Please note: You are viewing the unstyled version of this website. Either your browser does not support CSS (cascading style sheets) or it has been disabled. Skip navigation.

Current Research Projects (2018-2019)

   Print Change text to small (default) Change text to medium Change text to large

Enlarge Image

Much of our funding comes from the National Institute of Environmental Health Sciences (NIEHS), part of the U.S. National Institutes of Health. We are grateful to NIEHS and the American taxpayers for supporting this research.

Enlarge Image

The Superfund Research Program (formerly known as Superfund Basic Research Program) is part of NIEHS and supports our basic research on PCB- and dioxin-resistant fish. The long-term support provided by this program has allowed us to investigate the molecular components of the cellular pathways involved in the response to PCB exposure and how they differ in fish with evolved PCB resistance.

Our Superfund research is part of the Superfund Research Program at Boston University, in its 16th year.

Enlarge Image

Tomcod from the Hudson River have a variant protein that makes them less sensitive to the toxic effects of PCBs.  The effects of PCBs occur through their interaction with a protein called Aryl Hydrocarbon Receptor 2 (AHR2).  AHR2 is normally inactive, but when PCB molecules bind to it, AHR2 becomes activated and acts as a molecular switch to turn on other genes that lead to toxicity (“Effects” in the figure).  Tomcod such as those from Shinnecock Bay, Long Island, NY (left panel) have a normal version of the AHR2 protein, which has a high affinity for PCBs. Tomcod from the Hudson River (right panel) have a variant AHR2 protein that is missing two amino acids (building blocks of proteins). Without these two amino acids, the AHR2 from Hudson River fish has a reduced ability to bind PCBs as compared to the normal AHR2 protein. This makes the Hudson River fish less sensitive to the effects of PCBs.  Killifish from New Bedford Harbor also variants of AHR2, but the functional differences have not yet been identified.  For additional details, see Mechanisms and Impacts of Dioxin Resistance in Fish. (figure drawn by Jack Cook (WHOI))

Enlarge Image

The difference between AHR2 proteins in tomcod from Hudson River (right panel) and Shinnecock Bay (left panel) is the loss of two amino acids out of the 1,104 amino acids that normally make up the AHR protein. (figure drawn by Jack Cook (WHOI))

Cellular and molecular mechanisms underlying long-term effects of early-life exposure to HAB toxins
(Please see also Project 3 in the Woods Hole Center for Oceans and Human Health.)

The overall objective of the proposed research is to elucidate the cellular and molecular mechanisms by which early-life exposure to harmful algal bloom (HAB) toxins may interfere with neurodevelopment to cause persistent neurobehavioral changes later in life. The HAB toxins domoic acid and saxitoxin occur in seafood and levels are regulated to prevent acute toxicity. However, human exposure to these toxins at levels below regulatory limits is common, widespread, and may be increasing, posing risks to vulnerable subpopulations such as developing humans. It is now well known that the early life environment can profoundly influence health throughout the life course (the developmental origins of health and disease). However, the mechanisms by which developmental exposures elicit effects later in life are not well understood. The central hypothesis of this research is that early life, low-level exposure to domoic acid and saxitoxin targets neurotransmitter receptors and ion channels, leading to altered gene expression, functional changes in glial and neural cells, and long-term changes in neurobehavioral function in adults. These studies are being conducted using zebrafish, a powerful model organism in developmental neurotoxicology research. In Aim 1, we are testing the hypothesis that embryonic exposure to low levels of domoic acid, a glutamate receptor agonist, targets developing oligodendrocytes (OLs), thereby disrupting myelination of axons. We will measure the effects on OL-lineage cells using a variety of transgenic zebrafish lines that allow visualization of developing OLs and myelination. We will elucidate the functional consequences of these changes by assessing larval behavior. In addition, we will determine later life consequences of developmental exposure to domoic acid on neurobehavior using a battery of well-established behavioral assays and characterizing the gene expression patterns in the adult brain. In Aim 2, we are testing the hypothesis that developmental exposure to saxitoxin, an inhibitor of voltage-gated sodium channels, targets developing neurons, leading to defects in axonal growth. We will visualize the changes in axonal growth in motor neurons and determine functional changes in larval and adult behavior. In Aim 3, we are testing the hypothesis that combined early life exposure to low levels of domoic acid and saxitoxin targets OLs and neuronal cells, interfering with activity-dependent myelination and causing enhanced deficits in myelination and neurobehavior. We are also testing the hypothesis that domoic acid and saxitoxin can cause silent neurotoxicity that can be unmasked later in life by secondary stressors. Research in collaboration with Projects 1 and 2 and the Community Outreach Core will model human exposure and how it may change with a changing climate. This research will identify the cellular and molecular bases for neurobehavioral effects following early-life exposure to prominent HAB toxins, contributing to an understanding of the potential long-term health consequences of developmental exposure to domoic acid and saxitoxin in humans, critical for assessing public health risks associated with the possibly increasing exposure to these toxins.

Mechanisms and Impacts of PCB Resistance in Fish

The overall objective of the basic research proposed here is to understand the effects of long-term, multigenerational exposure to high levels of contaminants on natural populations of animals inhabiting Superfund sites. In one set of studies, we are using a fish model species, the Atlantic killifish Fundulus heteroclitus, populations of which have evolved resistance to dioxin-like compounds that act through the aryl hydrocarbon receptor (AHR) at numerous sites. Killifish inhabiting New Bedford Harbor (NBH), MA, a polychlorinated biphenyl (PCB)-contaminated Superfund site, exhibit heritable resistance to altered gene expression and toxicity of 2,3,7,8- tetrachlorodibenzo-p-dioxin (TCDD) and other AHR agonists as com pared to fish from a refe rence site, Scorto n Creek, MA (SC). We have identified and cloned four distinct AHRs (AHR1a, AHR2a, AHR1b, and AHR2b), ARNT2, hypoxia-inducible factors (HIFs), and an AHR repressor (AHRR) in killifish. Killifish AHR genes are highly polymorphic and allele frequencies differ between populations of dioxin-sensitive (SC) and dioxin-resistant (NBH) fish. To elucidate the role of each AHR in the sensitivity and resistance to PCBs, we are using CRISPR-Cas9 genome editing technology to know out each of the AHR genes. These studies seek to understand mechanisms underlying differential sensitivity to the developmental toxicity of HAHs and PAHs that act through AHR-dependent signaling, and to determine the impact of evolved HAH/PAH resistance on the sensitivity to other environmental stressors. 

Recent papers:

The genomic landscape of rapid repeated evolutionary adaptation to toxic pollution in wild fish.
Reid NM, Proestou DA, Clark BW, Warren WC, Colbourne JK, Shaw JR, Karchner SI, Hahn ME, Nacci D, Oleksiak MF, Crawford DL, Whitehead A (2016)
Science 354: 1305-1308.
WHOI Press release

Targeted mutagenesis of aryl hydrocarbon receptor 2a and 2b genes in Atlantic killifish (Fundulus heteroclitus).
Aluru N, Karchner SI, Franks DG, Nacci D, Champlin D, Hahn ME (2015)
Aquatic Toxicology 158: 192-201.

Genetic Variation at Aryl Hydrocarbon Receptor (AHR) Loci in populations of Atlantic Killifish (Fundulus heteroclitus) inhabiting Polluted and Reference Habitats. 
Reitzel, A. M., Karchner, S. I., Franks, D. G., Evans, B. R., Nacci, D. E., Champlin, D., Vieira, V. M., and Hahn, M. E. (2014). 
BMC Evolutionary Biology, 2014, 14:6.
WHOI Press release

Differential sensitivity to pro-oxidant exposure in two populations of killifish (Fundulus heteroclitus). 
Harbeitner, R. C., Hahn, M. E., and Timme-Laragy, A. R. (2013). 
Ecotoxicology22, 387–401 (doi:10.1007/s10646-10012-11033-x)

Transcriptomic assessment of resistance to effects of an aryl hydrocarbon receptor (AHR) agonist in embryos of Atlantic Killifish (Fundulus heteroclitus) from a Marine Superfund Site.  Oleksiak, M. F., Karchner, S. I., Jenny, M. J., Franks, D. G., Mark Welch, D. B., and Hahn, M. E.   (2011) BMC Genomics 12, 263.

Mechanistic Basis of Resistance to PCBs in Atlantic Tomcod from the Hudson River
Wirgin, I., Roy, N. K., Loftus, M., Chambers, R. C., Franks, D. G., and Hahn, M. E.  (2011) Science 331, 1322-1325 

Funded by the National Institute of Environmental Health Sciences (NIEHS) through the Superfund Basic Research Program at Boston University.

Superfund Research Program web site for M. Hahn.



AHR signaling in Mammalian and Nonmammalian Models

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) and polynuclear aromatic hydrocarbons are ubiquitous environmental contaminants implicated in adverse effects on human health. These compounds cause toxicity by activating the aryl hydrocarbon receptor (AHR). The AHR also has physiological roles regulating vascular development, immune function, and cell growth, suggesting a role in human disease. To understand these diverse functions and the possible role of AHR in human disease, it is important to determine how AHR signaling is regulated. The negative regulation of AHR signaling is poorly understood. An inhibitor of AHR transcriptional activation function, AHR repressor (AHRR), has been identified, but its role in regulating AHR signaling remains enigmatic, and possible functions beyond the AHR pathway have been virtually ignored. Recent epidemiological studies have linked AHRR Pr o185 and Ala185 polymorphisms to human reproductive disorders and AHRR has been identified as a likely tumo r suppressor gene in humans. However, fundamental questions concerning the biochemical and functional characteristics of the AHRR and its variants remain unresolved, preventing a full understanding of its roles in human disease.

These studies are utilizing established vertebrate model systems (human cells and zebrafish embryos) to determine the transcription factor specificity and gene selectivity of AHRR and its polymorphic variants, the mechanism by which AHRR represses AHR and hypoxia inducible factors (HIFs), and the role of AHRR in regulating embryonic development and the response to TCDD and hypoxia in vivo. 

Recent papers:

Identification of Cinnabarinic Acid as a Novel Endogenous Aryl Hydrocarbon Receptor Ligand That Drives IL-22 Production. 
Lowe, M. M., Mold, J. E., Kanwar, B., Huang, Y., Louie, A., Pollastri, M. P., Wang, C., Franks, D. G., Schlezinger, J., Sherr, D., Silverstone, A. E., Hahn, M. E., and McCune, J. M. (2014). 
PLoS ONE 9(2): e87877. doi:10.1371/journal.pone.0087877.

The African coelacanth genome provides insights into tetrapod evolution.
Amemiya, C. T., et al. (2013). 
Nature 496, 311-316.

Aryl hydrocarbon receptor (AHR) in the cnidarian Nematostella vectensis: comparative expression, protein interactions, and ligand binding. 
Reitzel, A. M., Passamaneck, Y. J., Karchner, S. I., Franks, D. G., Martindale, M. Q., Tarrant, A. M., and Hahn, M. E. (2013). 
Development Genes and Evolution, Nov 29. [Epub ahead of print].

Comparative Analysis of Homology Models of the Ah Receptor Ligand Binding Domain: Verification of Structure-Function Predictions by Site-Directed Mutagenesis  of a Non-Functional AHR. 

Fraccalvieri, D., Soshilov, A. A., Karchner, S. I., Franks, D. G., Pandini, A., Bonati, L., Hahn, M. E., and Denison, M. S. (2013). 
Biochemistry 52(4): 714–725.  

Regulation of Constitutive and Inducible AHR Signaling:  Complex Interactions Involving the AHR Repressor.
Hahn, M. E., Allan, L. L., and Sherr, D. H. (2009).
Biochemical Pharmacology 77, 485-497.

Distinct roles of two zebrafish AHR repressors (AHRRa and AHRRb) in embryonic development and regulating the response to 2,3,7,8-tetrachlorodibenzo-p-dioxin.
Jenny, M. J., Karchner, S. I., Franks, D. G., Woodin, B. R., Stegeman, J. J., and Hahn, M. E. (2009).
Toxicol Sci 110, 426-441.

The active form of human aryl hydrocarbon receptor repressor lacks exon 8 and its Pro185 and Ala185 variants repress both AHR and HIF.
Karchner, S. I., Jenny, M. J., Tarrant, A. M., Evans, B. R., Kang, H. J., Bae, I., Sherr, D. H., and Hahn, M. E. (2009).
Molecular and Cellular Biology 29, 3465-3477.

Funded by the National Institute of Environmental Health Sciences (NIEHS).

Mechanisms of embryo response to oxidative stress

Oxidative stress resulting from environmental exposures is associated with a variety of human diseases ranging from chemical teratogenesis to cardiovascular and neurodegenerative diseases. Developing animals appear to be especially sensitive to chemicals causing oxidative stress. The expression and inducibility of antioxidant defenses are critical factors affecting susceptibility to oxidants at these early life stages, but the ontogenic development of these responses in embryos is not well understood.

In adult animals, oxidants initiate an anti-oxidant response by activating NF-E2-related factor 2 (NRF2) and related proteins, which bind to the anti-oxidant response element and activate transcription of genes such as glutathione S-transferases, NAD(P)H-quinone oxidoreductase, glutamyl-cysteine ligase, and superoxide dismutase. The overall objective of the research proposed here is to elucidate the mechanisms by which vertebrate embryos respond to oxidative stress during development. These s tudies are being performed in vivo using embryos of the zebrafish (Danio rerio), a valuable model in which to examine mechanisms of toxicity in developing animals and to screen chemicals for developmental toxicity. The results of these studies will establish the composition and ontogeny of the transcriptional response to oxidative stress in vertebrate embryos, elucidate fundamental mechanisms underlying this response, generate tools for screening chemicals for activity as developmental toxicants or antioxidants, and provide insight into the role of oxidative stress in human disease.

Recent papers:

Glutathione redox dynamics and expression of glutathione-related genes in the developing embryo. 
Timme-Laragy, A. R., Goldstone, J. V., Imhoff, B. R., Stegeman, J. J., Hahn, M. E., and Hansen, J. M. (2013). 
Free Radical Biology & Medicine 65C, 89-101.

Developmental expression of the Nfe2-related factor (Nrf) transcription factor family.
Williams, L. M., Timme-Laragy, A. R., Goldstone, J. V., McArthur, A. G., Stegeman, J. J., Smolowitz, R. M., and Hahn, M. E. (2013). 
PLoS ONE 8, e79574.

Nrf2b: a novel zebrafish paralog of the oxidant-responsive transcription factor NF-E2-related factor 2 (Nrf2). 
Timme-Laragy, A. R., Karchner, S. I., Franks, D. G., Jenny, M. J., Harbeitner, R. C., Goldstone, J. V., McArthur, A. G., and Hahn, M. E. (2012). 
J. Biol. Chem. 287: 4609-4627.  

Funded by the National Institute of Environmental Health Sciences (NIEHS).

Molecular Indicators of Dioxin Sensitivity in Birds

Chlorinated dibenzo-p-dioxins such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) and related planar halogenated aromatic hydrocarbons (PHAHs) are highly toxic to most vertebrate animals, including mammals, birds, and fish. However, there are some dramatic species differences in sensitivity to TCDD and in the relative potencies of certain PHAHs, such as mono-ortho-substituted polychlorinated biphenyls (PCBs). These differences are a major limitation in ecological risk assessment, which often requires extrapolation among species. 

Most PHAH effects occur through binding and activation of the aryl hydrocarbon receptor (Ah receptor or AHR), a ligand-activated transcription factor that plays an essential role in the mechanism of PHAH toxicity. We rec ently identified two amino acid differences in the AHR protein, providing a mechanistic explanation for the difference in PHAH sensitivity between common terns (resistant) and chickens (sensitive). Based on these results and on the AHR sequences of other avian species of known sensitivity, we suggested that AHR sequences might serve as indicators of differential PHAH sensitivity among bird species. The overall objective of the research proposed here is to determine whether species differences in AHR structure can explain and predict avian species differences in AHR function and in vivo sensitivity to PHAHs.

Recent papers:

Species-specific relative AHR1 binding affinities of 2,3,4,7,8-pentachlorodibenzofuran explain avian species differences in its relative potency. 
Farmahin, R., Jones, S. P., Crump, D., Hahn, M. E., Giesy, J. P., Zwiernik, M. J., Bursian, S. J., and Kennedy, S. W. (2014). 
Comp Biochem Physiol C Toxicol Pharmacol  161: 21-25.

Amino Acid Sequence of the Ligand Binding Domain of the Aryl Hydrocarbon Receptor 1 (AHR1) Predicts Sensitivity of Wild Birds to Effects of Dioxin-like Compounds. 

Farmahin, R., Manning, G., Crump, D., Wu, D., Mundy, L., Jones, S., Hahn, M. E., Karchner, S., Giesy, J., Bursian, S., Zwiernik, M. J., Fredricks, T., and Kennedy, S. (2013). 
Toxicol Sci131: 139-152.

Sequence and In Vitro Function of Chicken, Ring-Necked Pheasant, and Japanese Quail AHR1 Predict In Vivo Sensitivity to Dioxins. 
Farmahin, R., Wu, D., Crump, D., Herve, J. C., Jones, S. P., Hahn, M. E., Karchner, S. I., Giesy, J. P., Bursian, S. J., Zwiernik, M. J., and Kennedy, S. W. (2012). 
Environmental Science & Technology 46, 2967-2975.

The molecular basis for differential dioxin sensitivity in birds: role of the aryl hydrocarbon receptor.  Karchner SI, Franks DG, Kennedy SW, Hahn ME. (2006) Proc Natl Acad Sci U S A. 103(16):6252-7.

Funded by NOAA through WHOI Sea Grant.

MicroRNAs in developmental toxicology

Congenital malformations are a major source of human morbidity and mortality. The role of chemical exposure and other environmental factors in the etiology of congenital malformations is not completely understood. However, many xenobiotic chemicals are known to be developmental toxicants or teratogens in experimental animals and several human birth defects are associated with embryonic exposure to xenobiotics. Despite this understanding, the mechanisms by which most developmental toxicants and teratogens disrupt embryonic development are not known. We are investigating a new potential mechanism of developmental toxicity—disruption of microRNA expression—and evaluating the zebrafish embryo as a model for studying the roles of microRNAs in developmental toxicology and teratogenicity. 

Recent papers:  

Developmental exposure to valproic acid alters the expression of microRNAs involved in neurodevelopment in zebrafish
Aluru, N., Deak, K. L., Jenny, M. J., and Hahn, M. E. (2013). 
Neurotoxicology and Teratology 40, 46-58.

Effects of Short-Term Exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin on MicroRNA Expression in Zebrafish Embryos. 
Jenny, M. J., Aluru, N., and Hahn, M. E. (2012). 
Toxicol Appl Pharmacol264: 262–273.

Funded by the National Institute of Environmental Health Sciences (NIEHS).

Last updated: September 14, 2018

whoi logo

Copyright ©2007 Woods Hole Oceanographic Institution, All Rights Reserved, Privacy Policy.
Problems or questions about the site, please contact