94143 USA
| | - Leslie Myatt
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239 USA
| | - Sheela Sathyanarayana
- Department of Pediatrics, University of Washington, Seattle, WA 98195 USA
- Center for Child Health, Behavior and Development, Seattle Children’s Research Institute, Seattle, WA 98101 USA
| | - Alison G. Paquette
- Center for Developmental Biology and Regenerative Medicine, Seattle Children’s Research Institute, 1900 9th Ave, Jack R. MacDonald Building, Seattle, WA 98101 USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195 USA
| |
Collapse
|
9
|
Petroff RL, Williams C, Li JL, MacDonald JW, Bammler TK, Richards T, English CN, Baldessari A, Shum S, Jing J, Isoherranen N, Crouthamel B, McKain N, Grant KS, Burbacher TM, Harry GJ. Prolonged, Low-Level Exposure to the Marine Toxin, Domoic Acid, and Measures of Neurotoxicity in Nonhuman Primates. Environ Health Perspect 2022; 130:97003. [PMID: 36102641 PMCID: PMC9472675 DOI: 10.1289/ehp10923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 07/21/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND The excitotoxic molecule, domoic acid (DA), is a marine algal toxin known to induce overt hippocampal neurotoxicity. Recent experimental and epidemiological studies suggest adverse neurological effects at exposure levels near the current regulatory limit (20 ppm, ∼0.075-0.1mg/kg). At these levels, cognitive effects occur in the absence of acute symptoms or evidence of neuronal death. OBJECTIVES This study aimed to identify adverse effects on the nervous system from prolonged, dietary DA exposure in adult, female Macaca fascicularis monkeys. METHODS Monkeys were orally exposed to 0, 0.075, and 0.15mg/kg per day for an average of 14 months. Clinical blood counts, chemistry, and cytokine levels were analyzed in the blood. In-life magnetic resonance (MR) imaging assessed volumetric and tractography differences in and between the hippocampus and thalamus. Histology of neurons and glia in the fornix, fimbria, internal capsule, thalamus, and hippocampus was evaluated. Hippocampal RNA sequencing was used to identify differentially expressed genes. Enrichment of gene networks for neuronal health, excitotoxicity, inflammation/glia, and myelin were assessed with Gene Set Enrichment Analysis. RESULTS Clinical blood counts, chemistry, and cytokine levels were not altered with DA exposure in nonhuman primates. Transcriptome analysis of the hippocampus yielded 748 differentially expressed genes (fold change≥1.5; p≤0.05), reflecting differences in a broad molecular profile of intermediate early genes (e.g., FOS, EGR) and genes related to myelin networks in DA animals. Between exposed and control animals, MR imaging showed comparable connectivity of the hippocampus and thalamus and histology showed no evidence of hypomyelination. Histological examination of the thalamus showed a larger microglia soma size and an extension of cell processes, but suggestions of a GFAP+astrocyte response showed no indication of astrocyte hypertrophy. DISCUSSION In the absence of overt hippocampal excitotoxicity, chronic exposure of Macaca fascicularis monkeys to environmentally relevant levels of DA suggested a subtle shift in the molecular profile of the hippocampus and the microglia phenotype in the thalamus that was possibly reflective of an adaptive response due to prolonged DA exposure. https://doi.org/10.1289/EHP10923.
Collapse
Affiliation(s)
- Rebekah L. Petroff
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Christopher Williams
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| | - Jian-Liang Li
- Epigenetics & Stem Cell Biology Laboratory, NIEHS, NIH, DHHS, Research Triangle Park, North Carolina, USA
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Todd Richards
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | | | - Audrey Baldessari
- Washington National Primate Research Center, Seattle, Washington, USA
| | - Sara Shum
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Jing Jing
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
| | - Nina Isoherranen
- Department of Pharmaceutics, University of Washington, Seattle, Washington, USA
- Center on Human Development and Disability, University of Washington, Seattle, Washington, USA
| | - Brenda Crouthamel
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Noelle McKain
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Kimberly S. Grant
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
- Washington National Primate Research Center, Seattle, Washington, USA
| | - Thomas M. Burbacher
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
- Washington National Primate Research Center, Seattle, Washington, USA
- Center on Human Development and Disability, University of Washington, Seattle, Washington, USA
| | - G. Jean Harry
- Mechanistic Toxicology Branch, Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Research Triangle Park, North Carolina, USA
| |
Collapse
|
10
|
Wander PL, Enquobahrie DA, Bammler TK, MacDonald JW, Srinouanprachanh S, Kaleru T, Khakpour D, Trikudanathan S. Associations of plasma miRNAs with waist circumference and insulin resistance among women with polycystic ovary syndrome - Pilot study. Mol Cell Endocrinol 2022; 554:111723. [PMID: 35843386 PMCID: PMC9552972 DOI: 10.1016/j.mce.2022.111723] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Insulin resistance (IR) and central obesity are common in polycystic ovary syndrome (PCOS), but pathomechanisms for IR in PCOS are not established. Circulating microRNAs (miRNAs) are non-invasive biomarkers of epigenetic regulation that may contribute to the pathogenesis of IR and central adiposity in PCOS. METHODS We conducted a pilot study to examine associations of circulating miRNAs with IR and central adiposity among women with PCOS (n = 11) using high-throughput miRNA sequencing. We fit generalized linear models examining associations of waist circumference and HOMA-IR with plasma miRNAs. We used false discovery rate (FDR)-adjusted cutoff p < 0.1 to correct for multiple testing. We used miRDB's Gene Ontology (GO) tool to identify predicted pathways for top hits. RESULTS Mean age and BMI of participants were 27.9 years and 32.5 kg/m2, respectively. Lower levels of miR-1294 were associated with higher waist circumference (β = -0.10, FDR = 0.095). While no miRNAs were associated with HOMA-IR at our FDR cut off <0.1, 11 miRNAs were associated with waist circumference and 14 miRNAs with HOMA-IR at unadjusted p < 0.01, including members of the highly conserved miR-17/92 cluster and miR-1294 (β = -0.10, p < 0.001). The GO analysis of miR-1294 identified 54 overrepresented pathways, including "negative regulation of insulin receptor signaling" (FDR = 0.019), and 6 underrepresented pathways. CONCLUSIONS Plasma miR-1294 along with members of the miR-17/92 cluster and miRNAs involved in insulin signaling may be associated with central obesity and insulin resistance in PCOS. Larger studies among women with and without PCOS are needed to validate these findings.
Collapse
Affiliation(s)
- Pandora L Wander
- Veterans Affairs Puget Sound Health Care System, Seattle, WA, United States; Division of General Internal Medicine, University of Washington, Seattle, WA, United States.
| | - Daniel A Enquobahrie
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Sengkeo Srinouanprachanh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Thanmai Kaleru
- Division of Metabolism, Endocrinology, and Nutrition, University of Washington, Seattle, WA, United States
| | - Dori Khakpour
- Division of Metabolism, Endocrinology, and Nutrition, University of Washington, Seattle, WA, United States
| | - Subbulaxmi Trikudanathan
- Division of Metabolism, Endocrinology, and Nutrition, University of Washington, Seattle, WA, United States
| |
Collapse
|
11
|
Sharma R, Frasch MG, Zelgert C, Zimmermann P, Fabre B, Wilson R, Waldenberger M, MacDonald JW, Bammler TK, Lobmaier SM, Antonelli MC. Maternal-fetal stress and DNA methylation signatures in neonatal saliva: an epigenome-wide association study. Clin Epigenetics 2022; 14:87. [PMID: 35836289 PMCID: PMC9281078 DOI: 10.1186/s13148-022-01310-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 07/05/2022] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Maternal stress before, during and after pregnancy has profound effects on the development and lifelong function of the infant's neurocognitive development. We hypothesized that the programming of the central nervous system (CNS), hypothalamic-pituitary-adrenal (HPA) axis and autonomic nervous system (ANS) induced by prenatal stress (PS) is reflected in electrophysiological and epigenetic biomarkers. In this study, we aimed to find noninvasive epigenetic biomarkers of PS in the newborn salivary DNA. RESULTS A total of 728 pregnant women were screened for stress exposure using Cohen Perceived Stress Scale (PSS), 164 women were enrolled, and 114 dyads were analyzed. Prenatal Distress Questionnaire (PDQ) was also administered to assess specific pregnancy worries. Transabdominal fetal electrocardiograms (taECG) were recorded to derive coupling between maternal and fetal heart rates resulting in a 'Fetal Stress Index' (FSI). Upon delivery, we collected maternal hair strands for cortisol measurements and newborn's saliva for epigenetic analyses. DNA was extracted from saliva samples, and DNA methylation was measured using EPIC BeadChip array (850 k CpG sites). Linear regression was used to identify associations between PSS/PDQ/FSI/Cortisol and DNA methylation. We found epigenome-wide significant associations for 5 CpG with PDQ and cortisol at FDR < 5%. Three CpGs were annotated to genes (Illumina Gene annotation file): YAP1, TOMM20 and CSMD1, and two CpGs were located approximately lay at 50 kb from SSBP4 and SCAMP1. In addition, two differentiated methylation regions (DMR) related to maternal stress measures PDQ and cortisol were found: DAXX and ARL4D. CONCLUSIONS Genes annotated to these CpGs were found to be involved in secretion and transportation, nuclear signaling, Hippo signaling pathways, apoptosis, intracellular trafficking and neuronal signaling. Moreover, some CpGs are annotated to genes related to autism, post-traumatic stress disorder (PTSD) and schizophrenia. However, our results should be viewed as hypothesis generating until replicated in a larger sample. Early assessment of such noninvasive PS biomarkers will allow timelier detection of babies at risk and a more effective allocation of resources for early intervention programs to improve child development. A biomarker-guided early intervention strategy is the first step in the prevention of future health problems, reducing their personal and societal impact.
Collapse
Affiliation(s)
- Ritika Sharma
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Munich, Munich, Germany
| | - Martin G Frasch
- Department of Obstetrics and Gynecology and Center On Human Development and Disability (CHDD), University of Washington, Seattle, WA, USA
| | - Camila Zelgert
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Peter Zimmermann
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Bibiana Fabre
- Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Rory Wilson
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Munich, Munich, Germany
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum Munich, Munich, Germany
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Silvia M Lobmaier
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany
| | - Marta C Antonelli
- Department of Obstetrics and Gynecology, Klinikum Rechts der Isar, Technical University of Munich, Munich, Germany.
- Instituto de Biología Celular y Neurociencia "Prof. E. De Robertis", Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina.
| |
Collapse
|
12
|
Li A, Hines KM, Ross DH, MacDonald JW, Xu L. Temporal changes in the brain lipidome during neurodevelopment of Smith-Lemli-Opitz syndrome mice. Analyst 2022; 147:1611-1621. [PMID: 35293916 PMCID: PMC9018458 DOI: 10.1039/d2an00137c] [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] [Indexed: 11/21/2022]
Abstract
Neurodevelopment is an intricately orchestrated program of cellular events that occurs with tight temporal and spatial regulation. While it is known that the development and proper functioning of the brain, which is the second most lipid rich organ behind adipose tissue, greatly rely on lipid metabolism and signaling, the temporal lipidomic changes that occur throughout the course of neurodevelopment have not been investigated. Smith-Lemli-Opitz syndrome is a metabolic disorder caused by genetic mutations in the DHCR7 gene, leading to defective 3β-hydroxysterol-Δ7-reductase (DHCR7), the enzyme that catalyzes the last step of the Kandutsch-Russell pathway of cholesterol synthesis. Due to the close regulatory relationship between sterol and lipid homeostasis, we hypothesize that altered or dysregulated lipid metabolism beyond the primary defect of cholesterol biosynthesis is present in the pathophysiology of SLOS. Herein, we applied our HILIC-IM-MS method and LiPydomics Python package to streamline an untargeted lipidomics analysis of developing mouse brains in both wild-type and Dhcr7-KO mice, identifying lipids at Level 3 (lipid species level: lipid class/subclass and fatty acid sum composition). We compared relative lipid abundances throughout development, from embryonic day 12.5 to postnatal day 0 and determined differentially expressed brain lipids between wild-type and Dhcr7-KO mice at specific developmental time points, revealing lipid metabolic pathways that are affected in SLOS beyond the cholesterol biosynthesis pathway, such as glycerolipid, glycerophospholipid, and sphingolipid metabolism. Implications of the altered lipid metabolic pathways in SLOS pathophysiology are discussed.
Collapse
Affiliation(s)
- Amy Li
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
| | - Kelly M Hines
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
| | - Dylan H Ross
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, USA.
| |
Collapse
|
13
|
C. Chi G, Liu Y, MacDonald JW, M. Reynolds L, Enquobahrie DA, L. Fitzpatrick A, Kerr KF, J. Budoff M, Lee SI, Siscovick D, D. Kaufman J. Epigenome-wide analysis of long-term air pollution exposure and DNA methylation in monocytes: results from the Multi-Ethnic Study of Atherosclerosis. Epigenetics 2022; 17:297-313. [PMID: 33818294 PMCID: PMC8920186 DOI: 10.1080/15592294.2021.1900028] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Air pollution might affect atherosclerosis through DNA methylation changes in cells crucial to atherosclerosis, such as monocytes. We conducted an epigenome-wide study of DNA methylation in CD14+ monocytes and long-term ambient air pollution exposure in adults participating in the Multi-Ethnic Study of Atherosclerosis (MESA). We also assessed the association between differentially methylated signals and cis-gene expression. Using spatiotemporal models, one-year average concentrations of outdoor fine particulate matter (PM2.5) and oxides of nitrogen (NOX) were estimated at participants' homes. We assessed DNA methylation and gene expression using Illumina 450k and HumanHT-12 v4 Expression BeadChips, respectively (n = 1,207). We used bump hunting and site-specific approaches to identify differentially methylated signals (false discovery rate of 0.05) and used linear models to assess associations between differentially methylated signals and cis-gene expression. Four differentially methylated regions (DMRs) located on chromosomes 5, 6, 7, and 16 (within or near SDHAP3, ZFP57, HOXA5, and PRM1, respectively) were associated with PM2.5. The DMRs on chromosomes 5 and 6 also associated with NOX. The DMR on chromosome 5 had the smallest p-value for both PM2.5 (p = 1.4×10-6) and NOX (p = 7.7×10-6). Three differentially methylated CpGs were identified for PM2.5, and cg05926640 (near TOMM20) had the smallest p-value (p = 5.6×10-8). NOX significantly associated with cg11756214 within ZNF347 (p = 5.6×10-8). Several differentially methylated signals were also associated with cis-gene expression. The DMR located on chromosome 7 was associated with the expression of HOXA5, HOXA9, and HOXA10. The DMRs located on chromosomes 5 and 16 were associated with expression of MRPL36 and DEXI, respectively. The CpG cg05926640 was associated with expression of ARID4B, IRF2BP2, and TOMM20. We identified differential DNA methylation in monocytes associated with long-term air pollution exposure. Methylation signals associated with gene expression might help explain how air pollution contributes to cardiovascular disease.
Collapse
Affiliation(s)
- Gloria C. Chi
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,CONTACT Gloria C. Chi 1 DNA Way, South San Francisco, CA 94080
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Lindsay M. Reynolds
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Daniel A. Enquobahrie
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Annette L. Fitzpatrick
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,Department of Family Medicine, School of Medicine, University of Washington, Seattle, Washington, USA,Department of Global Health, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Kathleen F. Kerr
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, Washington, USA
| | - Matthew J. Budoff
- Division of Cardiology, Los Angeles Biomedical Research Institute at Harbor–UCLA Medical Center, Torrance, California, USA
| | - Su-in Lee
- Department of Computer Science & Engineering, University of Washington, Seattle, Washington, USA,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | | | - Joel D. Kaufman
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, USA,Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington, USA
| |
Collapse
|
14
|
Okamura DM, Brewer CM, Wakenight P, Bahrami N, Bernardi K, Tran A, Olson J, Shi X, Yeh SY, Piliponsky A, Collins SJ, Nguyen ED, Timms AE, MacDonald JW, Bammler TK, Nelson BR, Millen KJ, Beier DR, Majesky MW. Spiny mice activate unique transcriptional programs after severe kidney injury regenerating organ function without fibrosis. iScience 2021; 24:103269. [PMID: 34849462 PMCID: PMC8609232 DOI: 10.1016/j.isci.2021.103269] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 09/02/2021] [Accepted: 10/12/2021] [Indexed: 12/13/2022] Open
Abstract
Fibrosis-driven solid organ failure is an enormous burden on global health. Spiny mice (Acomys) are terrestrial mammals that can regenerate severe skin wounds without scars to avoid predation. Whether spiny mice also regenerate internal organ injuries is unknown. Here, we show that despite equivalent acute obstructive or ischemic kidney injury, spiny mice fully regenerate nephron structure and organ function without fibrosis, whereas C57Bl/6 or CD1 mice progress to complete organ failure with extensive renal fibrosis. Two mechanisms for vertebrate regeneration have been proposed that emphasize either extrinsic (pro-regenerative macrophages) or intrinsic (surviving cells of the organ itself) controls. Comparative transcriptome analysis revealed that the Acomys genome appears poised at the time of injury to initiate regeneration by surviving kidney cells, whereas macrophage accumulation was not detected until about day 7. Thus, we provide evidence for rapid activation of a gene expression signature for regenerative wound healing in the spiny mouse kidney.
Collapse
Affiliation(s)
- Daryl M. Okamura
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Chris M. Brewer
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Paul Wakenight
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Nadia Bahrami
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Kristina Bernardi
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Amy Tran
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Jill Olson
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Xiaogang Shi
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Szu-Ying Yeh
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Adrian Piliponsky
- Center for Immunity & Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Sarah J. Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Elizabeth D. Nguyen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Andrew E. Timms
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - James W. MacDonald
- Department of Environmental & Occupational Health, University of Washington, Seattle, WA 98195, USA
| | - Theo K. Bammler
- Department of Environmental & Occupational Health, University of Washington, Seattle, WA 98195, USA
| | - Branden R. Nelson
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Kathleen J. Millen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Integrated Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - David R. Beier
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
| | - Mark W. Majesky
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98105, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
15
|
Al-Shaikhly T, MacDonald JW, Bammler TK, Altman MC, Ayars AG, Petroni DH, Tilles SA, Henderson WR. Unique basophil microRNA signature in chronic spontaneous urticaria patients who respond to omalizumab. Clin Exp Allergy 2021; 51:1648-1652. [PMID: 34519110 DOI: 10.1111/cea.14014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/30/2021] [Accepted: 09/09/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Taha Al-Shaikhly
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Interdisciplinary Center for Exposures, Diseases, Genomics & Environment, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Interdisciplinary Center for Exposures, Diseases, Genomics & Environment, Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Matthew C Altman
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew G Ayars
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | | | | | - William R Henderson
- Division of Allergy and Infectious Diseases, Department of Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| |
Collapse
|
16
|
Garrick JM, Cole TB, Bammler TK, MacDonald JW, Marsillach J, Furlong CE, Costa LG. Paraoxonase 2 deficiency in mice alters motor behavior and causes region-specific transcript changes in the brain. Neurotoxicol Teratol 2021; 87:107010. [PMID: 34216730 PMCID: PMC8440460 DOI: 10.1016/j.ntt.2021.107010] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 02/28/2021] [Revised: 06/07/2021] [Accepted: 06/28/2021] [Indexed: 01/01/2023]
Abstract
Paraoxonase 2 (PON2) is an intracellular antioxidant enzyme shown to play an important role in mitigating oxidative stress in the brain. Oxidative stress is a common mechanism of toxicity for neurotoxicants and is increasingly implicated in the etiology of multiple neurological diseases. While PON2 deficiency increases oxidative stress in the brain in-vitro, little is known about its effects on behavior in-vivo and what global transcript changes occur from PON2 deficiency. We sought to characterize the effects of PON2 deficiency on behavior in mice, with an emphasis on locomotion, and evaluate transcriptional changes with RNA-Seq. Behavioral endpoints included home-cage behavior (Noldus PhenoTyper), motor coordination (Rotarod) and various gait metrics (Noldus CatWalk). Home-cage behavior analysis showed PON2 deficient mice had increased activity at night compared to wildtype controls and spent more time in the center of the cage, displaying a possible anxiolytic phenotype. PON2 deficient mice had significantly shorter latency to fall when tested on the rotarod, suggesting impaired motor coordination. Minimal gait alterations were observed, with decreased girdle support posture noted as the only significant change in gait with PON2 deficiency. Beyond one home-cage metric, no significant sex-based behavioral differences were found in this study. Finally, A subset of samples were utilized for RNA-Seq analysis, looking at three discrete brain regions: cerebral cortex, striatum, and cerebellum. Highly regional- and sex-specific changes in RNA expression were found when comparing PON2 deficient and wildtype mice, suggesting PON2 may play distinct regional roles in the brain in a sex-specific manner. Taken together, these findings demonstrates that PON2 deficiency significantly alters the brain on both a biochemical and phenotypic level, with a specific impact on motor function. These data have implications for future gene-environment toxicological studies and warrants further investigation of the role of PON2 in the brain.
Collapse
Affiliation(s)
- Jacqueline M Garrick
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States..
| | - Toby B Cole
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States.; Center on Human Development and Disabilities, University of Washington, United States
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Judit Marsillach
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Clement E Furlong
- Depts. of Medicine (Div. Medical Genetics) and of Genome Sciences, University of Washington, United States
| | - Lucio G Costa
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States.; Dept. of Medicine and Surgery, University of Parma, Italy
| |
Collapse
|
17
|
Al‐Shaikhly T, MacDonald JW, Bammler TK, Altman MC, Ayars AG, Petroni DH, Tilles SA, Henderson WR. Extracellular vesicle microRNAs as predictors of response to omalizumab in chronic spontaneous urticaria. Allergy 2021; 76:1274-1277. [PMID: 33314187 DOI: 10.1111/all.14702] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/26/2020] [Accepted: 12/06/2020] [Indexed: 01/22/2023]
Affiliation(s)
- Taha Al‐Shaikhly
- Division of Allergy and Infectious Diseases Department of Medicine School of Medicine University of Washington Seattle WA USA
| | - James W. MacDonald
- Interdisciplinary Center for Exposures, Diseases, Genomics & Environment Department of Environmental and Occupational Health Sciences School of Public Health University of Washington Seattle WA USA
| | - Theo K. Bammler
- Interdisciplinary Center for Exposures, Diseases, Genomics & Environment Department of Environmental and Occupational Health Sciences School of Public Health University of Washington Seattle WA USA
| | - Matthew C. Altman
- Division of Allergy and Infectious Diseases Department of Medicine School of Medicine University of Washington Seattle WA USA
| | - Andrew G. Ayars
- Division of Allergy and Infectious Diseases Department of Medicine School of Medicine University of Washington Seattle WA USA
| | | | | | - William R. Henderson
- Division of Allergy and Infectious Diseases Department of Medicine School of Medicine University of Washington Seattle WA USA
| |
Collapse
|
18
|
Aldinger KA, Timms AE, MacDonald JW, McNamara HK, Herstein JS, Bammler TK, Evgrafov OV, Knowles JA, Levitt P. Transcriptome data of temporal and cingulate cortex in the Rett syndrome brain. Sci Data 2020; 7:192. [PMID: 32561870 PMCID: PMC7305197 DOI: 10.1038/s41597-020-0527-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 05/15/2020] [Indexed: 01/03/2023] Open
Abstract
Rett syndrome is an X-linked neurodevelopmental disorder caused by mutation in the methyl-CpG-binding protein 2 gene (MECP2) in the majority of cases. We describe an RNA sequencing dataset of postmortem brain tissue samples from four females clinically diagnosed with Rett syndrome and four age-matched female donors. The dataset contains 16 transcriptomes, including two brain regions, temporal and cingulate cortex, for each individual. We compared our dataset with published transcriptomic analyses of postmortem brain tissue from Rett syndrome and found consistent gene expression alterations among regions of the cerebral cortex. Our data provide a valuable resource to explore the biology of the human brain in Rett syndrome.
Collapse
Affiliation(s)
- Kimberly A Aldinger
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Jennifer S Herstein
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, USA
| | - Oleg V Evgrafov
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - James A Knowles
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Psychiatry and the Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Pat Levitt
- Department of Pediatrics and Program in Developmental Neuroscience and Developmental Neurogenetics, The Saban Research Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
19
|
Vornhagen J, Quach P, Santana-Ufret V, Alishetti V, Brokaw A, Armistead B, Qing Tang H, MacDonald JW, Bammler TK, Adams Waldorf KM, Uldbjerg N, Rajagopal L. Human Cervical Mucus Plugs Exhibit Insufficiencies in Antimicrobial Activity Towards Group B Streptococcus. J Infect Dis 2019; 217:1626-1636. [PMID: 29425317 DOI: 10.1093/infdis/jiy076] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Accepted: 02/05/2018] [Indexed: 01/31/2023] Open
Abstract
Preterm birth is a leading cause of neonatal mortality and lacks an effective therapy. Ascending microbial infections from the lower genital tract lead to infection of the placenta, amniotic fluid, and fetus causing preterm birth or stillbirth. Directly in the path of an ascending infection is the cervical mucus plug (CMP), a dense mucoid structure in the cervical canal with potential antimicrobial properties. In this study, we aimed to define the components of CMP responsible for antimicrobial activity against a common lower genital tract organism associated with preterm birth and stillbirths, namely, group B streptococcus (GBS). Using a quantitative proteomic approach, we identified antimicrobial factors in CMPs that were collected from healthy human pregnancies. However, we noted that the concentration of antimicrobial peptides present in the human CMPs were insufficient to directly kill GBS, and antimicrobial activity, when observed, was due to antibiotics retained in the CMPs. Despite this insufficiency, CMP proteins were able to activate leukocytes in whole blood resulting in increased rates of bacterial killing, suggesting a role for the CMP in enhancing complement-mediated killing or leukocyte activation. This study provides new insight into how the human CMP may limit ascending bacterial infection.
Collapse
Affiliation(s)
- Jay Vornhagen
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington.,Department of Global Health, University of Washington, Seattle
| | - Phoenicia Quach
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington
| | - Verónica Santana-Ufret
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington
| | - Varchita Alishetti
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington
| | - Alyssa Brokaw
- Department of Global Health, University of Washington, Seattle
| | - Blair Armistead
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington.,Department of Pediatrics, University of Washington, Seattle.,Department of Global Health, University of Washington, Seattle
| | - Hai Qing Tang
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Skejby, Denmark
| | - James W MacDonald
- Environmental and Occupational Health Sciences, University of Washington, Seattle
| | - Theo K Bammler
- Environmental and Occupational Health Sciences, University of Washington, Seattle
| | - Kristina M Adams Waldorf
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington.,Department of Obstetrics and Gynecology, University of Washington, Seattle.,Center for Innate Immunity and Immune Disease, University of Washington, Seattle.,Sahlgrenska Academy, University of Gothenburg, Sweden
| | - Niels Uldbjerg
- Department of Obstetrics and Gynecology, Aarhus University Hospital, Skejby, Denmark
| | - Lakshmi Rajagopal
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Washington.,Center for Innate Immunity and Immune Disease, University of Washington, Seattle.,Department of Pediatrics, University of Washington, Seattle.,Department of Global Health, University of Washington, Seattle
| |
Collapse
|
20
|
Chen H, Kichaev G, Bien SA, MacDonald JW, Wang L, Bammler TK, Auer P, Pasaniuc B, Lindström S. Genetic associations of breast and prostate cancer are enriched for regulatory elements identified in disease-related tissues. Hum Genet 2019; 138:1091-1104. [PMID: 31230194 DOI: 10.1007/s00439-019-02041-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 06/17/2019] [Indexed: 01/01/2023]
Abstract
Although genome-wide association studies (GWAS) have identified hundreds of risk loci for breast and prostate cancer, only a few studies have characterized the GWAS association signals across functional genomic annotations with a particular focus on single nucleotide polymorphisms (SNPs) located in DNA regulatory elements. In this study, we investigated the enrichment pattern of GWAS signals for breast and prostate cancer in genomic functional regions located in normal tissue and cancer cell lines. We quantified the overall enrichment of SNPs with breast and prostate cancer association p values < 1 × 10-8 across regulatory categories. We then obtained annotations for DNaseI hypersensitive sites (DHS), typical enhancers, and super enhancers across multiple tissue types, to assess if significant GWAS signals were selectively enriched in annotations found in disease-related tissue. Finally, we quantified the enrichment of breast and prostate cancer SNP heritability in regulatory regions, and compared the enrichment pattern of SNP heritability with GWAS signals. DHS, typical enhancers, and super enhancers identified in the breast cancer cell line MCF-7 were observed with the highest enrichment of genome-wide significant variants for breast cancer. For prostate cancer, GWAS signals were mostly enriched in DHS and typical enhancers identified in the prostate cancer cell line LNCaP. With progressively stringent GWAS p value thresholds, an increasing trend of enrichment was observed for both diseases in DHS, typical enhancers, and super enhancers located in disease-related tissue. Results from heritability enrichment analysis supported the selective enrichment pattern of functional genomic regions in disease-related cell lines for both breast and prostate cancer. Our results suggest the importance of studying functional annotations identified in disease-related tissues when characterizing GWAS results, and further demonstrate the role of germline DNA regulatory elements from disease-related tissue in breast and prostate carcinogenesis.
Collapse
Affiliation(s)
- Hongjie Chen
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Gleb Kichaev
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA
| | - Stephanie A Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Lu Wang
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Paul Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Bogdan Pasaniuc
- Bioinformatics Interdepartmental Program, University of California Los Angeles, Los Angeles, CA, USA.,Departments of Human Genetics, and Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Sara Lindström
- Department of Epidemiology, University of Washington, Seattle, WA, USA. .,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
| |
Collapse
|
21
|
Roy A, Murphy RM, Deng M, MacDonald JW, Bammler TK, Aldinger KA, Glass IA, Millen KJ. PI3K-Yap activity drives cortical gyrification and hydrocephalus in mice. eLife 2019; 8:45961. [PMID: 31094678 PMCID: PMC6544437 DOI: 10.7554/elife.45961] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/15/2019] [Indexed: 01/07/2023] Open
Abstract
Mechanisms driving the initiation of brain folding are incompletely understood. We have previously characterized mouse models recapitulating human PIK3CA-related brain overgrowth, epilepsy, dysplastic gyrification and hydrocephalus (Roy et al., 2015). Using the same, highly regulatable brain-specific model, here we report PI3K-dependent mechanisms underlying gyrification of the normally smooth mouse cortex, and hydrocephalus. We demonstrate that a brief embryonic Pik3ca activation was sufficient to drive subtle changes in apical cell adhesion and subcellular Yap translocation, causing focal proliferation and subsequent initiation of the stereotypic ‘gyrification sequence’, seen in naturally gyrencephalic mammals. Treatment with verteporfin, a nuclear Yap inhibitor, restored apical surface integrity, normalized proliferation, attenuated gyrification and rescued the associated hydrocephalus, highlighting the interrelated role of regulated PI3K-Yap signaling in normal neural-ependymal development. Our data defines apical cell-adhesion as the earliest known substrate for cortical gyrification. In addition, our preclinical results support the testing of Yap-related small-molecule therapeutics for developmental hydrocephalus.
Collapse
Affiliation(s)
- Achira Roy
- Center for Integrative Brain Research, Seattle Children's Research Institute, Washington, United States
| | - Rory M Murphy
- Center for Integrative Brain Research, Seattle Children's Research Institute, Washington, United States
| | - Mei Deng
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Washington, United States
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Washington, United States
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Washington, United States
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Washington, United States.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Washington, United States
| | - Ian A Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Washington, United States
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Washington, United States.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Washington, United States
| |
Collapse
|
22
|
Cao M, MacDonald JW, Liu HL, Weaver M, Cortes M, Durosier LD, Burns P, Fecteau G, Desrochers A, Schulkin J, Antonelli MC, Bernier RA, Dorschner M, Bammler TK, Frasch MG. α7 Nicotinic Acetylcholine Receptor Signaling Modulates Ovine Fetal Brain Astrocytes Transcriptome in Response to Endotoxin. Front Immunol 2019; 10:1063. [PMID: 31143190 PMCID: PMC6520997 DOI: 10.3389/fimmu.2019.01063] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 04/25/2019] [Indexed: 11/13/2022] Open
Abstract
Neuroinflammation in utero may result in lifelong neurological disabilities. Astrocytes play a pivotal role in this process, but the mechanisms are poorly understood. No early postnatal treatment strategies exist to enhance neuroprotective potential of astrocytes. We hypothesized that agonism on α7 nicotinic acetylcholine receptor (α7nAChR) in fetal astrocytes will augment their neuroprotective transcriptome profile, while the inhibition of α7nAChR will achieve the opposite. Using an in vivo–in vitro model of developmental programming of neuroinflammation induced by lipopolysaccharide (LPS), we validated this hypothesis in primary fetal sheep astrocytes cultures re-exposed to LPS in the presence of a selective α7nAChR agonist or antagonist. Our RNAseq findings show that a pro-inflammatory astrocyte transcriptome phenotype acquired in vitro by LPS stimulation is reversed with α7nAChR agonistic stimulation. Conversely, α7nAChR inhibition potentiates the pro-inflammatory astrocytic transcriptome phenotype. Furthermore, we conducted a secondary transcriptome analysis against the identical α7nAChR experiments in fetal sheep primary microglia cultures. Similar to findings in fetal microglia, in fetal astrocytes we observed a memory effect of in vivo exposure to inflammation, expressed in a perturbation of the iron homeostasis signaling pathway (hemoxygenase 1, HMOX1), which persisted under pre-treatment with α7nAChR antagonist but was reversed with α7nAChR agonist. For both glia cell types, common pathways activated due to LPS included neuroinflammation signaling and NF-κB signaling in some, but not all comparisons. However, overall, the overlap on the level of signaling pathways was rather minimal. Astrocytes, not microglia—the primary immune cells of the brain, were characterized by unique inhibition patterns of STAT3 pathway due to agonistic stimulation of α7nAChR prior to LPS exposure. Lastly, we discuss the implications of our findings for fetal and postnatal brain development.
Collapse
Affiliation(s)
- Mingju Cao
- Department of Obstetrics and Gynaecology and Department of Neurosciences, CHU Ste-Justine Research Centre, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Hai L Liu
- Department of Obstetrics and Gynaecology and Department of Neurosciences, CHU Ste-Justine Research Centre, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Molly Weaver
- UW Medicine Center for Precision Diagnostics, University of Washington, Seattle, WA, United States
| | - Marina Cortes
- Animal Reproduction Research Centre (CRRA), Faculty of Veterinary Medicine, Université de Montréal, Montréal, QC, Canada
| | - Lucien D Durosier
- Department of Obstetrics and Gynaecology and Department of Neurosciences, CHU Ste-Justine Research Centre, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Patrick Burns
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Montréal, QC, Canada
| | - Gilles Fecteau
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Montréal, QC, Canada
| | - André Desrochers
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Université de Montréal, Montréal, QC, Canada
| | - Jay Schulkin
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States
| | - Marta C Antonelli
- Instituto de Biología Celular y Neurociencia "Prof. Eduardo De Robertis", Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, United States
| | - Michael Dorschner
- UW Medicine Center for Precision Diagnostics, University of Washington, Seattle, WA, United States
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, United States
| | - Martin G Frasch
- Department of Obstetrics and Gynaecology and Department of Neurosciences, CHU Ste-Justine Research Centre, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,Animal Reproduction Research Centre (CRRA), Faculty of Veterinary Medicine, Université de Montréal, Montréal, QC, Canada.,Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, United States.,Center on Human Development and Disability, University of Washington, Seattle, WA, United States
| |
Collapse
|
23
|
Goodson JM, MacDonald JW, Bammler TK, Chien WM, Chin MT. In utero exposure to diesel exhaust is associated with alterations in neonatal cardiomyocyte transcription, DNA methylation and metabolic perturbation. Part Fibre Toxicol 2019; 16:17. [PMID: 30975218 PMCID: PMC6460812 DOI: 10.1186/s12989-019-0301-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 04/03/2019] [Indexed: 12/30/2022] Open
Abstract
Background Developmental exposure to particulate matter air pollution is harmful to cardiovascular health, but the mechanisms by which this exposure mediates susceptibility to heart disease is poorly understood. We have previously shown, in a mouse model, that gestational exposure to diesel exhaust (DE) results in increased cardiac hypertrophy, fibrosis and susceptibility to heart failure in the adult offspring following transverse aortic constriction. Results In this study, we have analyzed gene expression in neonatal cardiomyocytes after gestational exposure by RNA-sequencing and have identified 300 genes that are dysregulated, including many involved in cardiac metabolism. We subsequently determined that these cardiomyocytes exhibit reduced metabolic activity as measured by Seahorse extracellular flux analysis. We also surveyed for modifications in DNA methylation at global regulatory regions using reduced representation bisulfite sequencing and found hypomethylation of DNA in neonatal cardiomyocytes isolated from in utero DE exposed neonates. Conclusion We have demonstrated that in utero exposure to diesel exhaust alters the neonatal cardiomyocyte transcriptional and epigenetic landscapes, as well as the metabolic capability of these cells. Understanding how exposure alters the developing heart through dysregulation of gene expression, metabolism and DNA methylation is vital for identifying therapeutic interventions for air pollution-related heart failure.
Collapse
Affiliation(s)
- Jamie M Goodson
- Department of Pathology, University of Washington School of Medicine, Seattle, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, Seattle, USA
| | - Wei-Ming Chien
- Division of Cardiology, Department of Medicine, University of Washington School of Medicine, Seattle, USA
| | - Michael T Chin
- Division of Cardiology, Department of Medicine, University of Washington School of Medicine, Seattle, USA. .,Department of Pathology, University of Washington School of Medicine, Seattle, USA. .,Molecular Cardiology Research Institute, Tufts Medical Center, Seattle, USA. .,Tufts Hypertrophic Cardiomyopathy Center and Research Institute, MCRI/CVC, Tufts Medical Center, 800 Washington Street, Box 80, Boston, MA, 02111, USA.
| |
Collapse
|
24
|
Massaro AN, Wu YW, Bammler TK, MacDonald JW, Mathur A, Chang T, Mayock D, Mulkey SB, van Meurs K, Afsharinejad Z, Juul SE. Dried blood spot compared to plasma measurements of blood-based biomarkers of brain injury in neonatal encephalopathy. Pediatr Res 2019; 85:655-661. [PMID: 30661082 DOI: 10.1038/s41390-019-0298-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 01/04/2019] [Accepted: 01/08/2019] [Indexed: 12/25/2022]
Abstract
BACKGROUND Data correlating dried blood spots (DBS) and plasma concentrations for neonatal biomarkers of brain injury are lacking. We hypothesized that candidate biomarker levels determined from DBS can serve as a reliable surrogate for plasma levels. METHODS In the context of a phase II multi-center trial evaluating erythropoietin for neuroprotection in neonatal encephalopathy (NE), DBS were collected at enrollment ( < 24 h), day 2, 4, and 5. Plasma was collected with the first and last DBS. The relationship between paired DBS-plasma determinations of brain-specific proteins and cytokines was assessed by correlation and Bland-Altman analyses. For analytes with consistent DBS-plasma associations, DBS-derived biomarker levels were related to brain injury by MRI and 1-year outcomes. RESULTS We enrolled 50 newborns with NE. While S100B protein, tumor necrosis factor α, interleukin (IL)1 β, IL-6, IL-8 demonstrated significant DBS-plasma correlations, Bland-Altman plots demonstrated that the methods are not interchangeable, with a 2 to 4-fold error between measurements. No significant relationships were found between DBS levels of TNFα, IL-6, and IL-8 and outcomes. CONCLUSION Further work is needed to optimize elution and assay methods before using DBS specimens as a reliable surrogate for plasma levels of candidate brain injury biomarkers in NE.
Collapse
Affiliation(s)
- An N Massaro
- Pediatrics - Division of Neonatology, Children's National Health Systems and The George Washington University School of Medicine, Washington, DC, USA.
| | - Yvonne W Wu
- Neurology and Pediatrics, UCSF, San Francisco, CA, USA
| | - Theo K Bammler
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Amit Mathur
- Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Taeun Chang
- Neurology and Pediatrics, Children's National Health Systems and The George Washington University School of Medicine, Washington, DC, USA
| | - Dennis Mayock
- Pediatrics-Division of Neonatology, University of Washington, Seattle, WA, USA
| | - Sarah B Mulkey
- Neurology and Pediatrics, Children's National Health Systems and The George Washington University School of Medicine, Washington, DC, USA
| | | | - Zahra Afsharinejad
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Sandra E Juul
- Pediatrics-Division of Neonatology, University of Washington, Seattle, WA, USA
| |
Collapse
|
25
|
Vincow ES, Thomas RE, Merrihew GE, Shulman NJ, Bammler TK, MacDonald JW, MacCoss MJ, Pallanck LJ. Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective. Autophagy 2019; 15:1592-1605. [PMID: 30865561 DOI: 10.1080/15548627.2019.1586258] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The destruction of mitochondria through macroautophagy (autophagy) has been recognised as a major route of mitochondrial protein degradation since its discovery more than 50 years ago, but fundamental questions remain unanswered. First, how much mitochondrial protein turnover occurs through auto-phagy? Mitochondrial proteins are also degraded by nonautophagic mechanisms, and the proportion of mitochondrial protein turnover that occurs through autophagy is still unknown. Second, does auto-phagy degrade mitochondrial proteins uniformly or selectively? Autophagy was originally thought to degrade all mitochondrial proteins at the same rate, but recent work suggests that mitochondrial autophagy may be protein selective. To investigate these questions, we used a proteomics-based approach in the fruit fly Drosophila melanogaster, comparing mitochondrial protein turnover rates in autophagy-deficient Atg7 mutants and controls. We found that ~35% of mitochondrial protein turnover occurred via autophagy. Similar analyses using parkin mutants revealed that parkin-dependent mitophagy accounted for ~25% of mitochondrial protein turnover, suggesting that most mitochondrial autophagy specifically eliminates dysfunctional mitochondria. We also found that our results were incompatible with uniform autophagic turnover of mitochondrial proteins and consistent with protein-selective autophagy. In particular, the autophagic turnover rates of individual mitochondrial proteins varied widely, and only a small amount of the variation could be attributed to tissue differences in mitochondrial composition and autophagy rate. Furthermore, analyses comparing autophagy-deficient and control human fibroblasts revealed diverse autophagy-dependent turnover rates even in homogeneous cells. In summary, our work indicates that autophagy acts selectively on mitochondrial proteins, and that most mitochondrial protein turnover occurs through non-autophagic processes. Abbreviations: Atg5: Autophagy-related 5 (Drosophila); ATG5: autophagy related 5 (human); Atg7: Autophagy-related 7 (Drosophila); ATG7: autophagy related 7 (human); DNA: deoxyribonucleic acid; ER: endoplasmic reticulum; GFP: green fluorescent protein; MS: mass spectrometry; park: parkin (Drosophila); Pink1: PTEN-induced putative kinase 1 (Drosophila); PINK1: PTEN-induced kinase 1 (human); PRKN: parkin RBR E3 ubiquitin protein ligase (human); RNA: ribonucleic acid; SD: standard deviation; Ub: ubiquitin/ubiquitinated; WT: wild-type; YME1L: YME1 like ATPase (Drosophila); YME1L1: YME1 like 1 ATPase (human).
Collapse
Affiliation(s)
- Evelyn S Vincow
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Ruth E Thomas
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Gennifer E Merrihew
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Nicholas J Shulman
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Theo K Bammler
- b Department of Environmental and Occupational Health Sciences, University of Washington , Seattle , WA , USA
| | - James W MacDonald
- b Department of Environmental and Occupational Health Sciences, University of Washington , Seattle , WA , USA
| | - Michael J MacCoss
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| | - Leo J Pallanck
- a Department of Genome Sciences, University of Washington , Seattle , WA , USA
| |
Collapse
|
26
|
Williams CR, Dittman AH, McElhany P, Busch DS, Maher M, Bammler TK, MacDonald JW, Gallagher EP. Elevated CO 2 impairs olfactory-mediated neural and behavioral responses and gene expression in ocean-phase coho salmon (Oncorhynchus kisutch). Glob Chang Biol 2019; 25:963-977. [PMID: 30561876 PMCID: PMC7065673 DOI: 10.1111/gcb.14532] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [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: 09/12/2018] [Accepted: 11/06/2018] [Indexed: 05/16/2023]
Abstract
Elevated concentrations of CO2 in seawater can disrupt numerous sensory systems in marine fish. This is of particular concern for Pacific salmon because they rely on olfaction during all aspects of their life including during their homing migrations from the ocean back to their natal streams. We investigated the effects of elevated seawater CO2 on coho salmon (Oncorhynchus kisutch) olfactory-mediated behavior, neural signaling, and gene expression within the peripheral and central olfactory system. Ocean-phase coho salmon were exposed to three levels of CO2 , ranging from those currently found in ambient marine water to projected future levels. Juvenile coho salmon exposed to elevated CO2 levels for 2 weeks no longer avoided a skin extract odor that elicited avoidance responses in coho salmon maintained in ambient CO2 seawater. Exposure to these elevated CO2 levels did not alter odor signaling in the olfactory epithelium, but did induce significant changes in signaling within the olfactory bulb. RNA-Seq analysis of olfactory tissues revealed extensive disruption in expression of genes involved in neuronal signaling within the olfactory bulb of salmon exposed to elevated CO2 , with lesser impacts on gene expression in the olfactory rosettes. The disruption in olfactory bulb gene pathways included genes associated with GABA signaling and maintenance of ion balance within bulbar neurons. Our results indicate that ocean-phase coho salmon exposed to elevated CO2 can experience significant behavioral impairments likely driven by alteration in higher-order neural signal processing within the olfactory bulb. Our study demonstrates that anadromous fish such as salmon may share a sensitivity to rising CO2 levels with obligate marine species suggesting a more wide-scale ecological impact of ocean acidification.
Collapse
Affiliation(s)
- Chase R. Williams
- Department of Environmental and Occupational Health Sciences. University of Washington. Seattle, WA 98105
| | - Andrew H. Dittman
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E Seattle WA 98112, USA
- Corresponding author at NOAA fisheries, Andrew H. Dittman, Ph.D., Tel: 206-860-3392,
| | - Paul McElhany
- Conservation Biology Division, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 802 Front Street, Mukilteo, WA 98275, USA
| | - D. Shallin Busch
- Conservation Biology Division, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 802 Front Street, Mukilteo, WA 98275, USA
- Ocean Acidification Program, Office of Oceanic and Atmospheric Research, National Oceanic and Atmospheric Administration, 2725 Montlake Blvd E, Seattle WA 98112, USA
| | - Michael Maher
- Conservation Biology Division, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 802 Front Street, Mukilteo, WA 98275, USA
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences. University of Washington. Seattle, WA 98105
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences. University of Washington. Seattle, WA 98105
| | - Evan P. Gallagher
- Department of Environmental and Occupational Health Sciences. University of Washington. Seattle, WA 98105
- Corresponding author at the University of Washington, Evan P. Gallagher, Ph.D., Tel: 1-206-616-4739,
| |
Collapse
|
27
|
Weber EJ, Lidberg KA, Wang L, Bammler TK, MacDonald JW, Li MJ, Redhair M, Atkins WM, Tran C, Hines KM, Herron J, Xu L, Monteiro MB, Ramm S, Vaidya V, Vaara M, Vaara T, Himmelfarb J, Kelly EJ. Human kidney on a chip assessment of polymyxin antibiotic nephrotoxicity. JCI Insight 2018; 3:123673. [PMID: 30568031 DOI: 10.1172/jci.insight.123673] [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: 07/18/2018] [Accepted: 11/06/2018] [Indexed: 12/22/2022] Open
Abstract
Drug-induced kidney injury, largely caused by proximal tubular intoxicants, limits development and clinical use of new and approved drugs. Assessing preclinical nephrotoxicity relies on animal models that are frequently insensitive; thus, potentially novel techniques - including human microphysiological systems, or "organs on chips" - are proposed to accelerate drug development and predict safety. Polymyxins are potent antibiotics against multidrug-resistant microorganisms; however, clinical use remains restricted because of high risk of nephrotoxicity and limited understanding of toxicological mechanisms. To mitigate risks, structural analogs of polymyxins (NAB739 and NAB741) are currently in clinical development. Using a microphysiological system to model human kidney proximal tubule, we exposed cells to polymyxin B (PMB) and observed significant increases of injury signals, including kidney injury molecule-1 KIM-1and a panel of injury-associated miRNAs (each P < 0.001). Surprisingly, transcriptional profiling identified cholesterol biosynthesis as the primary cellular pathway induced by PMB (P = 1.22 ×10-16), and effluent cholesterol concentrations were significantly increased after exposure (P < 0.01). Additionally, we observed no upregulation of the nuclear factor (erythroid derived-2)-like 2 pathway, despite this being a common pathway upregulated in response to proximal tubule toxicants. In contrast with PMB exposure, minimal changes in gene expression, injury biomarkers, and cholesterol concentrations were observed in response to NAB739 and NAB741. Our findings demonstrate the preclinical safety of NAB739 and NAB741 and reveal cholesterol biosynthesis as a potentially novel pathway for PMB-induced injury. To our knowledge, this is the first demonstration of a human-on-chip platform used for simultaneous safety testing of new chemical entities and defining unique toxicological pathway responses of an FDA-approved molecule.
Collapse
Affiliation(s)
| | | | - Lu Wang
- Department of Environmental and Occupational Health Sciences, and
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, and
| | | | - Mavis J Li
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Michelle Redhair
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Cecilia Tran
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Kelly M Hines
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Josi Herron
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Maria Beatriz Monteiro
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts, USA
| | - Susanne Ramm
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts, USA
| | - Vishal Vaidya
- Laboratory of Systems Pharmacology, Harvard Program in Therapeutic Science, Harvard Medical School, Boston, Massachusetts, USA
| | - Martti Vaara
- Northern Antibiotics Ltd., Espoo, Finland.,Division of Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland.,Department of Bacteriology and Immunology, Helsinki University Medical School, Helsinki, Finland
| | - Timo Vaara
- Northern Antibiotics Ltd., Espoo, Finland
| | - Jonathan Himmelfarb
- Department of Medicine, Division of Nephrology, Kidney Research Institute, Seattle, Washington, USA
| | | |
Collapse
|
28
|
Elsen GE, Bedogni F, Hodge RD, Bammler TK, MacDonald JW, Lindtner S, Rubenstein JLR, Hevner RF. The Epigenetic Factor Landscape of Developing Neocortex Is Regulated by Transcription Factors Pax6→ Tbr2→ Tbr1. Front Neurosci 2018; 12:571. [PMID: 30186101 PMCID: PMC6113890 DOI: 10.3389/fnins.2018.00571] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022] Open
Abstract
Epigenetic factors (EFs) regulate multiple aspects of cerebral cortex development, including proliferation, differentiation, laminar fate, and regional identity. The same neurodevelopmental processes are also regulated by transcription factors (TFs), notably the Pax6→ Tbr2→ Tbr1 cascade expressed sequentially in radial glial progenitors (RGPs), intermediate progenitors, and postmitotic projection neurons, respectively. Here, we studied the EF landscape and its regulation in embryonic mouse neocortex. Microarray and in situ hybridization assays revealed that many EF genes are expressed in specific cortical cell types, such as intermediate progenitors, or in rostrocaudal gradients. Furthermore, many EF genes are directly bound and transcriptionally regulated by Pax6, Tbr2, or Tbr1, as determined by chromatin immunoprecipitation-sequencing and gene expression analysis of TF mutant cortices. Our analysis demonstrated that Pax6, Tbr2, and Tbr1 form a direct feedforward genetic cascade, with direct feedback repression. Results also revealed that each TF regulates multiple EF genes that control DNA methylation, histone marks, chromatin remodeling, and non-coding RNA. For example, Tbr1 activates Rybp and Auts2 to promote the formation of non-canonical Polycomb repressive complex 1 (PRC1). Also, Pax6, Tbr2, and Tbr1 collectively drive massive changes in the subunit isoform composition of BAF chromatin remodeling complexes during differentiation: for example, a novel switch from Bcl7c (Baf40c) to Bcl7a (Baf40a), the latter directly activated by Tbr2. Of 11 subunits predominantly in neuronal BAF, 7 were transcriptionally activated by Pax6, Tbr2, or Tbr1. Using EFs, Pax6→ Tbr2→ Tbr1 effect persistent changes of gene expression in cell lineages, to propagate features such as regional and laminar identity from progenitors to neurons.
Collapse
Affiliation(s)
- Gina E. Elsen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Francesco Bedogni
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Rebecca D. Hodge
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States
| | - Susan Lindtner
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, United States
| | - John L. R. Rubenstein
- Nina Ireland Laboratory of Developmental Neurobiology, University of California, San Francisco, San Francisco, CA, United States
- Department of Psychiatry, University of California, San Francisco, San Francisco, CA, United States
| | - Robert F. Hevner
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, United States
- Department of Neurological Surgery, School of Medicine, University of Washington, Seattle, WA, United States
| |
Collapse
|
29
|
Marcu R, Choi YJ, Xue J, Fortin CL, Wang Y, Nagao RJ, Xu J, MacDonald JW, Bammler TK, Murry CE, Muczynski K, Stevens KR, Himmelfarb J, Schwartz SM, Zheng Y. Human Organ-Specific Endothelial Cell Heterogeneity. iScience 2018; 4:20-35. [PMID: 30240741 PMCID: PMC6147238 DOI: 10.1016/j.isci.2018.05.003] [Citation(s) in RCA: 148] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 04/24/2018] [Accepted: 05/03/2018] [Indexed: 12/20/2022] Open
Abstract
The endothelium first forms in the blood islands in the extra-embryonic yolk sac and then throughout the embryo to establish circulatory networks that further acquire organ-specific properties during development to support diverse organ functions. Here, we investigated the properties of endothelial cells (ECs), isolated from four human major organs-the heart, lung, liver, and kidneys-in individual fetal tissues at three months' gestation, at gene expression, and at cellular function levels. We showed that organ-specific ECs have distinct expression patterns of gene clusters, which support their specific organ development and functions. These ECs displayed distinct barrier properties, angiogenic potential, and metabolic rate and support specific organ functions. Our findings showed the link between human EC heterogeneity and organ development and can be exploited therapeutically to contribute in organ regeneration, disease modeling, as well as guiding differentiation of tissue-specific ECs from human pluripotent stem cells.
Collapse
Affiliation(s)
- Raluca Marcu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Yoon Jung Choi
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jun Xue
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Chelsea L Fortin
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Yuliang Wang
- Department of Computer Science & Engineering, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Ryan J Nagao
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Jin Xu
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - James W MacDonald
- Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Theo K Bammler
- Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, USA
| | - Charles E Murry
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA
| | | | - Kelly R Stevens
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Department of Pathology, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Jonathan Himmelfarb
- Department of Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, University of Washington, Seattle, WA, USA
| | | | - Ying Zheng
- Department of Bioengineering, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Kidney Research Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
30
|
Mitchell T, MacDonald JW, Srinouanpranchanh S, Bammler TK, Merillat S, Boldenow E, Coleman M, Agnew K, Baldessari A, Stencel-Baerenwald JE, Tisoncik-Go J, Green RR, Gale MJ, Rajagopal L, Adams Waldorf KM. Evidence of cardiac involvement in the fetal inflammatory response syndrome: disruption of gene networks programming cardiac development in nonhuman primates. Am J Obstet Gynecol 2018; 218:438.e1-438.e16. [PMID: 29475580 PMCID: PMC6070341 DOI: 10.1016/j.ajog.2018.01.009] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 12/22/2017] [Accepted: 01/04/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Most early preterm births are associated with intraamniotic infection and inflammation, which can lead to systemic inflammation in the fetus. The fetal inflammatory response syndrome describes elevations in the fetal interleukin-6 level, which is a marker for inflammation and fetal organ injury. An understanding of the effects of inflammation on fetal cardiac development may lead to insight into the fetal origins of adult cardiovascular disease. OBJECTIVE The purpose of this study was to determine whether the fetal inflammatory response syndrome is associated with disruptions in gene networks that program fetal cardiac development. STUDY DESIGN We obtained fetal cardiac tissue after necropsy from a well-described pregnant nonhuman primate model (pigtail macaque, Macaca nemestrina) of intrauterine infection (n=5) and controls (n=5). Cases with the fetal inflammatory response syndrome (fetal plasma interleukin-6 >11 pg/mL) were induced by either choriodecidual inoculation of a hypervirulent group B streptococcus strain (n=4) or intraamniotic inoculation of Escherichia coli (n=1). RNA and protein were extracted from fetal hearts and profiled by microarray and Luminex (Millipore, Billerica, MA) for cytokine analysis, respectively. Results were validated by quantitative reverse transcriptase polymerase chain reaction. Statistical and bioinformatics analyses included single gene analysis, gene set analysis, Ingenuity Pathway Analysis (Qiagen, Valencia, CA), and Wilcoxon rank sum. RESULTS Severe fetal inflammation developed in the context of intraamniotic infection and a disseminated bacterial infection in the fetus. Interleukin-6 and -8 in fetal cardiac tissues were elevated significantly in fetal inflammatory response syndrome cases vs controls (P<.05). A total of 609 probe sets were expressed differentially (>1.5-fold change, P<.05) in the fetal heart (analysis of variance). Altered expression of select genes was validated by quantitative reverse transcriptase polymerase chain reaction that included several with known functions in cardiac injury, morphogenesis, angiogenesis, and tissue remodeling (eg, angiotensin I converting enzyme 2, STEAP family member 4, natriuretic peptide A, and secreted frizzled-related protein 4; all P<.05). Multiple gene sets and pathways that are involved in cardiac morphogenesis and vasculogenesis were downregulated significantly by gene set and Ingenuity Pathway Analysis (hallmark transforming growth factor beta signaling, cellular morphogenesis during differentiation, morphology of cardiovascular system; all P<.05). CONCLUSION Disruption of gene networks for cardiac morphogenesis and vasculogenesis occurred in the preterm fetal heart of nonhuman primates with preterm labor, intraamniotic infection, and severe fetal inflammation. Inflammatory injury to the fetal heart in utero may contribute to the development of heart disease later in life. Development of preterm labor therapeutics must also target fetal inflammation to lessen organ injury and potential long-term effects on cardiac function.
Collapse
Affiliation(s)
- Timothy Mitchell
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA
| | | | - Theodor K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA
| | - Sean Merillat
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Erica Boldenow
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | | | - Kathy Agnew
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA
| | - Audrey Baldessari
- Washington National Primate Research Center, University of Washington, Seattle, WA
| | - Jennifer E Stencel-Baerenwald
- Department of Immunology, University of Washington, Seattle, WA; Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Jennifer Tisoncik-Go
- Department of Immunology, University of Washington, Seattle, WA; Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Richard R Green
- Department of Immunology, University of Washington, Seattle, WA; Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Michael J Gale
- Department of Immunology, University of Washington, Seattle, WA; Department of Global Health, University of Washington, Seattle, WA; Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA
| | - Lakshmi Rajagopal
- Department of Pediatrics, University of Washington, Seattle, WA; Department of Global Health, University of Washington, Seattle, WA; Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA; Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Kristina M Adams Waldorf
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA; Department of Global Health, University of Washington, Seattle, WA; Center for Innate Immunity and Immune Disease, University of Washington, Seattle, WA; Sahlgrenska Academy, Gothenburg, Sweden.
| |
Collapse
|
31
|
Goodson JM, Weldy CS, MacDonald JW, Liu Y, Bammler TK, Chien WM, Chin MT. In utero exposure to diesel exhaust particulates is associated with an altered cardiac transcriptional response to transverse aortic constriction and altered DNA methylation. FASEB J 2017; 31:4935-4945. [PMID: 28751527 DOI: 10.1096/fj.201700032r] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 07/10/2017] [Indexed: 12/13/2022]
Abstract
In utero exposure to diesel exhaust air pollution has been associated with increased adult susceptibility to heart failure in mice, but the mechanisms by which this exposure promotes susceptibility to heart failure are poorly understood. To identify the potential transcriptional effects that mediate this susceptibility, we have performed RNA sequencing analysis on adult hearts from mice that were exposed to diesel exhaust in utero and that have subsequently undergone transverse aortic constriction. We identified 3 target genes, Mir133a-2, Ptprf, and Pamr1, which demonstrate dysregulation after exposure and aortic constriction. Examination of expression patterns in human heart tissues indicates a correlation between expression and heart failure. We subsequently assessed DNA methylation modifications at these candidate loci in neonatal cultured cardiac myocytes after in utero exposure to diesel exhaust and found that the promoter for Mir133a-2 is differentially methylated. These target genes in the heart are the first genes to be identified that likely play an important role in mediating adult sensitivity to heart failure. We have also shown a change in DNA methylation within cardiomyocytes as a result of in utero exposure to diesel exhaust.-Goodson, J. M., Weldy, C. S., MacDonald, J. W., Liu, Y., Bammler, T. K., Chien, W.-M., Chin, M. T. In utero exposure to diesel exhaust particulates is associated with an altered cardiac transcriptional response to transverse aortic constriction and altered DNA methylation.
Collapse
Affiliation(s)
- Jamie M Goodson
- Department of Pathology, University of Washington School of Medicine, University of Washington, Seattle, Washington, USA
| | - Chad S Weldy
- Department of Pathology, University of Washington School of Medicine, University of Washington, Seattle, Washington, USA.,Division of Cardiology, Department of Medicine, University of Washington School of Medicine, University of Washington, Seattle, Washington, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, University of Washington, Seattle, Washington, USA
| | - Yonggang Liu
- Division of Cardiology, Department of Medicine, University of Washington School of Medicine, University of Washington, Seattle, Washington, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington School of Public Health, University of Washington, Seattle, Washington, USA
| | - Wei-Ming Chien
- Division of Cardiology, Department of Medicine, University of Washington School of Medicine, University of Washington, Seattle, Washington, USA
| | - Michael T Chin
- Department of Pathology, University of Washington School of Medicine, University of Washington, Seattle, Washington, USA .,Division of Cardiology, Department of Medicine, University of Washington School of Medicine, University of Washington, Seattle, Washington, USA
| |
Collapse
|
32
|
Scoville DK, Botta D, Galdanes K, Schmuck SC, White CC, Stapleton PL, Bammler TK, MacDonald JW, Altemeier WA, Hernandez M, Kleeberger SR, Chen LC, Gordon T, Kavanagh TJ. Genetic determinants of susceptibility to silver nanoparticle-induced acute lung inflammation in mice. FASEB J 2017; 31:4600-4611. [PMID: 28716969 DOI: 10.1096/fj.201700187r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 03/03/2017] [Accepted: 06/19/2017] [Indexed: 12/12/2022]
Abstract
Silver nanoparticles (AgNPs) are employed in a variety of consumer products; however, in vivo rodent studies indicate that AgNPs can cause lung inflammation and toxicity in a strain- and particle type-dependent manner, but mechanisms of susceptibility remain unclear. The aim of this study was to assess the variation in AgNP-induced lung inflammation and toxicity across multiple inbred mouse strains and to use genome-wide association (GWA) mapping to identify potential candidate susceptibility genes. Mice received doses of 0.25 mg/kg of either 20-nm citrate-coated AgNPs or citrate buffer using oropharyngeal aspiration. Neutrophils in bronchoalveolar lavage fluid (BALF) served as markers of inflammation. We found significant strain- and treatment-dependent variation in neutrophils in BALF. GWA mapping identified 10 significant single-nucleotide polymorphisms (false discovery rate, 15%) in 4 quantitative trait loci on mouse chromosomes 1, 4, 15, and 18, and Nedd4l (neural precursor cell expressed developmentally downregulated gene 4-like; chromosome 18), Ano6 (anocatmin 6; chromosome 15), and Rnf220 (Ring finger protein 220; chromosome 4) were considered candidate genes. Quantitative RT-PCR revealed significant inverse associations between mRNA levels of these genes and neutrophil influx. Nedd4l, Ano6, and Rnf220 are candidate susceptibility genes for AgNP-induced lung inflammation that warrant additional exploration in future studies.-Scoville, D. K., Botta, D., Galdanes, K., Schmuck, S. C., White, C. C., Stapleton, P. L., Bammler, T. K., MacDonald, J. W., Altemeier, W. A., Hernandez, M., Kleeberger, S. R., Chen, L.-C., Gordon, T., Kavanagh, T. J. Genetic determinants of susceptibility to silver nanoparticle-induced acute lung inflammation in mice.
Collapse
Affiliation(s)
- David K Scoville
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Dianne Botta
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Karen Galdanes
- Department of Environmental Medicine, New York University, Tuxedo, New York, USA
| | - Stefanie C Schmuck
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Collin C White
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Patricia L Stapleton
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA
| | | | - Michelle Hernandez
- Department of Environmental Medicine, New York University, Tuxedo, New York, USA
| | - Steven R Kleeberger
- Immunity, Inflammation, and Disease Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA
| | - Lung-Chi Chen
- Department of Environmental Medicine, New York University, Tuxedo, New York, USA
| | - Terry Gordon
- Department of Environmental Medicine, New York University, Tuxedo, New York, USA
| | - Terrance J Kavanagh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, USA;
| |
Collapse
|
33
|
Chi GC, Liu Y, MacDonald JW, Barr RG, Donohue KM, Hensley MD, Hou L, McCall CE, Reynolds LM, Siscovick DS, Kaufman JD. Long-term outdoor air pollution and DNA methylation in circulating monocytes: results from the Multi-Ethnic Study of Atherosclerosis (MESA). Environ Health 2016; 15:119. [PMID: 27903268 PMCID: PMC5131503 DOI: 10.1186/s12940-016-0202-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/24/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND DNA methylation may mediate effects of air pollution on cardiovascular disease. The association between long-term air pollution exposure and DNA methylation in monocytes, which are central to atherosclerosis, has not been studied. We investigated the association between long-term ambient air pollution exposure and DNA methylation (candidate sites and global) in monocytes of adults (aged ≥55). METHODS One-year average ambient fine particulate matter (PM2.5) and oxides of nitrogen (NOX) concentrations were predicted at participants' (n = 1,207) addresses using spatiotemporal models. We assessed DNA methylation in circulating monocytes at 1) 2,713 CpG sites associated with mRNA expression of nearby genes and 2) probes mapping to Alu and LINE-1 repetitive elements (surrogates for global DNA methylation) using Illumina's Infinium HumanMethylation450 BeadChip. We used linear regression models adjusted for demographics, smoking, physical activity, socioeconomic status, methyl-nutrients, and technical variables. For significant air pollution-associated methylation sites, we also assessed the association between expression of gene transcripts previously associated with these CpG sites and air pollution. RESULTS At a false discovery rate of 0.05, five candidate CpGs (cg20455854, cg07855639, cg07598385, cg17360854, and cg23599683) had methylation significantly associated with PM2.5 and none were associated with NOX. Cg20455854 had the smallest p-value for the association with PM2.5 (p = 2.77 × 10-5). mRNA expression profiles of genes near three of the PM2.5-associated CpGs (ANKHD1, LGALS2, and ANKRD11) were also significantly associated with PM2.5 exposure. Alu and LINE-1 methylation were not associated with long-term air pollution exposure. CONCLUSIONS We observed novel associations between long-term ambient air pollution exposure and site-specific DNA methylation, but not global DNA methylation, in purified monocytes of a multi-ethnic adult population. Epigenetic markers may provide insights into mechanisms underlying environmental factors in complex diseases like atherosclerosis.
Collapse
Affiliation(s)
- Gloria C. Chi
- Department of Epidemiology, School of Public Health, University of Washington, 1959 NE Pacific St, Box 357236, Seattle, WA 98195 USA
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC USA
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA USA
| | - R. Graham Barr
- Division of General Medicine, Mailman School of Public Health, Columbia University, New York, NY USA
- Division of Pulmonary, Allergy & Critical Care, Columbia University Medical Center, New York, NY USA
| | - Kathleen M. Donohue
- Division of General Medicine, Mailman School of Public Health, Columbia University, New York, NY USA
- Division of Pulmonary, Allergy & Critical Care, Columbia University Medical Center, New York, NY USA
| | - Mark D. Hensley
- Department of Epidemiology, School of Public Health, University of Washington, 1959 NE Pacific St, Box 357236, Seattle, WA 98195 USA
| | - Lifang Hou
- Department of Preventive Medicine, Division of Cancer Epidemiology and Prevention, Feinberg School of Medicine, Northwestern University, Chicago, IL USA
| | - Charles E. McCall
- Section on Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC USA
| | - Lindsay M. Reynolds
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC USA
| | | | - Joel D. Kaufman
- Department of Epidemiology, School of Public Health, University of Washington, 1959 NE Pacific St, Box 357236, Seattle, WA 98195 USA
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA USA
| |
Collapse
|
34
|
Boldenow E, Gendrin C, Ngo L, Bierle C, Vornhagen J, Coleman M, Merillat S, Armistead B, Whidbey C, Alishetti V, Santana-Ufret V, Ogle J, Gough M, Srinouanprachanh S, MacDonald JW, Bammler TK, Bansal A, Liggitt HD, Rajagopal L, Adams Waldorf KM. Group B Streptococcus circumvents neutrophils and neutrophil extracellular traps during amniotic cavity invasion and preterm labor. Sci Immunol 2016; 1:1/4/eaah4576. [PMID: 27819066 DOI: 10.1126/sciimmunol.aah4576] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Preterm birth is a leading cause of neonatal morbidity and mortality. Although microbial invasion of the amniotic cavity (MIAC) is associated with the majority of early preterm births, the temporal events that occur during MIAC and preterm labor are not known. Group B Streptococci (GBS) are β-hemolytic, gram-positive bacteria, which commonly colonize the vagina but have been recovered from the amniotic fluid in preterm birth cases. To understand temporal events that occur during MIAC, we utilized a unique chronically catheterized nonhuman primate model that closely emulates human pregnancy. This model allows monitoring of uterine contractions, timing of MIAC and immune responses during pregnancy-associated infections. Here, we show that adverse outcomes such as preterm labor, MIAC, and fetal sepsis were observed more frequently during infection with hemolytic GBS when compared to nonhemolytic GBS. Although MIAC was associated with systematic progression in chorioamnionitis beginning with chorionic vasculitis and progressing to neutrophilic infiltration, the ability of the GBS hemolytic pigment toxin to induce neutrophil cell death and subvert killing by neutrophil extracellular traps (NETs) in placental membranes in vivo facilitated MIAC and fetal injury. Furthermore, compared to maternal neutrophils, fetal neutrophils exhibit decreased neutrophil elastase activity and impaired phagocytic functions to GBS. Collectively, our studies demonstrate how a unique bacterial hemolytic lipid toxin enables GBS to circumvent neutrophils and NETs in placental membranes to induce fetal injury and preterm labor.
Collapse
Affiliation(s)
- Erica Boldenow
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Claire Gendrin
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Lisa Ngo
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Craig Bierle
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Jay Vornhagen
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America; Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michelle Coleman
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Sean Merillat
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Blair Armistead
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America; Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Christopher Whidbey
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America; Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Varchita Alishetti
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Veronica Santana-Ufret
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Jason Ogle
- Washington National Primate Center, University of Washington, Seattle, Washington, United States of America
| | - Michael Gough
- Washington National Primate Center, University of Washington, Seattle, Washington, United States of America
| | - Sengkeo Srinouanprachanh
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Aasthaa Bansal
- Department of Pharmacy, University of Washington, Seattle, Washington, United States of America
| | - H Denny Liggitt
- Department of Comparative Medicine, University of Washington, Seattle, Washington, United States of America
| | - Lakshmi Rajagopal
- Department of Pediatric Infectious Diseases, University of Washington and Seattle Children's Research Institute, Seattle, Washington, United States of America; Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Kristina M Adams Waldorf
- Department of Obstetrics & Gynecology, University of Washington, Seattle, Washington, United States of America
| |
Collapse
|
35
|
Williams CR, MacDonald JW, Bammler TK, Paulsen MH, Simpson CD, Gallagher EP. From the Cover: Cadmium Exposure Differentially Alters Odorant-Driven Behaviors and Expression of Olfactory Receptors in Juvenile Coho Salmon (Oncorhynchus kisutch). Toxicol Sci 2016; 154:267-277. [PMID: 27621283 DOI: 10.1093/toxsci/kfw172] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Salmon exposed to waterborne metals can experience olfactory impairment leading to disrupted chemosensation. In the current study, we investigated the effects of cadmium (Cd) on salmon olfactory function by modeling an exposure scenario where juvenile salmon transiently migrate through a polluted waterway. Coho were exposed to environmentally relevant concentrations of waterborne Cd (2 and 30 µg/L) for 48 h and (0.3 and 2 μg/L) for 16 days, followed by a 16-day depuration associated with outmigration. Cadmium exposures inhibited behavioral responses towards L-cysteine and conspecific odorants, with effects persisting following the depuration. Behavioral alterations following the 30 µg/L exposure were associated with increased olfactory epithelial gene expression of metallothionein (mt1a) and heme oxygenase (hmox1); reduced expression of olfactory signal transduction (OST) molecules; and reduced expression of mRNAs encoding major coho odorant receptors (ORs). Salmon OR array analysis indicated that Cd preferentially impacted expression of OST and OR markers for ciliated olfactory sensory neurons (OSNs) relative to microvillus OSNs, suggesting a differential sensitivity of these two major OSN populations. Behavioral alterations on exposure to 0.3 and 2 µg/L Cd were associated with increased mt1a, but not with major histological or OR molecular changes, likely indicating disrupted OST as a major mechanism underlying the behavioral dysfunction at the low-level Cd exposures. Laser-ablation mass spectrometry analysis revealed that the OSN injury and behavioral dysfunction was associated with significant Cd bioaccumulation within the olfactory sensory epithelium. In summary, low-level Cd exposures associated with polluted waterways can induce differential and persistent olfactory dysfunction in juvenile coho salmon.
Collapse
Affiliation(s)
- Chase R Williams
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Michael H Paulsen
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Christopher D Simpson
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| | - Evan P Gallagher
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98105
| |
Collapse
|
36
|
Ligresti G, Nagao RJ, Xue J, Choi YJ, Xu J, Ren S, Aburatani T, Anderson SK, MacDonald JW, Bammler TK, Schwartz SM, Muczynski KA, Duffield JS, Himmelfarb J, Zheng Y. A Novel Three-Dimensional Human Peritubular Microvascular System. J Am Soc Nephrol 2015; 27:2370-81. [PMID: 26657868 DOI: 10.1681/asn.2015070747] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [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: 07/08/2015] [Accepted: 10/29/2015] [Indexed: 12/21/2022] Open
Abstract
Human kidney peritubular capillaries are particularly susceptible to injury, resulting in dysregulated angiogenesis, capillary rarefaction and regression, and progressive loss of kidney function. However, little is known about the structure and function of human kidney microvasculature. Here, we isolated, purified, and characterized human kidney peritubular microvascular endothelial cells (HKMECs) and reconstituted a three-dimensional human kidney microvasculature in a flow-directed microphysiologic system. By combining epithelial cell depletion and cell culture in media with high concentrations of vascular endothelial growth factor, we obtained HKMECs of high purity in large quantity. Unlike other endothelial cells, isolated HKMECs depended on high vascular endothelial growth factor concentration for survival and growth and exhibited high tubulogenic but low angiogenic potential. Furthermore, HKMECs had a different transcriptional profile. Under flow, HKMECs formed a thin fenestrated endothelium with a functional permeability barrier. In conclusion, this three-dimensional HKMEC-specific microphysiologic system recapitulates human kidney microvascular structure and function and shows phenotypic characteristics different from those of other microvascular endothelial cells.
Collapse
Affiliation(s)
| | | | - Jun Xue
- Departments of Bioengineering
| | | | - Jin Xu
- Departments of Bioengineering
| | | | | | | | | | | | | | | | | | | | - Ying Zheng
- Departments of Bioengineering, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| |
Collapse
|
37
|
Vleeshouwer-Neumann T, Phelps M, Bammler TK, MacDonald JW, Jenkins I, Chen EY. Histone Deacetylase Inhibitors Antagonize Distinct Pathways to Suppress Tumorigenesis of Embryonal Rhabdomyosarcoma. PLoS One 2015; 10:e0144320. [PMID: 26636678 PMCID: PMC4670218 DOI: 10.1371/journal.pone.0144320] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/15/2015] [Indexed: 02/01/2023] Open
Abstract
Embryonal rhabdomyosarcoma (ERMS) is the most common soft tissue cancer in children. The prognosis of patients with relapsed or metastatic disease remains poor. ERMS genomes show few recurrent mutations, suggesting that other molecular mechanisms such as epigenetic regulation might play a major role in driving ERMS tumor biology. In this study, we have demonstrated the diverse roles of histone deacetylases (HDACs) in the pathogenesis of ERMS by characterizing effects of HDAC inhibitors, trichostatin A (TSA) and suberoylanilide hydroxamic acid (SAHA; also known as vorinostat) in vitro and in vivo. TSA and SAHA suppress ERMS tumor growth and progression by inducing myogenic differentiation as well as reducing the self-renewal and migratory capacity of ERMS cells. Differential expression profiling and pathway analysis revealed downregulation of key oncogenic pathways upon HDAC inhibitor treatment. By gain-of-function, loss-of-function, and chromatin immunoprecipitation (ChIP) studies, we show that Notch1- and EphrinB1-mediated pathways are regulated by HDACs to inhibit differentiation and enhance migratory capacity of ERMS cells, respectively. Our study demonstrates that aberrant HDAC activity plays a major role in ERMS pathogenesis. Druggable targets in the molecular pathways affected by HDAC inhibitors represent novel therapeutic options for ERMS patients.
Collapse
Affiliation(s)
| | - Michael Phelps
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
| | - Theo K. Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - James W. MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington, United States of America
| | - Isaac Jenkins
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Eleanor Y. Chen
- Department of Pathology, University of Washington, Seattle, Washington, United States of America
- * E-mail:
| |
Collapse
|
38
|
Larson TA, Lent KL, Bammler TK, MacDonald JW, Wood WE, Caras ML, Thatra NM, Budzillo A, Perkel DJ, Brenowitz EA. Network analysis of microRNA and mRNA seasonal dynamics in a highly plastic sensorimotor neural circuit. BMC Genomics 2015; 16:905. [PMID: 26545368 PMCID: PMC4636775 DOI: 10.1186/s12864-015-2175-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/31/2015] [Indexed: 12/31/2022] Open
Abstract
Background Adult neurogenesis and the incorporation of adult-born neurons into functional circuits requires precise spatiotemporal coordination across molecular networks regulating a wide array of processes, including cell proliferation, apoptosis, neurotrophin signaling, and electrical activity. MicroRNAs (miRs) - short, non-coding RNA sequences that alter gene expression by post-transcriptional inhibition or degradation of mRNA sequences - may be involved in the global coordination of such diverse biological processes. To test the hypothesis that miRs related to adult neurogenesis and related cellular processes are functionally regulated in the nuclei of the avian song control circuit, we used microarray analyses to quantify changes in expression of miRs and predicted target mRNAs in the telencephalic nuclei HVC, the robust nucleus of arcopallium (RA), and the basal ganglia homologue Area X in breeding and nonbreeding Gambel’s white-crowned sparrows (Zonotrichia leucophrys gambelli). Results We identified 46 different miRs that were differentially expressed across seasons in the song nuclei. miR-132 and miR-210 showed the highest differential expression in HVC and Area X, respectively. Analyzing predicted mRNA targets of miR-132 identified 33 candidate target genes that regulate processes including cell cycle control, calcium signaling, and neuregulin signaling in HVC. Likewise, miR-210 was predicted to target 14 mRNAs differentially expressed across seasons that regulate serotonin, GABA, and dopamine receptor signaling and inflammation. Conclusions Our results identify potential miR–mRNA regulatory networks related to adult neurogenesis and provide opportunities to discover novel genetic control of the diverse biological processes and factors related to the functional incorporation of new neurons to the adult brain. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2175-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tracy A Larson
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.,Present Address: Basic Sciences Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA
| | - Karin L Lent
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, 98195, USA
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, WA, 98195, USA
| | - William E Wood
- Department of Otolaryngology, University of Washington, Seattle, WA, 98195, USA.,Graduate Program in Neuroscience, University of Washington, Seattle, WA, 98195, USA.,Present address: Centre National de la Recherche Scientifique, Laboratoire de Neurophysique et Physiologie, UMR 8119, Université Paris Descartes, 45, rue des Saints Pères, 75006, Paris, France
| | - Melissa L Caras
- Department of Psychology, University of Washington, Seattle, WA, 98195, USA.,Graduate Program in Neuroscience, University of Washington, Seattle, WA, 98195, USA.,Present address: Center for Neural Science, New York University, 4 Washington Place, New York, NY, 10003, USA
| | - Nivretta M Thatra
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.,Department of Psychology, University of Washington, Seattle, WA, 98195, USA
| | - Agata Budzillo
- Department of Otolaryngology, University of Washington, Seattle, WA, 98195, USA.,Graduate Program in Neuroscience, University of Washington, Seattle, WA, 98195, USA
| | - David J Perkel
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.,Department of Otolaryngology, University of Washington, Seattle, WA, 98195, USA
| | - Eliot A Brenowitz
- Department of Biology, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
39
|
Wang L, Espinoza HM, MacDonald JW, Bammler TK, Williams CR, Yeh A, Louie KW, Marcinek DJ, Gallagher EP. Olfactory Transcriptional Analysis of Salmon Exposed to Mixtures of Chlorpyrifos and Malathion Reveal Novel Molecular Pathways of Neurobehavioral Injury. Toxicol Sci 2015; 149:145-57. [PMID: 26494550 DOI: 10.1093/toxsci/kfv223] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Pacific salmon exposed to sublethal concentrations of organophosphate pesticides (OP) have impaired olfactory function that can lead to loss of behaviors that are essential for survival. These exposures often involve mixtures and can occur at levels below those which inhibit acetylcholinesterase (AChE). In this study, juvenile Coho salmon were exposed for 24 h to either 0.1, 0.5, or 2.5 ppb chlorpyrifos (CPF), 2, 10, or 50 ppb malathion (MAL), or binary mixtures of 0.1 CPF:2 ppb MAL, 0.5 CPF:10 ppb MAL, or 2.5 CPF:10 ppb MAL to mimic single and binary environmental exposures. Microarray analysis of olfactory rosettes from pesticide-exposed salmon revealed differentially expressed genes involved in nervous system function and signaling, aryl hydrocarbon receptor signaling, xenobiotic metabolism, and mitochondrial dysfunction. Coho exposed to OP mixtures exhibited a more pronounced loss in detection of a predatory olfactory cue relative to those exposed to single compounds, whereas respirometry experiments demonstrated that exposure to OPs, individually and in mixtures, reduced maximum respiratory capacity of olfactory rosette mitochondria. The observed molecular, biochemical, and behavioral effects occurred largely in the absence of effects on brain AChE. In summary, our results provide new insights associated with the sublethal neurotoxic effects of OP mixtures relevant to environmental exposures involving molecular and cellular pathways of injury to the salmon olfactory system that underlie neurobehavioral injury.
Collapse
Affiliation(s)
- Lu Wang
- *Department of Environmental and Occupational Health Sciences and
| | | | | | - Theo K Bammler
- *Department of Environmental and Occupational Health Sciences and
| | - Chase R Williams
- *Department of Environmental and Occupational Health Sciences and
| | - Andrew Yeh
- *Department of Environmental and Occupational Health Sciences and
| | - Ke'ale W Louie
- *Department of Environmental and Occupational Health Sciences and
| | - David J Marcinek
- Department of Radiology, University of Washington, Seattle, Washington
| | - Evan P Gallagher
- *Department of Environmental and Occupational Health Sciences and
| |
Collapse
|
40
|
Homayounfar N, Park SS, Afsharinejad Z, Bammler TK, MacDonald JW, Farin FM, Mecham BH, Cunningham ML. Transcriptional analysis of human cranial compartments with different embryonic origins. Arch Oral Biol 2015; 60:1450-60. [PMID: 26188427 DOI: 10.1016/j.archoralbio.2015.06.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [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: 06/17/2014] [Revised: 06/11/2015] [Accepted: 06/12/2015] [Indexed: 12/11/2022]
Abstract
OBJECTIVE Previous investigations suggest that the embryonic origins of the calvarial tissues (neural crest or mesoderm) may account for the molecular mechanisms underlying sutural development. The aim of this study was to evaluate the differences in the gene expression of human cranial tissues and assess the presence of an expression signature reflecting their embryonic origins. METHODS Using microarray technology, we investigated global gene expression of cells from the frontal and parietal bones and the metopic and sagittal intrasutural mesenchyme (ISM) of four human foetal calvaria. qRT-PCR of a selected group of genes was done to validate the microarray analysis. Paired comparison and correlation analyses were performed on microarray results. RESULTS Of six paired comparisons, frontal and parietal compartments (distinct tissue types of calvaria, either bone or intrasutural mesenchyme) had the most different gene expression profiles despite being composed of the same tissue type (bone). Correlation analysis revealed two distinct gene expression profiles that separate frontal and metopic compartments from parietal and sagittal compartments. TFAP2A, TFAP2B, ICAM1, SULF1, TNC and FOXF2 were among differentially expressed genes. CONCLUSION Transcriptional profiles of two groups of tissues, frontal and metopic compartments vs. parietal and sagittal compartments, suggest differences in proliferation, differentiation and extracellular matrix production. Our data suggest that in the second trimester of human foetal development, a gene expression signature of neural crest origin still exists in frontal and metopic compartments while gene expression of parietal and sagittal compartments is more similar to mesoderm.
Collapse
Affiliation(s)
- Negar Homayounfar
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 - 9th Avenue, Seattle, WA 98101, United States; Department of Oral Health Sciences, Dental School, University of Washington, United States; Department of Endodontics, Prosthodontics and Operative Dentistry, School of Dentistry, University of Maryland, Baltimore, United States.
| | - Sarah S Park
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 - 9th Avenue, Seattle, WA 98101, United States
| | - Zahra Afsharinejad
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, # 100, Seattle, WA 98105-6099, United States
| | - Theodor K Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, # 100, Seattle, WA 98105-6099, United States
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, # 100, Seattle, WA 98105-6099, United States
| | - Federico M Farin
- Department of Environmental and Occupational Health Sciences, University of Washington, 4225 Roosevelt Way NE, # 100, Seattle, WA 98105-6099, United States
| | - Brigham H Mecham
- Trialomics, 1700 7th Avenue, # 116, Seattle, WA 98101, United States
| | - Michael L Cunningham
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, 1900 - 9th Avenue, Seattle, WA 98101, United States; Seattle Children's Craniofacial Center, 4800 Sand Point Way NE, Seattle, WA 98105, United States
| |
Collapse
|
41
|
Anderson GD, Peterson TC, Vonder Haar C, Farin FM, Bammler TK, MacDonald JW, Kantor ED, Hoane MR. Effect of Traumatic Brain Injury, Erythropoietin, and Anakinra on Hepatic Metabolizing Enzymes and Transporters in an Experimental Rat Model. AAPS J 2015; 17:1255-67. [PMID: 26068867 DOI: 10.1208/s12248-015-9792-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 05/26/2015] [Indexed: 12/18/2022]
Abstract
In contrast to considerable data demonstrating a decrease in cytochrome P450 (CYP) activity in inflammation and infection, clinically, traumatic brain injury (TBI) results in an increase in CYP and UDP glucuronosyltransferase (UGT) activity. The objective of this study was to determine the effects of TBI alone and with treatment with erythropoietin (EPO) or anakinra on the gene expression of hepatic inflammatory proteins, drug-metabolizing enzymes, and transporters in a cortical contusion impact (CCI) injury model. Microarray-based transcriptional profiling was used to determine the effect on gene expression at 24 h, 72 h, and 7 days post-CCI. Plasma cytokine and liver protein concentrations of CYP2D4, CYP3A1, EPHX1, and UGT2B7 were determined. There was no effect of TBI, TBI + EPO, or TBI + anakinra on gene expression of the inflammatory factors shown to be associated with decreased expression of hepatic metabolic enzymes in models of infection and inflammation. IL-6 plasma concentrations were increased in TBI animals and decreased with EPO and anakinra treatment. There was no significant effect of TBI and/or anakinra on gene expression of enzymes or transporters known to be involved in drug disposition. TBI + EPO treatment decreased the gene expression of Cyp2d4 at 72 h with a corresponding decrease in CYP2D4 protein at 72 h and 7 days. CYP3A1 protein was decreased at 24 h. In conclusion, EPO treatment may result in a significant decrease in the metabolism of Cyp-metabolized drugs. In contrast to clinical TBI, there was not a significant effect of experimental TBI on CYP or UGT metabolic enzymes.
Collapse
Affiliation(s)
- Gail D Anderson
- Department of Pharmacy, University of Washington, Seattle, Washington, 98195, USA,
| | | | | | | | | | | | | | | |
Collapse
|
42
|
Mohanty AF, Farin FM, Bammler TK, MacDonald JW, Afsharinejad Z, Burbacher TM, Siscovick DS, Williams MA, Enquobahrie DA. Infant sex-specific placental cadmium and DNA methylation associations. Environ Res 2015; 138:74-81. [PMID: 25701811 PMCID: PMC4385453 DOI: 10.1016/j.envres.2015.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [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: 09/24/2014] [Revised: 01/26/2015] [Accepted: 02/03/2015] [Indexed: 05/18/2023]
Abstract
BACKGROUND Recent evidence suggests that maternal cadmium (Cd) burden and fetal growth associations may vary by fetal sex. However, mechanisms contributing to these differences are unknown. OBJECTIVES Among 24 maternal-infant pairs, we investigated infant sex-specific associations between placental Cd and placental genome-wide DNA methylation. METHODS We used ANOVA models to examine sex-stratified associations of placental Cd (dichotomized into high/low Cd using sex-specific Cd median cutoffs) with DNA methylation at each cytosine-phosphate-guanine site or region. Statistical significance was defined using a false discovery rate cutoff (<0.10). RESULTS Medians of placental Cd among females and males were 5 and 2 ng/g, respectively. Among females, three sites (near ADP-ribosylation factor-like 9 (ARL9), siah E3 ubiquitin protein ligase family member 3 (SIAH3), and heparin sulfate (glucosamine) 3-O-sulfotransferase 4 (HS3ST4) and one region on chromosome 7 (including carnitine O-octanoyltransferase (CROT) and TP5S target 1 (TP53TG1)) were hypomethylated in high Cd placentas. Among males, high placental Cd was associated with methylation of three sites, two (hypomethylated) near MDS1 and EVI1 complex locus (MECOM) and one (hypermethylated) near spalt-like transcription factor 1 (SALL1), and two regions (both hypomethylated, one on chromosome 3 including MECOM and another on chromosome 8 including rho guanine nucleotide exchange factor (GEF) 10 (ARHGEF10). Differentially methylated sites were at or close to transcription start sites of genes involved in cell damage response (SIAH3, HS3ST4, TP53TG1) in females and cell differentiation, angiogenesis and organ development (MECOM, SALL1) in males. CONCLUSIONS Our preliminary study supports infant sex-specific placental Cd-DNA methylation associations, possibly accounting for previously reported differences in Cd-fetal growth associations across fetal sex. Larger studies are needed to replicate and extend these findings. Such investigations may further our understanding of epigenetic mechanisms underlying maternal Cd burden with suboptimal fetal growth associations.
Collapse
Affiliation(s)
- April F Mohanty
- Cardiovascular Health Research Unit, University of Washington, 1730 Minor Ave, Seattle, WA 98101, USA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA.
| | - Fred M Farin
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, 4225 Roosevelt Way N.E., Suite #100, Seattle, WA 98105, USA.
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, 4225 Roosevelt Way N.E., Suite #100, Seattle, WA 98105, USA.
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, 4225 Roosevelt Way N.E., Suite #100, Seattle, WA 98105, USA.
| | - Zahra Afsharinejad
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, 4225 Roosevelt Way N.E., Suite #100, Seattle, WA 98105, USA.
| | - Thomas M Burbacher
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Box: 357234, 1705 N.E. Pacific Street, Seattle, WA 98195, USA.
| | - David S Siscovick
- Cardiovascular Health Research Unit, University of Washington, 1730 Minor Ave, Seattle, WA 98101, USA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Department of Medicine, University of Washington, Seattle, WA, USA.
| | - Michelle A Williams
- Department of Epidemiology, Harvard School of Public Health, Kresge Building, 9th Floor, 677 Huntington Ave., Boston, MA 02115, USA.
| | - Daniel A Enquobahrie
- Cardiovascular Health Research Unit, University of Washington, 1730 Minor Ave, Seattle, WA 98101, USA; Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA, USA; Center for Perinatal Studies, Swedish Medical Center, 1124 Columbia Street, Suite 750, Seattle, WA 98104, USA.
| |
Collapse
|
43
|
Peterson TC, Hoane MR, McConomy KS, Farin FM, Bammler TK, MacDonald JW, Kantor ED, Anderson GD. A Combination Therapy of Nicotinamide and Progesterone Improves Functional Recovery following Traumatic Brain Injury. J Neurotrauma 2015; 32:765-79. [PMID: 25313690 DOI: 10.1089/neu.2014.3530] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Neuroprotection, recovery of function, and gene expression were evaluated in an animal model of traumatic brain injury (TBI) after a combination treatment of nicotinamide (NAM) and progesterone (Prog). Animals received a cortical contusion injury over the sensorimotor cortex, and were treated with either Vehicle, NAM, Prog, or a NAM/Prog combination for 72 h and compared with a craniotomy only (Sham) group. Animals were assessed in a battery of behavioral, sensory, and both fine and gross motor tasks, and given histological assessments at 24 h post-injury to determine lesion cavity size, degenerating neurons, and reactive astrocytes. Microarray-based transcriptional profiling was used to determine treatment-specific changes on gene expression. Our results confirm the beneficial effects of treatment with either NAM or Prog, demonstrating significant improvements in recovery of function and a reduction in lesion cavitation, degenerating neurons, and reactive astrocytes 24 h post-injury. The combination treatment of NAM and Prog led to a significant improvement in both neuroprotection at 24 h post-injury and recovery of function in sensorimotor related tasks when compared with individual treatments. The NAM/Prog-treated group was the only treatment group to show a significant reduction of cortical loss 24 h post-injury. The combination appears to affect inflammatory and immune processes, reducing expression of a significant number of genes in both pathways. Further preclinical trials using NAM and Prog as a combination treatment should be conducted to identify the window of opportunity, determine the optimal duration of treatment, and evaluate the combination in other pre-clinical models of TBI.
Collapse
Affiliation(s)
- Todd C Peterson
- 1Department of Psychology, Southern Illinois University, Carbondale, Illinois
| | - Michael R Hoane
- 1Department of Psychology, Southern Illinois University, Carbondale, Illinois
| | - Keith S McConomy
- 1Department of Psychology, Southern Illinois University, Carbondale, Illinois
| | - Fred M Farin
- 2Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Theo K Bammler
- 2Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - James W MacDonald
- 2Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington
| | - Eric D Kantor
- 3Department of Pharmacy, University of Washington, Seattle, Washington
| | - Gail D Anderson
- 3Department of Pharmacy, University of Washington, Seattle, Washington
| |
Collapse
|
44
|
Cole TB, Li WF, Co AL, Hay AM, MacDonald JW, Bammler TK, Farin FM, Costa LG, Furlong CE. Repeated gestational exposure of mice to chlorpyrifos oxon is associated with paraoxonase 1 (PON1) modulated effects in maternal and fetal tissues. Toxicol Sci 2014; 141:409-22. [PMID: 25070982 DOI: 10.1093/toxsci/kfu144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chlorpyrifos oxon (CPO), the toxic metabolite of the organophosphorus (OP) insecticide chlorpyrifos, causes developmental neurotoxicity in humans and rodents. CPO is hydrolyzed by paraoxonase-1 (PON1), with protection determined by PON1 levels and the human Q192R polymorphism. To examine how the Q192R polymorphism influences fetal toxicity associated with gestational CPO exposure, we measured enzyme inhibition and fetal-brain gene expression in wild-type (PON1(+/+)), PON1-knockout (PON1(-/-)), and tgHuPON1R192 and tgHuPON1Q192 transgenic mice. Pregnant mice exposed dermally to 0, 0.50, 0.75, or 0.85 mg/kg/d CPO from gestational day (GD) 6 through 17 were sacrificed on GD18. Biomarkers of CPO exposure inhibited in maternal tissues included brain acetylcholinesterase (AChE), red blood cell acylpeptide hydrolase (APH), and plasma butyrylcholinesterase (BChE) and carboxylesterase (CES). Fetal plasma BChE was inhibited in PON1(-/-) and tgHuPON1Q192, but not PON1(+/+) or tgHuPON1R192 mice. Fetal brain AChE and plasma CES were inhibited in PON1(-/-) mice, but not in other genotypes. Weighted gene co-expression network analysis identified five gene modules based on clustering of the correlations among their fetal-brain expression values, allowing for correlation of module membership with the phenotypic data on enzyme inhibition. One module that correlated highly with maternal brain AChE activity had a large representation of homeobox genes. Gene set enrichment analysis revealed multiple gene sets affected by gestational CPO exposure in tgHuPON1Q192 but not tgHuPON1R192 mice, including gene sets involved in protein export, lipid metabolism, and neurotransmission. These data indicate that maternal PON1 status modulates the effects of repeated gestational CPO exposure on fetal-brain gene expression and on inhibition of both maternal and fetal biomarker enzymes.
Collapse
Affiliation(s)
- Toby B Cole
- Department of Medicine, Division of Medical Genetics Department of Environmental and Occupational Health Sciences Department of Genome Sciences Center on Human Development and Disability
| | - Wan-Fen Li
- Department of Medicine, Division of Medical Genetics
| | - Aila L Co
- Department of Medicine, Division of Medical Genetics Department of Genome Sciences
| | - Ariel M Hay
- Department of Medicine, Division of Medical Genetics Department of Genome Sciences
| | - James W MacDonald
- Department of Environmental and Occupational Health Sciences Center for Ecogenetics and Environmental Health, University of Washington, Seattle, Washington 98195
| | - Theo K Bammler
- Department of Environmental and Occupational Health Sciences Center for Ecogenetics and Environmental Health, University of Washington, Seattle, Washington 98195
| | - Federico M Farin
- Department of Environmental and Occupational Health Sciences Center for Ecogenetics and Environmental Health, University of Washington, Seattle, Washington 98195
| | - Lucio G Costa
- Department of Environmental and Occupational Health Sciences Department of Neuroscience, University of Parma, Parma, Italy
| | - Clement E Furlong
- Department of Medicine, Division of Medical Genetics Department of Genome Sciences
| |
Collapse
|
45
|
Vonder Haar C, Anderson GD, Elmore BE, Moore LH, Wright AM, Kantor ED, Farin FM, Bammler TK, MacDonald JW, Hoane MR. Comparison of the effect of minocycline and simvastatin on functional recovery and gene expression in a rat traumatic brain injury model. J Neurotrauma 2014; 31:961-75. [PMID: 24308531 DOI: 10.1089/neu.2013.3119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The goal of this study was to compare the effects of minocycline and simvastatin on functional recovery and brain gene expression after a cortical contusion impact (CCI) injury. Dosage regimens were designed to provide serum concentrations in a rat model in the range obtained with clinically approved doses; minocycline 60 mg/kg q12h and simvastatin 10 mg/kg q12h for 72 h. Functional recovery was assessed using motor and spatial learning tasks and neuropathological measurements. Microarray-based transcriptional profiling was used to determine the effect on gene expression at 24 h, 72 h, and 7 days post-CCI. Gene Ontology analysis (GOA) was used to evaluate the effect on relevant biological pathways. Both minocycline and simvastatin improved fine motor function, but not gross motor or cognitive function. Minocycline modestly decreased lesion size with no effect of simvastatin. At 24 h post-CCI, GOA identified a significant effect of minocycline on chemotaxis, blood circulation, immune response, and cell to cell signaling pathways. Inflammatory pathways were affected by minocycline only at the 72 h time point. There was a minimal effect of simvastatin on gene expression 24 h after injury, with increasing effects at 72 h and 7 days. GOA identified a significant effect of simvastatin on inflammatory response at 72 h and 7 days. In conclusion, treatment with minocycline and simvastatin resulted in significant effects on gene expression in the brain reflecting adequate brain penetration without producing significant neurorestorative effects.
Collapse
Affiliation(s)
- Cole Vonder Haar
- 1 Restorative Neuroscience Laboratory, Center for Integrated Research in Cognitive and Neural Sciences, Department of Psychology, Southern Illinois University , Carbondale, Illinois
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Doronin K, Flatt JW, Di Paolo NC, Khare R, Kalyuzhniy O, Acchione M, Sumida JP, Ohto U, Shimizu T, Akashi-Takamura S, Miyake K, MacDonald JW, Bammler TK, Beyer RP, Farin FM, Stewart PL, Shayakhmetov DM. Coagulation factor X activates innate immunity to human species C adenovirus. Science 2012; 338:795-8. [PMID: 23019612 DOI: 10.1126/science.1226625] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Although coagulation factors play a role in host defense for "living fossils" such as horseshoe crabs, the role of the coagulation system in immunity in higher organisms remains unclear. We modeled the interface of human species C adenovirus (HAdv) interaction with coagulation factor X (FX) and introduced a mutation that abrogated formation of the HAdv-FX complex. In vivo genome-wide transcriptional profiling revealed that FX-binding-ablated virus failed to activate a distinct network of nuclear factor κB-dependent early-response genes that are activated by HAdv-FX complex downstream of TLR4/MyD88/TRIF/TRAF6 signaling. Our study implicates host factor "decoration" of the virus as a mechanism to trigger an innate immune sensor that responds to a misplacement of coagulation FX from the blood into intracellular macrophage compartments upon virus entry into the cell.
Collapse
Affiliation(s)
- Konstantin Doronin
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Abstract
Mutations in the transcription factors PROP1 and PIT1 (POU1F1) lead to pituitary hormone deficiency and hypopituitarism in mice and humans. The dysmorphology of developing Prop1 mutant pituitaries readily distinguishes them from those of Pit1 mutants and normal mice. This and other features suggest that Prop1 controls the expression of genes besides Pit1 that are important for pituitary cell migration, survival, and differentiation. To identify genes involved in these processes we used microarray analysis of gene expression to compare pituitary RNA from newborn Prop1 and Pit1 mutants and wild-type littermates. Significant differences in gene expression were noted between each mutant and their normal littermates, as well as between Prop1 and Pit1 mutants. Otx2, a gene critical for normal eye and pituitary development in humans and mice, exhibited elevated expression specifically in Prop1 mutant pituitaries. We report the spatial and temporal regulation of Otx2 in normal mice and Prop1 mutants, and the results suggest Otx2 could influence pituitary development by affecting signaling from the ventral diencephalon and regulation of gene expression in Rathke's pouch. The discovery that Otx2 expression is affected by Prop1 deficiency provides support for our hypothesis that identifying molecular differences in mutants will contribute to understanding the molecular mechanisms that control pituitary organogenesis and lead to human pituitary disease.
Collapse
Affiliation(s)
- Amanda H Mortensen
- Department of Human Genetics, Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109-5618, USA
| | | | | | | |
Collapse
|
48
|
Brinkmeier ML, Davis SW, Carninci P, MacDonald JW, Kawai J, Ghosh D, Hayashizaki Y, Lyons RH, Camper SA. Retraction notice to “Discovery of transcriptional regulators and signaling pathways in the developing pituitary gland by bioinformatic and genomic approaches” [Genomics 93 (2009) 449–460]. Genomics 2011. [DOI: 10.1016/j.ygeno.2011.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
49
|
Davis SW, Potok MA, Brinkmeier ML, Carninci P, Lyons RH, MacDonald JW, Fleming MT, Mortensen AH, Egashira N, Ghosh D, Steel KP, Osamura RY, Hayashizaki Y, Camper SA. Genetics, gene expression and bioinformatics of the pituitary gland. Horm Res 2009; 71 Suppl 2:101-15. [PMID: 19407506 DOI: 10.1159/000192447] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Genetic cases of congenital pituitary hormone deficiency are common and many are caused by transcription factor defects. Mouse models with orthologous mutations are invaluable for uncovering the molecular mechanisms that lead to problems in organ development and typical patient characteristics. We are using mutant mice defective in the transcription factors PROP1 and POU1F1 for gene expression profiling to identify target genes for these critical transcription factors and candidates for cases of pituitary hormone deficiency of unknown aetiology. These studies reveal critical roles for Wnt signalling pathways, including the TCF/LEF transcription factors and interacting proteins of the groucho family, bone morphogenetic protein antagonists and targets of notch signalling. Current studies are investigating the roles of novel homeobox genes and pathways that regulate the transition from proliferation to differentiation, cell adhesion and cell migration. Pituitary adenomas are a common human health problem, yet most cases are sporadic, necessitating alternative approaches to traditional Mendelian genetic studies. Mouse models of adenoma formation offer the opportunity for gene expression profiling during progressive stages of hyperplasia, adenoma and tumorigenesis. This approach holds promise for the identification of relevant pathways and candidate genes as risk factors for adenoma formation, understanding mechanisms of progression, and identifying drug targets and clinically relevant biomarkers.
Collapse
|
50
|
Krebs CJ, Khan S, MacDonald JW, Sorenson M, Robins DM. Regulator of sex-limitation KRAB zinc finger proteins modulate sex-dependent and -independent liver metabolism. Physiol Genomics 2009; 38:16-28. [PMID: 19351907 DOI: 10.1152/physiolgenomics.90391.2008] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Krüppel-related zinc finger proteins (KRAB-zfps) comprise the largest mammalian transcription factor family, but their specific functions are largely unknown. Two KRAB-zfps, regulator of sex-limitation (Rsl) 1 and Rsl2, repress expression of the mouse sex-limited protein (Slp) gene, the hallmark of Rsl activity, as well as some other male-predominant liver genes. This phenotype suggests Rsl modifies sex-specific transcription. The scope of Rsl control was determined by expression profiling of liver RNA from wild-type (wt), rsl, and transgenic mice with hepatic overexpression of Rsl1 or Rsl2. About 7.5% of the liver transcriptome was Rsl-responsive. More genes in males than females were affected by the loss of Rsl (e.g., in rsl mice), whereas Rsl overexpression altered more transcripts in females than males. Rsl dramatically repressed some female-predominant genes, but most were modestly (1.25- to 2-fold) influenced. In males, most Rsl-responsive genes unexpectedly expressed at lower levels in rsl than wt, suggesting not all are direct targets of Rsl repression. Gene Ontology analysis showed Rsl targets enriched in pathways of cholesterol, steroid, and lipid metabolism, linking Rsl to energy balance. In accord with this, blood glucose levels were less in male rsl than wt mice, and less responsive to fasting and refeeding. rsl mice were also leaner than wt, consistent with their hepatic regulation of phosphoenolpyruvate carboxykinase 1 and stearoyl-Coenzyme A desaturase 1. Altogether, Rsl's effect on sexually dimorphic and metabolically sensitive liver gene expression suggests a role for KRAB-zfps as broad genetic modulators of individual adaptation.
Collapse
Affiliation(s)
- Christopher J Krebs
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109-0618, USA
| | | | | | | | | |
Collapse
|