Professional Education

  • Bachelor of Science, University of Wisconsin Madison (2007)
  • Doctor of Philosophy, Harvard University (2012)

Stanford Advisors


All Publications

  • Viral-genetic tracing of the input-output organization of a central noradrenaline circuit. Nature Schwarz, L. A., Miyamichi, K., Gao, X. J., Beier, K. T., Weissbourd, B., DeLoach, K. E., Ren, J., Ibanes, S., Malenka, R. C., Kremer, E. J., Luo, L. 2015; 524 (7563): 88-92


    Deciphering how neural circuits are anatomically organized with regard to input and output is instrumental in understanding how the brain processes information. For example, locus coeruleus noradrenaline (also known as norepinephrine) (LC-NE) neurons receive input from and send output to broad regions of the brain and spinal cord, and regulate diverse functions including arousal, attention, mood and sensory gating. However, it is unclear how LC-NE neurons divide up their brain-wide projection patterns and whether different LC-NE neurons receive differential input. Here we developed a set of viral-genetic tools to quantitatively analyse the input-output relationship of neural circuits, and applied these tools to dissect the LC-NE circuit in mice. Rabies-virus-based input mapping indicated that LC-NE neurons receive convergent synaptic input from many regions previously identified as sending axons to the locus coeruleus, as well as from newly identified presynaptic partners, including cerebellar Purkinje cells. The 'tracing the relationship between input and output' method (or TRIO method) enables trans-synaptic input tracing from specific subsets of neurons based on their projection and cell type. We found that LC-NE neurons projecting to diverse output regions receive mostly similar input. Projection-based viral labelling revealed that LC-NE neurons projecting to one output region also project to all brain regions we examined. Thus, the LC-NE circuit overall integrates information from, and broadcasts to, many brain regions, consistent with its primary role in regulating brain states. At the same time, we uncovered several levels of specificity in certain LC-NE sub-circuits. These tools for mapping output architecture and input-output relationship are applicable to other neuronal circuits and organisms. More broadly, our viral-genetic approaches provide an efficient intersectional means to target neuronal populations based on cell type and projection pattern.

    View details for DOI 10.1038/nature14600

    View details for PubMedID 26131933

  • Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms JOURNAL OF COMPARATIVE NEUROLOGY Mundell, N. A., Beier, K. T., Pan, Y. A., Lapan, S. W., Aytuerk, D. G., Berezovskii, V. K., Wark, A. R., Drokhlyansky, E., Bielecki, J., Born, R. T., Schier, A. F., Cepko, C. L. 2015; 523 (11): 1639-1663


    Current limitations in technology have prevented an extensive analysis of the connections among neurons, particularly within nonmammalian organisms. We developed a transsynaptic viral tracer originally for use in mice, and then tested its utility in a broader range of organisms. By engineering the vesicular stomatitis virus (VSV) to encode a fluorophore and either the rabies virus glycoprotein (RABV-G) or its own glycoprotein (VSV-G), we created viruses that can transsynaptically label neuronal circuits in either the retrograde or anterograde direction, respectively. The vectors were investigated for their utility as polysynaptic tracers of chicken and zebrafish visual pathways. They showed patterns of connectivity consistent with previously characterized visual system connections, and revealed several potentially novel connections. Further, these vectors were shown to infect neurons in several other vertebrates, including Old and New World monkeys, seahorses, axolotls, and Xenopus. They were also shown to infect two invertebrates, Drosophila melanogaster, and the box jellyfish, Tripedalia cystophora, a species previously intractable for gene transfer, although no clear evidence of transsynaptic spread was observed in these species. These vectors provide a starting point for transsynaptic tracing in most vertebrates, and are also excellent candidates for gene transfer in organisms that have been refractory to other methods.

    View details for DOI 10.1002/cne.23761

    View details for Web of Science ID 000355836700004

    View details for PubMedID 25688551

  • Circuit Architecture of VTA Dopamine Neurons Revealed by Systematic Input-Output Mapping CELL Beier, K. T., Steinberg, E. E., DeLoach, K. E., Xie, S., Miyamichi, K., Schwarz, L., Gao, X. J., Kremer, E. J., Malenka, R. C., Luo, L. 2015; 162 (3): 622-634
  • Intact-Brain Analyses Reveal Distinct Information Carried by SNc Dopamine Subcircuits CELL Lerner, T. N., Shilyansky, C., Davidson, T. J., Evans, K. E., Beier, K. T., Zalocusky, K. A., Crow, A. K., Malenka, R. C., Luo, L., Tomer, R., Deisseroth, K. 2015; 162 (3): 635-647
  • Diversity of Transgenic Mouse Models for Selective Targeting of Midbrain Dopamine Neurons NEURON Lammel, S., Steinberg, E. E., Foeldy, C., Wall, N. R., Beier, K., Luo, L., Malenka, R. C. 2015; 85 (2): 429-438


    Ventral tegmental area (VTA) dopamine (DA) neurons have been implicated in reward, aversion, salience, cognition, and several neuropsychiatric disorders. Optogenetic approaches involving transgenic Cre-driver mouse lines provide powerful tools for dissecting DA-specific functions. However, the emerging complexity of VTA circuits requires Cre-driver mouse lines that restrict transgene expression to a precisely defined cell population. Because of recent work reporting that VTA DA neurons projecting to the lateral habenula release GABA, but not DA, we performed an extensive anatomical, molecular, and functional characterization of prominent DA transgenic mouse driver lines. We find that transgenes under control of the tyrosine hydroxylase, but not the dopamine transporter, promoter exhibit dramatic non-DA cell-specific expression patterns within and around VTA nuclei. Our results demonstrate how Cre expression in unintentionally targeted cells in transgenic mouse lines can confound the interpretation of supposedly cell-type-specific experiments. This Matters Arising paper is in response to Stamatakis et al. (2013), published in Neuron. See also the Matters Arising Response paper by Stuber et al. (2015), published concurrently with this Matters Arising in Neuron.

    View details for DOI 10.1016/j.neuron.2014.12.036

    View details for Web of Science ID 000348296000019

  • Neuroanatomy goes viral! Frontiers in neuroanatomy Nassi, J. J., Cepko, C. L., Born, R. T., Beier, K. T. 2015; 9: 80-?


    The nervous system is complex not simply because of the enormous number of neurons it contains but by virtue of the specificity with which they are connected. Unraveling this specificity is the task of neuroanatomy. In this endeavor, neuroanatomists have traditionally exploited an impressive array of tools ranging from the Golgi method to electron microscopy. An ideal method for studying anatomy would label neurons that are interconnected, and, in addition, allow expression of foreign genes in these neurons. Fortuitously, nature has already partially developed such a method in the form of neurotropic viruses, which have evolved to deliver their genetic material between synaptically connected neurons while largely eluding glia and the immune system. While these characteristics make some of these viruses a threat to human health, simple modifications allow them to be used in controlled experimental settings, thus enabling neuroanatomists to trace multi-synaptic connections within and across brain regions. Wild-type neurotropic viruses, such as rabies and alpha-herpes virus, have already contributed greatly to our understanding of brain connectivity, and modern molecular techniques have enabled the construction of recombinant forms of these and other viruses. These newly engineered reagents are particularly useful, as they can target genetically defined populations of neurons, spread only one synapse to either inputs or outputs, and carry instructions by which the targeted neurons can be made to express exogenous proteins, such as calcium sensors or light-sensitive ion channels, that can be used to study neuronal function. In this review, we address these uniquely powerful features of the viruses already in the neuroanatomist's toolbox, as well as the aspects of their biology that currently limit their utility. Based on the latter, we consider strategies for improving viral tracing methods by reducing toxicity, improving control of transsynaptic spread, and extending the range of species that can be studied.

    View details for DOI 10.3389/fnana.2015.00080

    View details for PubMedID 26190977

  • Lineage Analysis of the Late Otocyst Stage Mouse Inner Ear by Transuterine Microinjection of A Retroviral Vector Encoding Alkaline Phosphatase and an Oligonucleotide Library PLOS ONE Jiang, H., Wang, L., Beier, K. T., Cepko, C. L., Fekete, D. M., Brigande, J. V. 2013; 8 (7)


    The mammalian inner ear subserves the special senses of hearing and balance. The auditory and vestibular sensory epithelia consist of mechanically sensitive hair cells and associated supporting cells. Hearing loss and balance dysfunction are most frequently caused by compromise of hair cells and/or their innervating neurons. The development of gene- and cell-based therapeutics will benefit from a thorough understanding of the molecular basis of patterning and cell fate specification in the mammalian inner ear. This includes analyses of cell lineages and cell dispersals across anatomical boundaries (such as sensory versus nonsensory territories). The goal of this study was to conduct retroviral lineage analysis of the embryonic day 11.5(E11.5) mouse otic vesicle. A replication-defective retrovirus encoding human placental alkaline phosphatase (PLAP) and a variable 24-bp oligonucleotide tag was microinjected into the E11.5 mouse otocyst. PLAP-positive cells were microdissected from cryostat sections of the postnatal inner ear and subjected to nested PCR. PLAP-positive cells sharing the same sequence tag were assumed to have arisen from a common progenitor and are clonally related. Thirty five multicellular clones consisting of an average of 3.4 cells per clone were identified in the auditory and vestibular sensory epithelia, ganglia, spiral limbus, and stria vascularis. Vestibular hair cells in the posterior crista were related to one another, their supporting cells, and nonsensory epithelial cells lining the ampulla. In the organ of Corti, outer hair cells were related to a supporting cell type and were tightly clustered. By contrast, spiral ganglion neurons, interdental cells, and Claudius' cells were related to cells of the same type and could be dispersed over hundreds of microns. These data contribute new information about the developmental potential of mammalian otic precursors in vivo.

    View details for DOI 10.1371/journal.pone.0069314

    View details for Web of Science ID 000322433300031

    View details for PubMedID 23935981

  • Pseudotyped retroviruses for infecting axolotl in vivo and in vitro DEVELOPMENT Whited, J. L., Tsai, S. L., Beier, K. T., White, J. N., Piekarski, N., Hanken, J., Cepko, C. L., Tabin, C. J. 2013; 140 (5): 1137-1146


    Axolotls are poised to become the premiere model system for studying vertebrate appendage regeneration. However, very few molecular tools exist for studying crucial cell lineage relationships over regeneration or for robust and sustained misexpression of genetic elements to test their function. Furthermore, targeting specific cell types will be necessary to understand how regeneration of the diverse tissues within the limb is accomplished. We report that pseudotyped, replication-incompetent retroviruses can be used in axolotls to permanently express markers or genetic elements for functional study. These viruses, when modified by changing their coat protein, can infect axolotl cells only when they have been experimentally manipulated to express the receptor for that coat protein, thus allowing for the possibility of targeting specific cell types. Using viral vectors, we have found that progenitor populations for many different cell types within the blastema are present at all stages of limb regeneration, although their relative proportions change with time.

    View details for DOI 10.1242/dev.087734

    View details for Web of Science ID 000314879800021

    View details for PubMedID 23344705

  • Vesicular stomatitis virus with the rabies virus glycoprotein directs retrograde transsynaptic transport among neurons in vivo FRONTIERS IN NEURAL CIRCUITS Beier, K. T., Saunders, A. B., Oldenburg, I. A., Sabatini, B. L., Cepko, C. L. 2013; 7


    Defining the connections among neurons is critical to our understanding of the structure and function of the nervous system. Recombinant viruses engineered to transmit across synapses provide a powerful approach for the dissection of neuronal circuitry in vivo. We recently demonstrated that recombinant vesicular stomatitis virus (VSV) can be endowed with anterograde or retrograde transsynaptic tracing ability by providing the virus with different glycoproteins. Here we extend the characterization of the transmission and gene expression of recombinant VSV (rVSV) with the rabies virus glycoprotein (RABV-G), and provide examples of its activity relative to the anterograde transsynaptic tracer form of rVSV. rVSV with RABV-G was found to drive strong expression of transgenes and to spread rapidly from neuron to neuron in only a retrograde manner. Depending upon how the RABV-G was delivered, VSV served as a polysynaptic or monosynaptic tracer, or was able to define projections through axonal uptake and retrograde transport. In animals co-infected with rVSV in its anterograde form, rVSV with RABV-G could be used to begin to characterize the similarities and differences in connections to different areas. rVSV with RABV-G provides a flexible, rapid, and versatile tracing tool that complements the previously described VSV-based anterograde transsynaptic tracer.

    View details for DOI 10.3389/fncir.2013.00011

    View details for Web of Science ID 000314834200001

    View details for PubMedID 23403489

  • Transsynaptic Tracing with Vesicular Stomatitis Virus Reveals Novel Retinal Circuitry JOURNAL OF NEUROSCIENCE Beier, K. T., Borghuis, B. G., El-Danaf, R. N., Huberman, A. D., Demb, J. B., Cepko, C. L. 2013; 33 (1): 35-51


    The use of neurotropic viruses as transsynaptic tracers was first described in the 1960s, but only recently have such viruses gained popularity as a method for labeling neural circuits. The development of retrograde monosynaptic tracing vectors has enabled visualization of the presynaptic sources onto defined sets of postsynaptic neurons. Here, we describe the first application of a novel viral tracer, based on vesicular stomatitis virus (VSV), which directs retrograde transsynaptic viral spread between defined cell types. We use this virus in the mouse retina to show connectivity between starburst amacrine cells (SACs) and their known synaptic partners, direction-selective retinal ganglion cells, as well as to discover previously unknown connectivity between SACs and other retinal ganglion cell types. These novel connections were confirmed using physiological recordings. VSV transsynaptic tracing enables cell type-specific dissection of neural circuitry and can reveal synaptic relationships among neurons that are otherwise obscured due to the complexity and density of neuropil.

    View details for DOI 10.1523/JNEUROSCI.0245-12.2013

    View details for Web of Science ID 000313046500006

    View details for PubMedID 23283320

  • Viral Tracing of Genetically Defined Neural Circuitry JOVE-JOURNAL OF VISUALIZED EXPERIMENTS Beier, K., Cepko, C. 2012

    View details for DOI 10.3791/4253

    View details for Web of Science ID 000209225700031

  • Transcription factor Olig2 defines subpopulations of retinal progenitor cells biased toward specific cell fates PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hafler, B. P., Surzenko, N., Beier, K. T., Punzo, C., Trimarchi, J. M., Kong, J. H., Cepko, C. L. 2012; 109 (20): 7882-7887


    Previous lineage analyses have shown that retinal progenitor cells (RPCs) are multipotent throughout development, and expression-profiling studies have shown a great deal of molecular heterogeneity among RPCs. To determine if the molecular heterogeneity predicts that an RPC will produce particular types of progeny, clonal lineage analysis was used to investigate the progeny of a subset of RPCs, those that express the basic helix-loop-helix transcription factor, Olig2. The embryonic Olig2(+) RPCs underwent terminal divisions, producing small clones with primarily two of the five cell types being made by the pool of RPCs at that time. The later, postnatal Olig2(+) RPCs also made terminal divisions, which were biased toward production of rod photoreceptors and amacrine cell interneurons. These data indicate that the multipotent progenitor pool is made up of distinctive types of RPCs, which have biases toward producing subsets of retinal neurons in a terminal division, with the types of neurons produced varying over time. This strategy is similar to that of the developing Drosophila melanogaster ventral nerve cord, with the Olig2(+) cells behaving as ganglion mother cells.

    View details for DOI 10.1073/pnas.1203138109

    View details for Web of Science ID 000304369800066

    View details for PubMedID 22543161

  • Anterograde or retrograde transsynaptic labeling of CNS neurons with vesicular stomatitis virus vectors PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Beier, K. T., Saunders, A., Oldenburg, I. A., Miyamichi, K., Akhtar, N., Luo, L., Whelan, S. P., Sabatini, B., Cepko, C. L. 2011; 108 (37): 15414-15419


    To understand how the nervous system processes information, a map of the connections among neurons would be of great benefit. Here we describe the use of vesicular stomatitis virus (VSV) for tracing neuronal connections in vivo. We made VSV vectors that used glycoprotein (G) genes from several other viruses. The G protein from lymphocytic choriomeningitis virus endowed VSV with the ability to spread transsynaptically, specifically in an anterograde direction, whereas the rabies virus glycoprotein gave a specifically retrograde transsynaptic pattern. The use of an avian G protein fusion allowed specific targeting of cells expressing an avian receptor, which allowed a demonstration of monosynaptic anterograde tracing from defined cells. Synaptic connectivity of pairs of virally labeled cells was demonstrated by using slice cultures and electrophysiology. In vivo infections of several areas in the mouse brain led to the predicted patterns of spread for anterograde or retrograde tracers.

    View details for DOI 10.1073/pnas.1110854108

    View details for Web of Science ID 000294804900082

    View details for PubMedID 21825165

  • A Class of Human Proteins that Deliver Functional Proteins into Mammalian Cells In Vitro and In Vivo CHEMISTRY & BIOLOGY Cronican, J. J., Beier, K. T., Davis, T. N., Tseng, J., Li, W., Thompson, D. B., Shih, A. F., May, E. M., Cepko, C. L., Kung, A. L., Zhou, Q., Liu, D. R. 2011; 18 (7): 833-838


    We discovered a class of naturally occurring human proteins with unusually high net positive charge that can potently deliver proteins in functional form into mammalian cells both in vitro and also in murine retina, pancreas, and white adipose tissues in vivo. These findings represent diverse macromolecule delivery agents for in vivo applications, and also raise the possibility that some of these human proteins may penetrate cells as part of their native biological functions.

    View details for DOI 10.1016/j.chembiol.2011.07.003

    View details for Web of Science ID 000294085200006

    View details for PubMedID 21802004

  • Conditional expression of the TVA receptor allows clonal analysis of descendents from Cre-expressing progenitor cells DEVELOPMENTAL BIOLOGY Beier, K. T., Samson, M. E., Matsuda, T., Cepko, C. L. 2011; 353 (2): 309-320


    An understanding of the number and types of progeny produced by progenitor cells during development provides a foundation for studies of when and where cell fate determination takes place. Lineal relationships can be revealed by the identification of descendents of cells that express a recombinase, such as Cre or Flp. This method provides data concerning gene expression history, but does not provide clonal resolution among the descendents. An alternative method employs retroviral labeling, which permits the identification of clones, but does not allow for the tracking of gene expression history. Here we report a combination of these methods to circumvent each method's limitations. By employing the specificity of Cre expression, and by selecting only a subset of cells with a Cre history for retroviral infection, clones with a gene expression history can be labeled. The method utilizes a conditional allele of the avian tumor virus receptor A (TVA), which allows infection of mouse cells following Cre activity, with mammalian retroviral vectors pseudotyped with the ASLV-A envelope glycoprotein (EnvA). We quantified the efficiency and specificity of this system in vivo and in vitro. We also generated a series of retroviral vectors encoding a variety of histochemical and fluorescent reporter genes that enable the tracking of mixtures of clones, thus enabling better resolution of clonal boundaries. This method and new vectors can be used to further our understanding of the gene expression patterns of progenitor cells that make particular daughter cells, as well as provide a platform for manipulating identified subsets of developing cells.

    View details for DOI 10.1016/j.ydbio.2011.03.004

    View details for Web of Science ID 000290192900014

    View details for PubMedID 21397594

  • Elevation of blood urea nitrogen is predictive of long-term mortality in critically ill patients independent of "normal" creatinine CRITICAL CARE MEDICINE Beier, K., Eppanapally, S., Bazick, H. S., Chang, D., Mahadevappa, K., Gibbons, F. K., Christopher, K. B. 2011; 39 (2): 305-313


    We hypothesized that elevated blood urea nitrogen can be associated with all-cause mortality independent of creatinine in a heterogeneous critically ill population.Multicenter observational study of patients treated in medical and surgical intensive care units.Twenty intensive care units in two teaching hospitals in Boston, MA.A total of 26,288 patients, age ≥ 18 yrs, hospitalized between 1997 and 2007 with creatinine of 0.80-1.30 mg/dL.None.Blood urea nitrogen at intensive care unit admission was categorized as 10-20, 20-40, and >40 mg/dL. Logistic regression examined death at days 30, 90, and 365 after intensive care unit admission as well as in-hospital mortality. Adjusted odds ratios were estimated by multivariable logistic regression models.Blood urea nitrogen at intensive care unit admission was predictive for short- and long-term mortality independent of creatinine. Thirty days following intensive care unit admission, patients with blood urea nitrogen of >40 mg/dL had an odds ratio for mortality of 5.12 (95% confidence interval, 4.30-6.09; p < .0001) relative to patients with blood urea nitrogen of 10-20 mg/dL. Blood urea nitrogen remained a significant predictor of mortality at 30 days after intensive care unit admission following multivariable adjustment for confounders; patients with blood urea nitrogen of >40 mg/dL had an odds ratio for mortality of 2.78 (95% confidence interval, 2.27-3.39; p < .0001) relative to patients with blood urea nitrogen of 10-20 mg/dL. Thirty days following intensive care unit admission, patients with blood urea nitrogen of 20-40 mg/dL had an odds ratio of 2.15 (95% confidence interval, 1.98-2.33; <.0001) and a multivariable odds ratio of 1.53 (95% confidence interval, 1.40-1.68; p < .0001) relative to patients with blood urea nitrogen of 10-20 mg/dL. Results were similar at 90 and 365 days following intensive care unit admission as well as for in-hospital mortality. A subanalysis of patients with blood cultures (n = 7,482) demonstrated that blood urea nitrogen at intensive care unit admission was associated with the risk of blood culture positivity.Among critically ill patients with creatinine of 0.8-1.3 mg/dL, an elevated blood urea nitrogen was associated with increased mortality, independent of serum creatinine.

    View details for DOI 10.1097/CCM.0b013e3181ffe22a

    View details for Web of Science ID 000286426400010

    View details for PubMedID 21099426

  • Potent Delivery of Functional Proteins into Mammalian Cells in Vitro and in Vivo Using a Supercharged Protein ACS CHEMICAL BIOLOGY Cronican, J. J., Thompson, D. B., Beier, K. T., McNaughton, B. R., Cepko, C. L., Liu, D. R. 2010; 5 (8): 747-752


    The inability of proteins to potently penetrate mammalian cells limits their usefulness as tools and therapeutics. When fused to superpositively charged GFP, proteins rapidly (within minutes) entered five different types of mammalian cells with potency up to approximately 100-fold greater than that of corresponding fusions with known protein transduction domains (PTDs) including Tat, oligoarginine, and penetratin. Ubiquitin-fused supercharged GFP when incubated with human cells was partially deubiquitinated, suggesting that proteins delivered with supercharged GFP can access the cytosol. Likewise, supercharged GFP delivered functional, nonendosomal recombinase enzyme with greater efficiencies than PTDs in vitro and also delivered functional recombinase enzyme to the retinae of mice when injected in vivo.

    View details for DOI 10.1021/cb1001153

    View details for Web of Science ID 000281029500005

    View details for PubMedID 20545362

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