ECD Group Research Interests
The
ECD Group has many ongoing projects and collaborators, and we are always open to new projects and new collaborations. These are a few of the currently funded projects going on in the lab right now:
Mechanisms of cognitive impairment following early-life seizures (5R01NS108765: Holmes)
Epilepsy is a complex disorder which involves much more than seizures. As emphasized by the National Academy of Science-sponsored Committee on the Public Health Dimensions of the Epilepsies,1 epilepsy may be accompanied by a range of associated co-morbid
health conditions that can have significant health and quality of life implications. Of these comorbidities, cognitive impairment is one of the most common and distressing aspects of epilepsy. Because the risk of cognitive impairment is greatest
in young children, the educational, vocational, social and economic implications are enormous. Remarkably, there are only a handful of laboratories attempting to understand the pathophysiological basis of cognitive disturbances in early-life seizures
(ELS). It is the view of our laboratory that prior to preventing, limiting and reversing cognitive comorbidities, it is essential to understand the neurobiological basis of developmental cognitive dysfunction associated with ELS. One of the major
difficulties in decoding the complex issue of cognitive outcomes following ELS in children is the gulf between the behavioral/mental spheres in which these deficits are substantiated and the underlying physiological/developmental domains that
are both the cause of these deficits and the most likely domains for therapy and intervention. Based on strong preliminary data showing abnormalities in rate and temporal coding in cognitive impairment following ELS, we propose that aberrant neural
circuit dynamics are the neurophysiological underpinnings of cognitive impairment. In this proposal, we wish to rigorously study the consequences of ELS on temporal coding using multi-site single cell and local field potentials. To move from correlative
to causal experimentation, we will first determine if cognitive rehabilitation following ELS reverses coding abnormalities. Secondly, we will use optogenetic-induced modulation of neuronal circuits to modify coding abnormalities and correct spatial
cognitive deficits. Based on compelling preliminary data, we believe our findings will support the concept of dynamic neural discoordination as a causal factor of cognitive dysfunction following ELS.
Cognitive deficits after experimental febrile seizures: neurobiology and biomarkers (5R01NS108296: Holmes and Baram)
Epilepsy is a complex disorder which involves much more than seizures. It may also be accompanied by a range of associated comorbid health conditions with significant health and quality of life implications as emphasized by the National Academy of
Science-sponsored Committee on the Public Health Dimensions of the Epilepsies.1 Our research laboratories have generated a rodent model of experimental febrile status epilepticus (eFSE), which provokes both temporal lobe epilepsy-like seizures
and cognitive deficits, thereby providing a powerful tool to probe the mechanisms underlying these conditions. Following eFSE, rats exhibit significant deficits in the active avoidance test—a test of spatial cognition—and show altered
hippocampal oscillatory activity and abnormal temporal coding of action potentials when compared with controls. Recently, we identified some of the mechanisms underlying epilepsy-promoting functional changes in the hippocampal network provoked
by eFSE. Specifically, we observed coordinated transcriptionally-regulated changes in the expression of multiple genes governing neuronal behavior which resulted from eFSE-induced up-regulated expression and function of the neuron-restrictive
silencing factor (NRSF). Remarkably, our preliminary studies indicate that both the cognitive deficits and the neuronal discoordination can be prevented by blocking NRSF following status epilepticus. While the therapeutic implications of our findings
are exciting, it is not yet known how eFSE-induced abnormal NRSF activities contribute to disruption of gene expression and maturation of specific cell populations throughout the circuit affected by eFSE. This proposal aims to determine the biological
underpinnings of eFSE-induced cognitive deficits at the molecular, single cell and circuit levels, and to establish how NRSF-blockade reverses these deficits. In addition, we will determine if NRSF is involved in memory problems associated with
other developmental seizures as this will be a requisite for translation of our discoveries. The proposed multidisciplinary, multidimensional and cutting-edge experiments will address the mechanisms involved in eFSE-induced memory disorders and
establish how such disorders can be reversed through genetic methods. These studies will also provide novel insights into mechanisms of memory-circuit maturation and have a potential major impact on a large population of children with febrile
status epilepticus.
Modification of neural circuits with interneuron transplantation (5R21NS098162-02: Scott)
Temporal lobe epilepsy associated with mesial temporal sclerosis (MTS) is common, frequently difficult to treat medically and therefore many patients have epilepsy surgery. Although temporal lobe resections are often successful at stopping seizures
this approach usually fails to improve the commonly identified memory comorbidities and can make those impairments worse. A therapeutic approach in which MTS is modified in a way that reduces epileptic phenomena and leads to an improvement in
memory would have a major impact on the quality of life of many patients with MTS. Implantation of interneuron precursors has been shown to reduce seizures and improve cognition. We hypothesize that transplanted interneuron precursors will restore
temporal organization of hippocampal pyramidal cells thereby improving abnormalities in rate, temporal and population coding that underpins normal cognitive behavior. In addition they will also minimize hypersynchrony leading to seizure reduction.
We propose to study interactions between multiple simultaneously firing hippocampal neurons recorded from CA1 and CA3 bilaterally in awake, freely moving rodents during foraging and during an active place-avoidance task. Systems level changes
at the level of rate coding, temporal coding and population coding will be compared between implanted and non-implanted rats. We will use standard and novel analytical tools developed in our laboratories to apply to these data. A detailed systems
level understanding of how neural networks need to change in order to improve disease outcomes will guide optimization of cell based therapies and will provide a target for other interventions such as electrical stimulation or optogenetics.
Synaptic changes and hypersynchronous network activity in mTORopathies (1R01NS110945: Weston)
Genetic variants that hyperactivate mechanistic target of rapamycin (mTOR) signaling are among the most common pathological substrates associated with intractable pediatric epilepsy, and hyperactivation of the mTOR pathway is also proposed to mediate
epileptogenesis in response to brain injury. Although altered neuronal migration and morphology are hallmarks of many known mTOR-related neurological diseases (mTORopathies) in humans, studies in animal models show that abnormal synaptic transmission
and network activity precede or occur in the absence of overt structural changes, and that preventing structural changes does not prevent the neurological symptoms. This highlights the need for a better understanding of the functional changes
in the brain. This proposal will test the hypothesis that abnormal synchronous neuronal activity caused by genetic hyperactivation of the mTOR signaling pathway is driven by changes in synaptic transmission. The long-term goal is to understand
the genesis of, and then prevent or rescue, this abnormal activity, which may underlie both the high incidence of epilepsy and autism in humans with mTORopathies. In Aim 1, we will address this by testing four genetic models of mTORopathies (Tsc1,
Pten, Pik3ca, Szt2) and determining whether there are common synaptic changes. Whether different mTORopathies share common synaptic alterations is an essential question to understanding the mechanistic similarity of these molecularly related diseases.
In Aim 2, we will use molecular genetic rescue strategies that dissociate the morphological and synaptic effects of mTOR hyperactivation to test whether synaptic changes are sufficient to induce hypersynchronous activity and epilepsy. In Aim 3,
we will use a combination of widefield and 2-photon calcium imaging to track the development and characteristics of hypersynchronous activity in vivo. We will then test whether the synaptic changes we observe in vitro are present at the time and
place of hypersynchronous activity onset, and whether they can drive aberrant network activity. We anticipate that defining the functional consequences of mTOR hyperactivation relevant to enhanced neuronal excitability will lead to significant
advances in the understanding of disease mechanisms, and aid the development of treatment strategies for mTORpathies and other neurological diseases
Mechanisms for improving cognitive outcome in epilepsy with ACTH (1K22NS104230-01: Hernan)
Epilepsy, particularly pediatric epilepsy, is associated with a very high incidence of cognitive, behavioral and psychiatric comorbidities that are often more detrimental to overall quality of life than the seizures themselves. Aggressive treatment
of seizures has been the gold standard, with the belief that this will also minimize cognitive and psychiatric comorbidities. However, very little focus has been placed on treatment of these comorbidities directly and clinical data suggest that
focusing on seizure treatment alone does not effectively treat cognitive impairment. We have recently found that ACTH, an endogenous part of the hypothalamic- pituitary-adrenal axis that is often exogenously administered to children with severe
epilepsies, can improve cognitive outcome in rats without altering seizure parameters. While it was previously thought that the primary mechanism of action for ACTH was through the release of corticosteroids, new research suggests that melanocortin
4 receptor (MC4R) activation in neuronal and glial populations is neuroprotective and can improve outcomes in other disease models. We hypothesize that MC4R agonism in the CNS with ACTH is a key mechanism of action by which it can improve cognitive
outcomes after early life seizures (ELS). We further hypothesize that early treatment with ACTH will normalized functional organization of neural networks within and between the prefrontal cortex and the hippocampus, and that this improvement
will provide a systems-level mechanism underpinning its mechanism of action. Understanding how ACTH can prevent cognitive deficits without altering seizure parameters is crucial for finding novel treatment approaches for these deficits. Therefore,
the scientific aims of this study are to: 1) determine the role of MC4R signaling in the brain on subsequent cognition in control animals and ELS animals, 2) determine the effect of early treatment with ACTH on synaptic plasticity in adult neuronal
networks in the PFC after ELS and finally 3) determine the effect of early treatment with ACTH on adult neuronal networks in vivo and executive dysfunction associated with ELS. The studies proposed are designed to understand the developmental
role of ACTH and MC4Rs on cognitive networks in ELS. Successful completion of this project has the potential to change the way we think about treatment of pediatric epilepsy, and may have implications for the treatment of other neurodevelopmental
disorders as well.
Inferring molecular mechanisms of complex disease by integrating patterns of epistasis with functional genomic networks (5R21LM012615: Mahoney and Tyler)
The goal of this proposal is to develop computational methods that will identify genes driving epistasis between quantitative trait loci. Genetic association studies in both humans and model organisms have been increasingly able to detect interactions
among genetic variants that influence disease risk and pathogenesis. However, identifying which genes are represented by individual variants is a major challenge. Many variants influencing disease are situated between genes, and even those that
are in genes may be representing an effect from a neighboring gene. In model organism studies the situation is even more problematic. In breeding experiments, genetic associations with phenotypes typically encompass large regions of DNA with many
genes, and experimental follow-up to identify the genes responsible for the association is resource-intensive. To address this problem, we are developing computational tools to prioritize putative gene interactions in interacting genomic regions
for biological follow-up. We use machine learning classifiers trained on functional gene-gene interaction networks and combinatorial optimization to identify likely candidate gene-gene interactions responsible for epistatic interactions between
genomic regions. Our methods sift through enormous spaces of candidate interactions, retaining only those whose functional interactions identify as plausible for supporting the epistatic interaction. These tools hold promise to dramatically limit
the resource-intensity of biological follow up of putative epistasis and to clarify the genetic architecture of complex disease.
COBRE project 4 (1P20GM130454: Mahoney)
The goal of this project is to develop network-based methods to predict tissue-specific pathways that underlie diseases and drug responses. Successfully treating systemic diseases requires targeting diverse, tissue- specific disease processes, which
are not easy to measure directly. Internal organ biopsies are rare and almost never taken in healthy subjects due to their inherent risks. Experiments probing disease states and drug responses with high-throughput (HTP) gene expression have to
mediate a tradeoff between the accessibility and tractability of the assayed biological system and the direct translatability of results to target tissues. For example, peripheral tissues such as skin and blood are easily acquired and typically
contain important information about the pathobiology of diseases, but HTP data in peripheral tissue is not a perfect surrogate for HTP data in other tissues. Likewise, drug screening in cell culture allows for rapid and scalable determination
of gene-expression-response signatures to therapeutic compounds, but translating these results to target tissues is not straightforward. The overarching goal of this project is to predict tissue-specific pathways from easily obtained HTP data
from outside that tissue. This project develops and validates a novel machine- learning framework called “tissue network knowledge transfer” (TINKER), which predicts tissue-specific pathways using HTP data from outside that tissue
by mining tissue-specific gene-gene interaction networks. TINKER will be used to predict differential gene expression in internal organs from HTP gene signatures obtained from skin and blood from the same disease condition. TINKER will be tested
by using it to predict known drug targets in tissues from HTP gene signatures in cell culture. Finally, this project will systematically optimize TINKER by incorporating nonlinear machine learning algorithms and network feature representations
that incorporate indirect connections among genes.
Systems genetics of tuberous sclerosis complex outcomes using BXD recombinant inbred mice (W81XWH-19-1-0251: Mahoney)
The goal of this project is to improve mouse models of tuberous sclerosis complex (TSC) in order to identify genetic factors conferring resilience to neurological symptoms. TSC is a profoundly complex disease characterized by cortical tubers and accompanied
by epilepsy and TSC-associated neurological disorders (TANDs), including intellectual disability, developmental delay, anxiety, and autism spectrum disorder (ASD). Although TSC has been traced to gene mutations in the human TSC1 and TSC2 genes,
patients with TSC-causing mutations have widely varying outcomes, ranging from intractable epilepsy and autism to no seizures or psychiatric comorbidities. Even within families sharing an identical TSC mutation, case reports indicate that some
members can be clinically unaffected, while others are developmentally delayed and suffer from treatment-resistant epilepsy. Thus, there must be other genetic factors beyond the TSC gene mutation that determine outcomes. Identifying genetic factors
conferring either resilience or susceptibility to adverse outcomes is a potentially powerful way to identify new possibilities for therapy. Mouse models are ideal for this work because they can be genetically controlled and extensively characterized
biologically. In this project, we will develop a novel family of mouse models called the BXD-TSC mice to model patient heterogeneity and identify new genetic factors determining resilience or susceptibility to adverse outcomes. The objective of
this project is to: (1) breed mice carrying a TSC-causing mutation to a diverse panel of mice called the BXD lines; (2) characterize their behavior, seizures, and brain abnormalities; and (3) genetically map these traits to identify resilience
and susceptibility factors. The rationale for this study is that behavior, seizures, and brain abnormalities are intricately linked to each other and determine the complex neurological and psychiatric outcomes in patients with TSC. Because these
outcomes are major determinants of quality of life, improved modeling of patient heterogeneity––and the subsequent effect on therapeutic development––is expected to benefit this group specifically. Such efforts are critical,
as neurological and psychiatric outcomes are poorly controlled and even more poorly understood. Developing and validating a model system for patient heterogeneity is an investment to improve our ability to probe the basic biology of TSC and robustly
preclinically test potential therapies. Improved TSC mouse models are expected to have a long-term translational impact on TSC research over the next 5 to 10 years. In the interim, this project will establish that genetic modifiers of TSC outcomes
exist in the BXD-TSC mice, leading to near-term efforts to pinpoint these factors and determine their mechanisms. Beyond genetic research, this project will also provide the TSC research community with a new set of easily generated models to study
the diversity of outcomes (including non-neurological outcomes). Moreover, this project will establish a novel experimental paradigm for identifying genetic modifiers of other TSC mutations, beyond the specific mutation in this project. The near-term
adoption of this paradigm will therefore provide a platform to radically expand our ability to probe the pathophysiology of TSC leading to long-term improvements in patient care.