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Publication Genome-Wide DNA Methylation Analysis in Cohesin Mutant Human Cell Lines(2010-09-01) Liu, Jinglan; Zhang, Zhe; Deardorff, Matthew A; Bando, Masashige; Itoh, Takehiko; Li, Jennifer R; Clark, Dinah; Kaur, Maninder; Tatsuro, Kondo; Kline, Antonie D; Chang, Celia; Spinner, Nancy B; Vega, Hugo; Jackson, Laird G; Krantz, Ian D; Shirahige, KatsuhikoThe cohesin complex has recently been shown to be a key regulator of eukaryotic gene expression, although the mechanisms by which it exerts its effects are poorly understood. We have undertaken a genome-wide analysis of DNA methylation in cohesin-deficient cell lines from probands with Cornelia de Lange syndrome (CdLS). Heterozygous mutations in NIPBL, SMC1A and SMC3 genes account for ∼65% of individuals with CdLS. SMC1A and SMC3 are subunits of the cohesin complex that controls sister chromatid cohesion, whereas NIPBL facilitates cohesin loading and unloading. We have examined the methylation status of 27 578 CpG dinucleotides in 72 CdLS and control samples. We have documented the DNA methylation pattern in human lymphoblastoid cell lines (LCLs) as well as identified specific differential DNA methylation in CdLS. Subgroups of CdLS probands and controls can be classified using selected CpG loci. The X chromosome was also found to have a unique DNA methylation pattern in CdLS. Cohesin preferentially binds to hypo-methylated DNA in control LCLs, whereas the differential DNA methylation alters cohesin binding in CdLS. Our results suggest that in addition to DNA methylation multiple mechanisms may be involved in transcriptional regulation in human cells and in the resultant gene misexpression in CdLS.Publication mGluR5-Antagonist Mediated Reversal of Elevated Stereotyped, Repetitive Behaviors in the VPA Model of Autism(2011-10-07) Mehta, Mili V; Gandal, Michael J.; Siegel, Steven JAutism spectrum disorders (ASD) are highly disabling developmental disorders with a population prevalence of 1–3%. Despite a strong genetic etiology, there are no current therapeutic options that target the core symptoms of ASD. Emerging evidence suggests that dysfunction of glutamatergic signaling, in particular through metabotropic glutamate receptor 5 (mGluR5) receptors, may contribute to phenotypic deficits and may be appropriate targets for pharmacologic intervention. This study assessed the therapeutic potential of 2-methyl-6-phenylethyl-pyrididine (MPEP), an mGluR5-receptor antagonist, on repetitive and anxiety-like behaviors in the valproic acid (VPA) mouse model of autism. Mice were exposed prenatally on day E13 to VPA and assessed for repetitive self-grooming and marble burying behaviors as adults. Anxiety-like behavior and locomotor activity were measured in an open-field. VPA-exposed mice displayed increased repetitive and anxiety-like behaviors, consistent with previously published results. Across both marble burying and self-grooming assays, MPEP significantly reduced repetitive behaviors in VPA-treated mice, but had no effect on locomotor activity. These results are consistent with emerging preclinical literature that mGluR5-antagonists may have therapeutic efficacy for core symptoms of autism.Publication Complementary Control of Sensory Adaptation by Two Types of Cortical Interneurons(2015-10-13) Natan, Ryan G; Briguglio, John J; Aizenberg, Mark; Mwilambwe-Tshilobo, Laetitia; Jones, Sara I; Geffen, Maria N; Goldberg, Ethan MReliably detecting unexpected sounds is important for environmental awareness and survival. By selectively reducing responses to frequently, but not rarely, occurring sounds, auditory cortical neurons are thought to enhance the brain's ability to detect unexpected events through stimulus-specific adaptation (SSA). The majority of neurons in the primary auditory cortex exhibit SSA, yet little is known about the underlying cortical circuits. We found that two types of cortical interneurons differentially amplify SSA in putative excitatory neurons. Parvalbumin-positive interneurons (PVs) amplify SSA by providing non-specific inhibition: optogenetic suppression of PVs led to an equal increase in responses to frequent and rare tones. In contrast, somatostatin-positive interneurons (SOMs) selectively reduce excitatory responses to frequent tones: suppression of SOMs led to an increase in responses to frequent, but not to rare tones. A mutually coupled excitatory-inhibitory network model accounts for distinct mechanisms by which cortical inhibitory neurons enhance the brain's sensitivity to unexpected sounds.Publication Remyelination Reporter Reveals Prolonged Refinement of Spontaneously Regenerated Myelin(2013-03-05) Powers, Berit E; Sellers, Drew L; Lovelett, Emilie A; Cheung, Willy; Aalami, Sheida A; Zapertov, Nikolai; Maris, Don O; Horner, Phillip JNeurological diseases and trauma often cause demyelination, resulting in the disruption of axonal function and integrity. Endogenous remyelination promotes recovery, but the process is not well understood because no method exists to definitively distinguish regenerated from preexisting myelin. To date, remyelinated segments have been defined as anything abnormally short and thin, without empirical data to corroborate these morphological assumptions. To definitively identify regenerated myelin, we used a transgenic mouse with an inducible membrane-bound reporter and targeted Cre recombinase expression to a subset of glial progenitor cells after spinal cord injury, yielding remarkably clear visualization of spontaneously regenerated myelin in vivo. Early after injury, the mean length of sheaths regenerated by Schwann cells and oligodendrocytes (OLs) was significantly shorter than control, uninjured myelin, confirming past assumptions. However, OL-regenerated sheaths elongated progressively over 6 mo to approach control values. Moreover, OL-regenerated myelin thickness was not significantly different from control myelin at most time points after injury. Thus, many newly formed OL sheaths were neither thinner nor shorter than control myelin, vitiating accepted dogmas of what constitutes regenerated myelin. We conclude that remyelination, once thought to be static, is dynamic and elongates independently of axonal growth, in contrast to stretch-based mechanisms proposed in development. Further, without clear identification, past assessments have underestimated the extent and quality of regenerated myelin.Publication Action Concepts in the Brain: An Activation Likelihood Estimation Meta-Analysis(2013-08-01) Watson, Christine E; Cardillo, Eileen R; Chatterjee, Anjan; Ianni, Geena RMany recent neuroimaging studies have investigated the representation of semantic memory for actions in the brain. We used activation likelihood estimation (ALE) meta-analyses to answer two outstanding questions about the neural basis of action concepts. First, on an “embodied” view of semantic memory, evidence to date is unclear regarding whether visual motion or motor systems are more consistently engaged by action concepts. Second, few studies have directly investigated the possibility that action concepts accessed verbally or nonverbally recruit different areas of the brain. Because our meta-analyses did not include studies requiring the perception of dynamic depictions of actions or action execution, we were able to determine whether conceptual processing alone recruits visual motion and motor systems. Significant concordance in brain regions within or adjacent to visual motion areas emerged in all meta-analyses. By contrast, we did not observe significant concordance in motor or premotor cortices in any analysis. Neural differences between action images and action verbs followed a gradient of abstraction among representations derived from visual motion information in the left lateral temporal and occipital cortex. The consistent involvement of visual motion but not motor brain regions in representing action concepts may reflect differences in the variability of experience across individuals with perceiving versus performing actions.Publication HDAC I Inhibition in the Dorsal and Ventral Hippocampus Differentially Modulates Predator-Odor Fear Learning and Generalization(2015-09-22) Yuan, Robin K; Thomas, Arthur S; Hebert, Jenna C; Wann, Ellen G; Muzzio, Isabel AAlthough predator odors are ethologically relevant stimuli for rodents, the molecular pathways and contribution of some brain regions involved in predator odor conditioning remain elusive. Inhibition of histone deacetylases (HDACs) in the dorsal hippocampus has been shown to enhance shock-induced contextual fear learning, but it is unknown if HDACs have differential effects along the dorso-ventral hippocampal axis during predator odor fear learning. We injected MS-275, a class I HDAC inhibitor, bilaterally in the dorsal or ventral hippocampus of mice and found that it had no effects on innate anxiety in either region. We then assessed the effects of MS-275 at different stages of fear learning along the longitudinal hippocampal axis. Animals were injected with MS-275 or vehicle after context pre-exposure (pre-conditioning injections), when a representation of the context is first formed, or after exposure to coyote urine (post-conditioning injections), when the context becomes associated with predator odor. When MS-275 was administered after context pre-exposure, dorsally injected animals showed enhanced fear in the training context but were able to discriminate it from a neutral environment. Conversely, ventrally injected animals did not display enhanced learning in the training context but generalized the fear response to a neutral context. However, when MS-275 was administered after conditioning, there were no differences between the MS-275 and vehicle control groups in either the dorsal or ventral hippocampus. Surprisingly, all groups displayed generalization to a neutral context, suggesting that predator odor exposure followed by a mild stressor such as restraint leads to fear generalization. These results may elucidate distinct functions of the dorsal and ventral hippocampus in predator odor-induced fear conditioning as well as some of the molecular mechanisms underlying fear generalization.Publication NR4A Nuclear Receptors Support Memory Enhancement by Histone Deacetylase Inhibitors(2012-10-01) Hawk, Joshua Davis; Poplawski, Shane Gary; Bridi, Morgan; Sulewski, Michael E; Bookout, Angie L; Abel, Ted; Rao, Allison J; Kroener, Brian T; Manglesdorf, David JThe formation of a long-lasting memory requires a transcription-dependent consolidation period that converts a short-term memory into a long-term memory. Nuclear receptors compose a class of transcription factors that regulate diverse biological processes, and several nuclear receptors have been implicated in memory formation. Here, we examined the potential contribution of nuclear receptors to memory consolidation by measuring the expression of all 49 murine nuclear receptors after learning. We identified 13 nuclear receptors with increased expression after learning, including all 3 members of the Nr4a subfamily. These CREB-regulated Nr4a genes encode ligand-independent “orphan” nuclear receptors. We found that blocking NR4A activity in memory-supporting brain regions impaired long-term memory but did not impact short-term memory in mice. Further, expression of Nr4a genes increased following the memory-enhancing effects of histone deacetylase (HDAC) inhibitors. Blocking NR4A signaling interfered with the ability of HDAC inhibitors to enhance memory. These results demonstrate that the Nr4a gene family contributes to memory formation and is a promising target for improving cognitive function.Publication Ventromedial Frontal Lobe Damage Disrupts Value Maximization in Humans(2011-05-18) Camille, Nathalie; Griffiths, Cathryn A; Vo, Khoi; Fellows, Lesley K; Kable, Joseph WRecent work in neuroeconomics has shown that regions in orbitofrontal and medial prefrontal cortex encode the subjective value of different options during choice. However, these electrophysiological and neuroimaging studies cannot demonstrate whether such signals are necessary for value-maximizing choices. Here we used a paradigm developed in experimental economics to empirically measure and quantify violations of utility theory in humans with damage to the ventromedial frontal lobe (VMF). We show that people with such damage are more likely to make choices that violate the generalized axiom of revealed preference, which is the one necessary and sufficient condition for choices to be consistent with value maximization. These results demonstrate that the VMF plays a critical role in value-maximizing choice.Publication Mechanically- and Chemically-Tunable Cell Culture System to Study Myofibroblast Phenotype(2014-05-01) Saums, Michele K; Wang, Weifeng; Han, Biao; Madhavan, Lakshmi; Lee, Daeyeon; Han, Lin; Wells, Rebecca GCell culture systems for studying the combined effects of matrix proteins and mechanical forces on the behavior of soft tissue cells have not been well developed. Here, we describe a new biomimetic cell culture system that allows for the study of mixtures of matrix proteins while controlling mechanical stiffness in a range that is physiological for soft tissues. This system consists of layer-by-layer (LbL)-assembled films of native matrix proteins atop mechanically tunable soft supports. We used hepatic stellate cells, which differentiate to myofibroblasts in liver fibrosis, for proof-of-concept studies. By culturing cells on collagen and lumican LbL-modified hydrogels, we demonstrate that this system is noncytotoxic and offers a valid control substrate, that the hydrogel determines the overall system mechanics, and that the addition of lumican to collagen influences the stellate cell phenotype. LbL-modified hydrogels offer the potential to study the influence of complex environmental factors on soft-tissue cells in culture.Publication Dielectrophoretic Capture and Genetic Analysis of Single Neuroblastoma Cells(2014-07-31) Carpenter, Erica L; Rader, JulieAnn; Hallberg, Paul L; Ruden, Jacob; Rappaport, Eric F; O'Dwyer, Peter J; Hunter, Kristen N; Mosse, Yael; Krystka, KateOur understanding of the diversity of cells that escape the primary tumor and seed micrometastases remains rudimentary, and approaches for studying circulating and disseminated tumor cells have been limited by low throughput and sensitivity, reliance on single parameter sorting, and a focus on enumeration rather than phenotypic and genetic characterization. Here, we utilize a highly sensitive microfluidic and dielectrophoretic approach for the isolation and genetic analysis of individual tumor cells. We employed fluorescence labeling to isolate 208 single cells from spiking experiments conducted with 11 cell lines, including 8 neuroblastoma cell lines, and achieved a capture sensitivity of 1 tumor cell per 106 white blood cells (WBCs). Sample fixation or freezing had no detectable effect on cell capture. Point mutations were accurately detected in the whole genome amplification product of captured single tumor cells but not in negative control WBCs. We applied this approach to capture 144 single tumor cells from 10 bone marrow samples of patients suffering from neuroblastoma. In this pediatric malignancy, high-risk patients often exhibit wide-spread hematogenous metastasis, but access to primary tumor can be difficult or impossible. Here, we used flow-based sorting to pre-enrich samples with tumor involvement below 0.02%. For all patients for whom a mutation in the Anaplastic Lymphoma Kinase gene had already been detected in their primary tumor, the same mutation was detected in single cells from their marrow. These findings demonstrate a novel, non-invasive, and adaptable method for the capture and genetic analysis of single tumor cells from cancer patients.