Comparing molecular and computational approaches for detecting viral integration of AAV gene therapy constructs

Many current gene therapy targets use recombinant adeno-associated virus (AAV). The majority of delivered AAV therapeutics persist as episomes, separate from host DNA, yet some viral DNA can integrate into host DNA in different proportions and at genomic locations. The potential for viral integration leading to oncogenic transformation has led regulatory agencies to require investigation into AAV integration events following gene therapy in preclinical species. In the present study, tissues were collected from cynomolgus monkeys and mice 6 and 8 weeks, respectively, following administration of an AAV vector delivering transgene cargo. We compared three different next-generation sequencing approaches (shearing extension primer tag selection ligation-mediated PCR, targeted enrichment sequencing [TES], and whole-genome sequencing) to contrast the specificity, scope, and frequency of integration detected by each method. All three methods detected dose-dependent insertions with a limited number of hotspots and expanded clones. While the functional outcome was similar for all three methods, TES was the most cost-effective and comprehensive method of detecting viral integration. Our findings aim to inform the direction of molecular efforts to ensure a thorough hazard assessment of AAV viral integration in our preclinical gene therapy studies.

Adaptive introgression enables evolutionary rescue from extreme environmental pollution

Radical environmental change that provokes population decline can impose constraints on the sources of genetic variation that may enable evolutionary rescue. Adaptive toxicant resistance has rapidly evolved in Gulf killifish (Fundulus grandis) that occupy polluted habitats. We show that resistance scales with pollution level and negatively correlates with inducibility of aryl hydrocarbon receptor (AHR) signaling. Loci with the strongest signatures of recent selection harbor genes regulating AHR signaling. Two of these loci introgressed recently (18 to 34 generations ago) from Atlantic killifish (F. heteroclitus). One introgressed locus contains a deletion in AHR that confers a large adaptive advantage [selection coefficient (s) = 0.8]. Given the limited migration of killifish, recent adaptive introgression was likely mediated by human-assisted transport. We suggest that interspecies connectivity may be an important source of adaptive variation during extreme environmental change.

Polychlorinated biphenyl (PCB) contamination in Galveston Bay, Texas: Comparing concentrations and profiles in sediments, passive samplers, and fish

The industrialized portion of the Houston Ship Channel (HSC) is heavily contaminated with anthropogenic contaminants, most prominent of which are the polychlorinated biphenyls (PCBs). This contamination has driven adaptive evolution in a keystone species for Galveston Bay, the Gulf killifish (Fundulus grandis). We investigated the geographical extent of PCB impacts by sampling 12 sites, ranging from the heavily industrialized upper portion of the HSC to Galveston Island. At each site, PCB concentrations and profiles were determined in three environmental compartments: sediment, water (polyethylene passive samplers), and fish tissue (resident Gulf killifish). We observed a steep gradient of PCB contamination, ranging from 4.00 to 100,000 ng/g organic carbon in sediment, 290-110,000 ng/g lipid in fish, and 4.5-2300 ng/g polyethylene in passive samplers. The PCB congener profiles in Gulf killifish at the most heavily contaminated sites were shifted toward the higher chlorinated PCBs and were highly similar to the sediment contamination profiles. In addition, while magnitude of total PCB concentrations in sediment and total fish contamination levels were highly correlated between sites, the relative PCB congener profiles in fish and passive samplers were more alike. This strong correlation, along with a lack of dependency of biota-sediment accumulation factors with total contamination rates, confirm the likely non-migratory nature of Gulf killifish and suggest their contamination levels are a good site-specific indicator of contamination in the Galveston Bay area. The spatial gradient of PCB contamination in Galveston Bay was evident in all three matrices studied and was observed effectively using Gulf killifish contamination as an environmentally relevant bioindicator of localized contamination in this environment.

EROD activity, chromosomal damage, and oxidative stress in response to contaminants exposure in tree swallow (Tachycineta bicolor) nestlings from Great Lakes Areas of Concern

Tree swallow, Tachycineta bicolor, nestlings were collected from 60 sites in the Great Lakes, which included multiple sites within 27 Areas of Concern (AOCs) and six sites not listed as AOCs from 2010 to 2014. Nestlings, approximately 12 days-of-age, were evaluated for ethoxyresorufin-O-dealkylase (EROD) activity, chromosomal damage, and six measures of oxidative stress. Data on each of these biomarkers were divided into four equal numbered groups from the highest to lowest values and the groups were compared to contaminant concentrations using multivariate analysis. Contaminant concentrations, from the same nestlings, included polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), perfluorinated compounds (PFCs), and 17 elements. Alkylated polycyclic aromatic hydrocarbons (aPAHs) and parent PAHs (pPAHs) were measured in pooled nestling dietary samples. Polychlorinated dibenzo-p-dioxins, polychlorinated dibenzofurans, and pesticides were measured in sibling eggs. Concentrations of aPAHs, pPAHs, chlordane, dieldrin, heptachlor, and PCBs, in that order, were the major contributors to the significant differences between the lowest and highest EROD activities; PFCs, PBDEs, the remaining pesticides, and all elements were of secondary importance. The four categories of chromosomal damage did not separate out well based on the contaminants measured. Concentrations of aPAHs, pPAHs, heptachlor, PCBs, chlordane, and dieldrin were the major contributors to the significant differences between the lowest and highest activities of two oxidative stress measures, total sulfhydryl (TSH) activity and protein bound sulfhydryl (PBSH) activity. The four categories of thiobarbituric acid reacting substances (TBARS), oxidized glutathione (GSSG), reduced glutathione (GSH), and the ratio of GSSG/GSH did not separate well based on the contaminants measured.

A non-destructive BFCOD assay for in vivo measurement of cytochrome P450 3A (CYP3A) enzyme activity in fish embryos and larvae

There is increasing interest in quantifying the exposure and effects of anthropogenic contaminants in fish. Determination of exposures in wild fish is routinely performed, but methods to investigate potential effects are less established. One of the most relevant approaches would be the use of in vivo assays, but existing assays are often limited to in vitro determination of enzyme activity. Many pharmaceuticals and some persistent pollutants activate, and are metabolized by cytochrome P4503A (CYP3A), which make it a relevant and desirable target for biomarker research. We altered the established 7-benzyloxy-4-trifluoromethylcoumarin-O-debenzylation (BFCOD) in vitro protocol for CYP3A activity determination, developing a rapid and inexpensive method to measure in vivo (and in ovo) CYP3A activity in two fish systems: Gulf killifish (Fundulus grandis) and zebrafish (Danio rerio) early life stages. Even with very low concentrations of 7-benzyloxy-4-trifluoromethyl coumarin (BFC, 0.06 µM or 20 µg/L), we were able to detect significant induction in CYP3A activity in embryos of F. grandis, as well as in larvae of D. rerio in response to benzo[a]pyrene (BaP) and fluoranthene (FL) exposures. Because of concerns regarding the possible contribution of CYP1A to BFCOD activity from previous research, we have used a CYP1A post-translational inhibitor (FL) in order to calculate the contribution of CYP1A to the BFCOD assay. We also dosed with benzo[k]fluoranthene (BkF) and showed significant induction of CYP1A activity, with no concurrent increase in CYP3A activity. In this paper, we have taken an established in vitro CYP3A activity assay, and utilized the reaction in a novel way to allow for the non-destructive determination of CYP3A. In summary, we describe a sensitive, cheap, fast and easy modified BFCOD assay for in ovo and in vivo determination of CYP3A activity for use in moderate throughput early-life-stage fish experiments.

Induced pesticide tolerance results from detoxification pathway priming

Few studies in developmental toxicology have focused on whether early life contaminant exposure affects future susceptibility. Investigations in frogs suggested that early life exposure to a pesticide resulted in higher tolerance to a subsequent challenge. This led to the hypothesis that early-life stage exposures can alter phenotypically plastic traits during development, resulting in induced tolerance. Here, we used Gulf killifish (Fundulus grandis) to test the role of detoxification pathway priming in this inducible tolerance. In frogs, the induced tolerance is present five days after the end of the pre-exposure, but absent after a month. We show that a pre-exposure early in life with carbaryl, induces the activity of cytochrome P450 1A (CYP1A) and increases the ability of pre-exposed groups to metabolize carbaryl, likely because of activation of the aryl hydrocarbon receptor (AHR) pathway. Embryos pre-exposed to carbaryl had a 350-500% increase in CYP1A activity, threefold greater capacity to metabolize carbaryl and were more tolerant to a lethal challenge five days after the end of pre-exposure. However, ten days later the differences in CYP1A activity, metabolic capacity and tolerance between pre-exposed and control groups were no longer present. Thus, we conclude that the increase in tolerance observed in pre-exposed fish embryos was due to the activation of the AHR and other metabolic pathways, resulting in a prolonged increase in biotransformation capacity. This allowed individuals to more efficiently deal with subsequent chemical challenges for a short period after the initial pre-exposure. However, this induced tolerance was only short-lived due to the recycling of biotransformation enzymes in the cells as part of general cellular protein maintenance. These findings suggest that induced tolerance was likely due to induction of defense mechanisms during the duration of response to the original stressor, rather than a more permanent change in their ability to respond to future challenges.

Evolutionary toxicology in an omics world

Evolutionary toxicology is a young field that has grown rapidly in the past two decades. The potential of this field comes from the ability to link chemical contamination to multigenerational and population-wide effects in various species. The advancements and rapidly decreasing costs of -omic tools are improving the power and resolution of evolutionary toxicology studies. In this manuscript, we aim to address the trajectories and perspectives for conducting evolutionary toxicology studies with -omic approaches. We discuss the complementarity of using multiple -omic tools (genomics, eDNA, transcriptomics, proteomics, and metabolomics) for utility in understanding the toxicological relevance of adaptive responses in populations. In addition, we discuss phenotypic plasticity and its relevance to transcriptomic studies in toxicology. As evolutionary toxicology grows and expands its capacity to link toxicology with population-wide end points, we emphasize the applications of such studies in answering questions about ecological and population health, as well as future applicability to regulation. Thus, we aim to emphasize the enormous potential for evolutionary toxicology in an -omics world and give perspectives on the directions of future investigations.

Evolutionary toxicology: Meta-analysis of evolutionary events in response to chemical stressors

The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and PAHs that would improve comparability among evolutionary toxicology investigations, and with regulatory guidelines. In addition, we identify studies documenting evolutionary change in the presence of PCB and PAH contamination levels below applicable regulatory benchmarks.

Cross-resistance in Gulf killifish (Fundulus grandis) populations resistant to dioxin-like compounds

The Houston Ship Channel (HSC) in Houston, Texas is an aquatic environment with a long history of contamination, including polychlorinated dibenzodioxins (PCDD), polychlorinated dibenzofurans (PCDF), polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs), and heavy metals. Populations of Gulf killifish (Fundulus grandis) from the HSC have adapted to resist developmental cardiac deformities caused by dioxin-like compounds (DLCs). Contaminants in the HSC have acted as a strong selective pressure on resident Gulf killifish populations. Rapid adaptation can lead to fitness costs, some as a direct result of the mechanisms involved in the adaptive process, whereas other adaptations may be more general. To explore potential fitness costs, we evaluated two Gulf killifish populations with documented resistance to DLC-induced cardiac teratogenesis (Patrick Bayou and Vince Bayou), and one previously characterized reference population (Gangs Bayou). We also characterized a previously unstudied population from Galveston Bay as an additional reference population (Smith Point). We tested the sensitivity of F1 larvae from these four populations to two classes of pesticides (pyrethroid (permethrin) and carbamate (carbaryl)) and two model pro-oxidants (tert-butyl hydroquinone (tBHQ) and tert-butyl hydroperoxide (tBOOH)). In addition, we explored their responses to hypoxia and measured resting metabolic rates (M.O2). Both adapted populations were cross-resistant to the toxicity of carbaryl and both pro-oxidants tested. There were no population differences in sensitivity to permethrin. On the other hand, one reference population (Gangs Bayou) was less sensitive to hypoxia, and maintained a lower M.O2 . However, there were no differences in hypoxia tolerance or resting metabolic rate between the second reference and the two adapted populations. This investigation emphasizes the importance of including multiple reference populations to clearly link fitness costs or cross-resistance to pollution adaptation, rather than to unrelated environmental or ecological differences. When compared to previous literature on adapted populations of Fundulus heteroclitus, we see a mixture of similarities and differences, suggesting that F. grandis adapted phenotypes likely involve multiple mechanisms, which may not be completely consistent among adapted populations.

Insights into the evolution of longevity from the bowhead whale genome

The bowhead whale (Balaena mysticetus) is estimated to live over 200 years and is possibly the longest-living mammal. These animals should possess protective molecular adaptations relevant to age-related diseases, particularly cancer. Here, we report the sequencing and comparative analysis of the bowhead whale genome and two transcriptomes from different populations. Our analysis identifies genes under positive selection and bowhead-specific mutations in genes linked to cancer and aging. In addition, we identify gene gain and loss involving genes associated with DNA repair, cell-cycle regulation, cancer, and aging. Our results expand our understanding of the evolution of mammalian longevity and suggest possible players involved in adaptive genetic changes conferring cancer resistance. We also found potentially relevant changes in genes related to additional processes, including thermoregulation, sensory perception, dietary adaptations, and immune response. Our data are made available online (http://www.bowhead-whale.org) to facilitate research in this long-lived species.

Evolved resistance to PCB- and PAH-induced cardiac teratogenesis, and reduced CYP1A activity in Gulf killifish (Fundulus grandis) populations from the Houston Ship Channel, Texas

The Houston Ship Channel (HSC), connecting Houston, Texas to Galveston Bay and ultimately the Gulf of Mexico, is heavily industrialized and includes several areas that have historically been identified as containing significant levels of mercury, dioxins, furans, polychlorinated biphenyls (PCBs), and polycyclic aromatic hydrocarbons (PAHs). Gulf killifish, Fundulus grandis, inhabit this entire estuarine system, including the most contaminated areas. F. grandis is the sister species of the well-established estuarine model organism Fundulus heteroclitus, for which heritable resistance to both PCB and PAH toxicity has been documented in several populations. F. grandis collected from two Superfund sites on the HSC and from a reference population were used to establish breeding colonies. F1 embryos from HSC populations were approximately 1000-fold more resistant to PCB126- and 2-5-fold more resistant to coal tar-induced cardiovascular teratogenesis, relative to embryos from the reference population. Reciprocal crosses between reference and contaminated populations exhibit an intermediate level of resistance, confirming that observed protection is genetic and biparentally inherited. Ethoxyresorufin-O-deethylase (EROD) data confirm a reduction in basal and induced cytochrome P4501A (CYP1A) activity in resistant populations of F. grandis. This result is consistent with responses previously described for resistant populations of F. heteroclitus, specifically a recalcitrant aryl hydrocarbon receptor (AHR) pathway. The decreased levels of cardiovascular teratogenesis, and decrease in CYP1A inducibility in response to PCB126 and a PAH mixture, suggest that HSC F. grandis populations have adapted to chronic contaminants exposures via a mechanism similar to that previously described for F. heteroclitus. To the best of our knowledge, this is the first documentation of evolved pollution resistance in F. grandis. Additionally, the mechanistic similarities between the population adaptation observed in this study and previous work in F. heteroclitus suggest that genetic variation predating the evolutionary divergence of these two species may best explain the apparent rapid parallel evolution of pollution resistance in genetically and geographically distinct species and populations.