Honors & Awards
Stanley Fahn Junior Faculty Award, Parkinson's Foundation (2021-2024)
NARSAD Young Investigator Award, Brain and Behavior Research Foundation (2019-2020)
K99 Pathway to Independence Award, NIMH (2016-2018)
Award for Scientific Excellence, Gladstone Institutes (2017)
F32 - Ruth L. Kirschstein National Research Service Award (NRSA), NINDS (2014-2016)
Above and Beyond Award, Gladstone Institutes (2012)
F31 - Ruth L. Kirschstein National Research Service Award (NRSA), NIMH (2008-2010)
NDSEG Graduate Fellowship, Department of Defense (2005-2008)
Bassett Physics Prize, Amherst College (1999)
Boards, Advisory Committees, Professional Organizations
Faculty Member, Society for Neuroscience NeurOnline Training Series (2018 - 2018)
Chair, Gordon-Kenan Research Seminar on Inhibition in the CNS (2015 - 2015)
Panelist, National Defense Science and Engineering Graduate Fellowship Selection Committee (2015 - 2015)
Co-Chair, Gordon-Kenan Research Seminar on Interneuron Diversity (2013 - 2013)
Visiting Scientist, The Allen Institute, Neuroscience (2020)
Post-Doc, Gladstone Institutes, UCSF, Neuroscience (2019)
PhD, Stanford University, Molecular and Cellular Physiology (2012)
AB, Amherst College, Physics (2002)
Doctoral Dissertation Advisor (AC)
Deniz Bingul, Rennie Kendrick, Emmalyn Leonard
A multimodal cell census and atlas of the mammalian primary motor cortex
2021; 598 (7879): 86-102
Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input-output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1-5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
View details for DOI 10.1038/s41586-021-03950-0
View details for Web of Science ID 000705847500002
View details for PubMedID 34616075
View details for PubMedCentralID PMC8494634
Comparative cellular analysis of motor cortex in human, marmoset and mouse.
2021; 598 (7879): 111-119
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally conserved across mammals1. Here, using high-throughput transcriptomic and epigenomic profiling of more than 450,000 single nuclei in humans, marmoset monkeys and mice, we demonstrate a broadly conserved cellular makeup of this region, with similarities that mirror evolutionary distance and are consistent between the transcriptome and epigenome. The core conserved molecular identities of neuronal and non-neuronal cell types allow us to generate a cross-species consensus classification of cell types, and to infer conserved properties of cell types across species. Despite the overall conservation, however, many species-dependent specializations are apparent, including differences in cell-type proportions, gene expression, DNA methylation and chromatin state. Few cell-type marker genes are conserved across species, revealing a short list of candidate genes and regulatory mechanisms that are responsible for conserved features of homologous cell types, such as the GABAergic chandelier cells. This consensus transcriptomic classification allows us to use patch-seq (a combination of whole-cell patch-clamp recordings, RNA sequencing and morphological characterization) to identify corticospinal Betz cells from layer 5 in non-human primates and humans, and to characterize their highly specialized physiology and anatomy. These findings highlight the robust molecular underpinnings of cell-type diversity in M1 across mammals, and point to the genes and regulatory pathways responsible for the functional identity of cell types and their species-specific adaptations.
View details for DOI 10.1038/s41586-021-03465-8
View details for PubMedID 34616062
View details for PubMedCentralID PMC8494640
Signature morpho-electric, transcriptomic, and dendritic properties of human layer 5 neocortical pyramidal neurons.
2021; 109 (18): 2914-2927.e5
In the neocortex, subcerebral axonal projections originate largely from layer 5 (L5) extratelencephalic-projecting (ET) neurons. The unique morpho-electric properties of these neurons have been mainly described in rodents, where retrograde tracers or transgenic lines can label them. Similar labeling strategies are infeasible in the human neocortex, rendering the translational relevance of findings in rodents unclear. We leveraged the recent discovery of a transcriptomically defined L5 ET neuron type to study the properties of human L5 ET neurons in neocortical brain slices derived from neurosurgeries. Patch-seq recordings, where transcriptome, physiology, and morphology were assayed from the same cell, revealed many conserved morpho-electric properties of human and rodent L5 ET neurons. Divergent properties were often subtler than differences between L5 cell types within these two species. These data suggest a conserved function of L5 ET neurons in the neocortical hierarchy but also highlight phenotypic divergence possibly related to functional specialization of human neocortex.
View details for DOI 10.1016/j.neuron.2021.08.030
View details for PubMedID 34534454
View details for PubMedCentralID PMC8570452
Thermal constraints on in vivo optogenetic manipulations.
2019; 22 (7): 1061-1065
A key assumption of optogenetics is that light only affects opsin-expressing neurons. However, illumination invariably heats tissue, and many physiological processes are temperature-sensitive. Commonly used illumination protocols increased the temperature by 0.2-2 °C and suppressed spiking in multiple brain regions. In the striatum, light delivery activated an inwardly rectifying potassium conductance and biased rotational behavior. Thus, careful consideration of light-delivery parameters is required, as even modest intracranial heating can confound interpretation of optogenetic experiments.
View details for DOI 10.1038/s41593-019-0422-3
View details for PubMedID 31209378
View details for PubMedCentralID PMC6592769
An open-source control system for in vivo fluorescence measurements from deep-brain structures.
Journal of neuroscience methods
2019; 311: 170-177
Intracranial photometry through chronically implanted optical fibers is a widely adopted technique for measuring signals from fluorescent probes in deep-brain structures. The recent proliferation of bright, photo-stable, and specific genetically encoded fluorescent reporters for calcium and for other neuromodulators has greatly increased the utility and popularity of this technique.Here we describe an open-source, cost-effective, microcontroller-based solution for controlling optical components in an intracranial photometry system and processing the resulting signal.We show proof-of-principle that this system supports high quality intracranial photometry recordings from dorsal striatum in freely moving mice. A single system supports simultaneous fluorescence measurements in two independent color channels, but multiple systems can be integrated together if additional fluorescence channels are required. This system is designed to work in combination with either commercially available or custom-built optical components. Parts can be purchased for less than one tenth the cost of commercially available alternatives and complete assembly takes less than one day for an inexperienced user.Currently available hardware draws on a variety of commercial, custom-built, or hybrid elements for both optical and electronic components. Many of these hardware systems are either specialized and inflexible, or over-engineered and expensive.This open-source system increases experimental flexibility while reducing cost relative to current commercially available components. All software and firmware are open-source and customizable, affording a degree of experimental flexibility that is not available in current commercial systems.
View details for DOI 10.1016/j.jneumeth.2018.10.022
View details for PubMedID 30342106
View details for PubMedCentralID PMC6258340
Targeted genomic CRISPR-Cas9 screen identifies MAP4K4 as essential for glioblastoma invasion.
2019; 9 (1): 14020
Among high-grade brain tumors, glioblastoma is particularly difficult to treat, in part due to its highly infiltrative nature which contributes to the malignant phenotype and high mortality in patients. In order to better understand the signaling pathways underlying glioblastoma invasion, we performed the first large-scale CRISPR-Cas9 loss of function screen specifically designed to identify genes that facilitate cell invasion. We tested 4,574 genes predicted to be involved in trafficking and motility. Using a transwell invasion assay, we discovered 33 genes essential for invasion. Of the 11 genes we selected for secondary testing using a wound healing assay, 6 demonstrated a significant decrease in migration. The strongest regulator of invasion was mitogen-activated protein kinase 4 (MAP4K4). Targeting of MAP4K4 with single guide RNAs or a MAP4K4 inhibitor reduced migration and invasion in vitro. This effect was consistent across three additional patient derived glioblastoma cell lines. Analysis of epithelial-mesenchymal transition markers in U138 cells with lack or inhibition of MAP4K4 demonstrated protein expression consistent with a non-invasive state. Importantly, MAP4K4 inhibition limited migration in a subset of human glioma organotypic slice cultures. Our results identify MAP4K4 as a novel potential therapeutic target to limit glioblastoma invasion.
View details for DOI 10.1038/s41598-019-50160-w
View details for PubMedID 31570734
A Genetically Encoded Fluorescent Sensor Enables Rapid and Specific Detection of Dopamine in Flies, Fish, and Mice.
2018; 174 (2): 481-496.e19
Dopamine (DA) is a central monoamine neurotransmitter involved in many physiological and pathological processes. A longstanding yet largely unmet goal is to measure DA changes reliably and specifically with high spatiotemporal precision, particularly in animals executing complex behaviors. Here, we report the development of genetically encoded GPCR-activation-based-DA (GRABDA) sensors that enable these measurements. In response to extracellular DA, GRABDA sensors exhibit large fluorescence increases (ΔF/F0 ∼90%) with subcellular resolution, subsecond kinetics, nanomolar to submicromolar affinities, and excellent molecular specificity. GRABDA sensors can resolve a single-electrical-stimulus-evoked DA release in mouse brain slices and detect endogenous DA release in living flies, fish, and mice. In freely behaving mice, GRABDA sensors readily report optogenetically elicited nigrostriatal DA release and depict dynamic mesoaccumbens DA signaling during Pavlovian conditioning or during sexual behaviors. Thus, GRABDA sensors enable spatiotemporally precise measurements of DA dynamics in a variety of model organisms while exhibiting complex behaviors.
View details for DOI 10.1016/j.cell.2018.06.042
View details for PubMedID 30007419
View details for PubMedCentralID PMC6092020
Fast-Spiking Interneurons Supply Feedforward Control of Bursting, Calcium, and Plasticity for Efficient Learning.
2018; 172 (4): 683-695.e15
Fast-spiking interneurons (FSIs) are a prominent class of forebrain GABAergic cells implicated in two seemingly independent network functions: gain control and network plasticity. Little is known, however, about how these roles interact. Here, we use a combination of cell-type-specific ablation, optogenetics, electrophysiology, imaging, and behavior to describe a unified mechanism by which striatal FSIs control burst firing, calcium influx, and synaptic plasticity in neighboring medium spiny projection neurons (MSNs). In vivo silencing of FSIs increased bursting, calcium transients, and AMPA/NMDA ratios in MSNs. In a motor sequence task, FSI silencing increased the frequency of calcium transients but reduced the specificity with which transients aligned to individual task events. Consistent with this, ablation of FSIs disrupted the acquisition of striatum-dependent egocentric learning strategies. Together, our data support a model in which feedforward inhibition from FSIs temporally restricts MSN bursting and calcium-dependent synaptic plasticity to facilitate striatum-dependent sequence learning.
View details for DOI 10.1016/j.cell.2018.01.005
View details for PubMedID 29425490
View details for PubMedCentralID PMC5810594
Oxytocin enhances hippocampal spike transmission by modulating fast-spiking interneurons
2013; 500 (7463): 458-?
Neuromodulatory control by oxytocin is essential to a wide range of social, parental and stress-related behaviours. Autism spectrum disorders (ASD) are associated with deficiencies in oxytocin levels and with genetic alterations of the oxytocin receptor (OXTR). Thirty years ago, Mühlethaler et al. found that oxytocin increases the firing of inhibitory hippocampal neurons, but it remains unclear how elevated inhibition could account for the ability of oxytocin to improve information processing in the brain. Here we describe in mammalian hippocampus a simple yet powerful mechanism by which oxytocin enhances cortical information transfer while simultaneously lowering background activity, thus greatly improving the signal-to-noise ratio. Increased fast-spiking interneuron activity not only suppresses spontaneous pyramidal cell firing, but also enhances the fidelity of spike transmission and sharpens spike timing. Use-dependent depression at the fast-spiking interneuron-pyramidal cell synapse is both necessary and sufficient for the enhanced spike throughput. We show the generality of this novel circuit mechanism by activation of fast-spiking interneurons with cholecystokinin or channelrhodopsin-2. This provides insight into how a diffusely delivered neuromodulator can improve the performance of neural circuitry that requires synapse specificity and millisecond precision.
View details for DOI 10.1038/nature12330
View details for Web of Science ID 000323316100035
View details for PubMedID 23913275
Ca(v)1 and Ca(v)2 Channels Engage Distinct Modes of Ca2+ Signaling to Control CREB-Dependent Gene Expression
2012; 149 (5): 1112-1124
Activity-dependent gene expression triggered by Ca(2+) entry into neurons is critical for learning and memory, but whether specific sources of Ca(2+) act distinctly or merely supply Ca(2+) to a common pool remains uncertain. Here, we report that both signaling modes coexist and pertain to Ca(V)1 and Ca(V)2 channels, respectively, coupling membrane depolarization to CREB phosphorylation and gene expression. Ca(V)1 channels are advantaged in their voltage-dependent gating and use nanodomain Ca(2+) to drive local CaMKII aggregation and trigger communication with the nucleus. In contrast, Ca(V)2 channels must elevate [Ca(2+)](i) microns away and promote CaMKII aggregation at Ca(V)1 channels. Consequently, Ca(V)2 channels are ~10-fold less effective in signaling to the nucleus than are Ca(V)1 channels for the same bulk [Ca(2+)](i) increase. Furthermore, Ca(V)2-mediated Ca(2+) rises are preferentially curbed by uptake into the endoplasmic reticulum and mitochondria. This source-biased buffering limits the spatial spread of Ca(2+), further attenuating Ca(V)2-mediated gene expression.
View details for DOI 10.1016/j.cell.2012.03.041
View details for Web of Science ID 000304453900016
View details for PubMedID 22632974
View details for PubMedCentralID PMC3654514
Mouse model of Timothy syndrome recapitulates triad of autistic traits
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
2011; 108 (37): 15432-15437
Autism and autism spectrum disorder (ASD) typically arise from a mixture of environmental influences and multiple genetic alterations. In some rare cases, such as Timothy syndrome (TS), a specific mutation in a single gene can be sufficient to generate autism or ASD in most patients, potentially offering insights into the etiology of autism in general. Both variants of TS (the milder TS1 and the more severe TS2) arise from missense mutations in alternatively spliced exons that cause the same G406R replacement in the Ca(V)1.2 L-type calcium channel. We generated a TS2-like mouse but found that heterozygous (and homozygous) animals were not viable. However, heterozygous TS2 mice that were allowed to keep an inverted neomycin cassette (TS2-neo) survived through adulthood. We attribute the survival to lowering of expression of the G406R L-type channel via transcriptional interference, blunting deleterious effects of mutant L-type channel overactivity, and addressed potential effects of altered gene dosage by studying Ca(V)1.2 knockout heterozygotes. Here we present a thorough behavioral phenotyping of the TS2-neo mouse, capitalizing on this unique opportunity to use the TS mutation to model ASD in mice. Along with normal general health, activity, and anxiety level, TS2-neo mice showed markedly restricted, repetitive, and perseverative behavior, altered social behavior, altered ultrasonic vocalization, and enhanced tone-cued and contextual memory following fear conditioning. Our results suggest that when TS mutant channels are expressed at levels low enough to avoid fatality, they are sufficient to cause multiple, distinct behavioral abnormalities, in line with the core aspects of ASD.
View details for DOI 10.1073/pnas.1112667108
View details for PubMedID 21878566
Inhibitory Neurons Hear Themselves during Development
2010; 66 (2): 164-166
Miniature synaptic events, resulting from spontaneous presynaptic release of neurotransmitter in the absence of an action potential, are often used to assay neural connectivity and are thought to play a pivotal role in the development and maintenance of neuronal circuits. In this issue of Neuron, Trigo et al. identify a new class of miniature synaptic event, called "preminis," that originate from and are subsequently detected by the presynaptic terminals of GABAergic neurons in the molecular layer of cerebellum. Remarkably, these events easily outnumber conventional minis. Their restriction to a relatively narrow time window (<15 days after birth) is a clue that they may play a critical role in wiring up interneurons within the developing cerebellar circuitry.
View details for DOI 10.1016/j.neuron.2010.04.021
View details for Web of Science ID 000277308200002
View details for PubMedID 20434993
- Excitation-transcription coupling mechanisms engaged by specific calcium channel types ELSEVIER IRELAND LTD. 2010: E20
- Fast line-based experiment timing system for LabVIEW REVIEW OF SCIENTIFIC INSTRUMENTS 2004; 75 (1): 259–65