Honors & Awards


  • The Walter V. and Idun Berry Fellowship, The Walter V. and Idun Berry Postdoctoral Fellowship Program (9/1/2021)

Stanford Advisors


All Publications


  • Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Cell Kishi, K. E., Kim, Y. S., Fukuda, M., Inoue, M., Kusakizako, T., Wang, P. Y., Ramakrishnan, C., Byrne, E. F., Thadhani, E., Paggi, J. M., Matsui, T. E., Yamashita, K., Nagata, T., Konno, M., Quirin, S., Lo, M., Benster, T., Uemura, T., Liu, K., Shibata, M., Nomura, N., Iwata, S., Nureki, O., Dror, R. O., Inoue, K., Deisseroth, K., Kato, H. E. 1800

    Abstract

    ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0A resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.

    View details for DOI 10.1016/j.cell.2022.01.007

    View details for PubMedID 35114111

  • Genetically targeted chemical assembly of functional materials in living cells, tissues, and animals. Science (New York, N.Y.) Liu, J. n., Kim, Y. S., Richardson, C. E., Tom, A. n., Ramakrishnan, C. n., Birey, F. n., Katsumata, T. n., Chen, S. n., Wang, C. n., Wang, X. n., Joubert, L. M., Jiang, Y. n., Wang, H. n., Fenno, L. E., Tok, J. B., Pașca, S. P., Shen, K. n., Bao, Z. n., Deisseroth, K. n. 2020; 367 (6484): 1372–76

    Abstract

    The structural and functional complexity of multicellular biological systems, such as the brain, are beyond the reach of human design or assembly capabilities. Cells in living organisms may be recruited to construct synthetic materials or structures if treated as anatomically defined compartments for specific chemistry, harnessing biology for the assembly of complex functional structures. By integrating engineered-enzyme targeting and polymer chemistry, we genetically instructed specific living neurons to guide chemical synthesis of electrically functional (conductive or insulating) polymers at the plasma membrane. Electrophysiological and behavioral analyses confirmed that rationally designed, genetically targeted assembly of functional polymers not only preserved neuronal viability but also achieved remodeling of membrane properties and modulated cell type-specific behaviors in freely moving animals. This approach may enable the creation of diverse, complex, and functional structures and materials within living systems.

    View details for DOI 10.1126/science.aay4866

    View details for PubMedID 32193327

  • Comprehensive Dual- and Triple-Feature Intersectional Single-Vector Delivery of Diverse Functional Payloads to Cells of Behaving Mammals. Neuron Fenno, L. E., Ramakrishnan, C. n., Kim, Y. S., Evans, K. E., Lo, M. n., Vesuna, S. n., Inoue, M. n., Cheung, K. Y., Yuen, E. n., Pichamoorthy, N. n., Hong, A. S., Deisseroth, K. n. 2020

    Abstract

    The resolution and dimensionality with which biologists can characterize cell types have expanded dramatically in recent years, and intersectional consideration of such features (e.g., multiple gene expression and anatomical parameters) is increasingly understood to be essential. At the same time, genetically targeted technology for writing in and reading out activity patterns for cells in living organisms has enabled causal investigation in physiology and behavior; however, cell-type-specific delivery of these tools (including microbial opsins for optogenetics and genetically encoded Ca2+ indicators) has thus far fallen short of versatile targeting to cells jointly defined by many individually selected features. Here, we develop a comprehensive intersectional targeting toolbox including 39 novel vectors for joint-feature-targeted delivery of 13 molecular payloads (including opsins, indicators, and fluorophores), systematic approaches for development and optimization of new intersectional tools, hardware for in vivo monitoring of expression dynamics, and the first versatile single-virus tools (Triplesect) that enable targeting of triply defined cell types.

    View details for DOI 10.1016/j.neuron.2020.06.003

    View details for PubMedID 32574559

  • Cortical layer-specific critical dynamics triggering perception. Science (New York, N.Y.) Marshel, J. H., Kim, Y. S., Machado, T. A., Quirin, S. n., Benson, B. n., Kadmon, J. n., Raja, C. n., Chibukhchyan, A. n., Ramakrishnan, C. n., Inoue, M. n., Shane, J. C., McKnight, D. J., Yoshizawa, S. n., Kato, H. E., Ganguli, S. n., Deisseroth, K. n. 2019

    Abstract

    Perceptual experiences may arise from neuronal activity patterns in mammalian neocortex. We probed mouse neocortex during visual discrimination using a red-shifted channelrhodopsin (ChRmine, discovered through structure-guided genome mining) alongside multiplexed multiphoton-holography (MultiSLM), achieving control of individually-specified neurons spanning large cortical volumes with millisecond precision. Stimulating a critical number of stimulus-orientation-selective neurons drove widespread recruitment of functionally-related neurons, a process enhanced by (but not requiring) orientation-discrimination task learning. Optogenetic targeting of orientation-selective ensembles elicited correct behavioral discrimination. Cortical layer specific-dynamics were apparent, as emergent neuronal activity asymmetrically propagated from layer-2/3 to layer-5, and smaller layer-5 ensembles were as effective as larger layer-2/3 ensembles in eliciting orientation discrimination behavior. Population dynamics emerging after optogenetic stimulation both correctly predicted behavior and resembled natural neural representations of visual stimuli.

    View details for DOI 10.1126/science.aaw5202

    View details for PubMedID 31320556

  • Structural mechanisms of selectivity and gating in anion channelrhodopsins NATURE Kato, H. E., Kim, Y., Paggi, J. M., Evans, K. E., Allen, W. E., Richardson, C., Inoue, K., Ito, S., Ramakrishnan, C., Fenno, L. E., Yamashita, K., Hilger, D., Lee, S., Berndt, A., Shen, K., Kandori, H., Dror, R. O., Kobilka, B. K., Deisseroth, K. 2018; 561 (7723): 349-+
  • Crystal structure of the natural anion-conducting channelrhodopsin GtACR1 NATURE Kim, Y., Kato, H. E., Yamashita, K., Ito, S., Inoue, K., Ramakrishnan, C., Fenno, L. E., Evans, K. E., Paggi, J. M., Dror, R. O., Kandori, H., Kobilka, B. K., Deisseroth, K. 2018; 561 (7723): 343-+
  • Sox6 expression distinguishes dorsally and ventrally biased dopamine neurons in the substantia nigra with distinctive properties and embryonic origins. Cell reports Pereira Luppi, M., Azcorra, M., Caronia-Brown, G., Poulin, J., Gaertner, Z., Gatica, S., Moreno-Ramos, O. A., Nouri, N., Dubois, M., Ma, Y. C., Ramakrishnan, C., Fenno, L., Kim, Y. S., Deisseroth, K., Cicchetti, F., Dombeck, D. A., Awatramani, R. 2021; 37 (6): 109975

    Abstract

    Dopamine (DA) neurons in the ventral tier of the substantia nigra pars compacta (SNc) degenerate prominently in Parkinson's disease, while those in the dorsal tier are relatively spared. Defining the molecular, functional, and developmental characteristics of each SNc tier is crucial to understand their distinct susceptibility. We demonstrate that Sox6 expression distinguishes ventrally and dorsally biased DA neuron populations in the SNc. The Sox6+ population in the ventral SNc includes an Aldh1a1+ subset and is enriched in gene pathways that underpin vulnerability. Sox6+ neurons project to the dorsal striatum and show activity correlated with acceleration. Sox6- neurons project to the medial, ventral, and caudal striatum and respond to rewards. Moreover, we show that this adult division is encoded early in development. Overall, our work demonstrates a dual origin of the SNc that results in DA neuron cohorts with distinct molecular profiles, projections, and functions.

    View details for DOI 10.1016/j.celrep.2021.109975

    View details for PubMedID 34758317

  • IDENTIFICATION OF A NEUROLIGIN-3 BINDING PARTNER IN HIGH-GRADE GLIOMAS AND NORMAL PROGENITORS Gillespie, S., Kim, Y., Geraghty, A., Quezada, M., Reed, J., Woo, P., Monje, M. OXFORD UNIV PRESS INC. 2021: 204
  • Transcriptional and functional divergence in lateral hypothalamic glutamate neurons projecting to the lateral habenula and ventral tegmental area. Neuron Rossi, M. A., Basiri, M. L., Liu, Y., Hashikawa, Y., Hashikawa, K., Fenno, L. E., Kim, Y. S., Ramakrishnan, C., Deisseroth, K., Stuber, G. D. 2021

    Abstract

    The lateral hypothalamic area (LHA) regulates feeding- and reward-related behavior, but because of its molecular and anatomical heterogeneity, the functions of defined neuronal populations are largely unclear. Glutamatergic neurons within the LHA (LHAVglut2) negatively regulate feeding and appetitive behavior. However, this population comprises transcriptionally distinct and functionally diverse neurons that project to diverse brain regions, including the lateral habenula (LHb) and ventral tegmental area (VTA). To resolve the function of distinct LHAVglut2 populations, we systematically compared projections to the LHb and VTA using viral tracing, single-cell sequencing, electrophysiology, and in vivo calcium imaging. LHAVglut2 neurons projecting to the LHb or VTA are anatomically, transcriptionally, electrophysiologically, and functionally distinct. While both populations encode appetitive and aversive stimuli, LHb projecting neurons are especially sensitive to satiety state and feeding hormones. These data illuminate the functional heterogeneity of LHAVglut2 neurons, suggesting that reward and aversion are differentially processed in divergent efferent pathways.

    View details for DOI 10.1016/j.neuron.2021.09.020

    View details for PubMedID 34624220

  • Distinct Signaling by Ventral Tegmental Area Glutamate, GABA, and Combinatorial Glutamate-GABA Neurons in Motivated Behavior. Cell reports Root, D. H., Barker, D. J., Estrin, D. J., Miranda-Barrientos, J. A., Liu, B., Zhang, S., Wang, H., Vautier, F., Ramakrishnan, C., Kim, Y. S., Fenno, L., Deisseroth, K., Morales, M. 2020; 32 (9): 108094

    Abstract

    Ventral tegmental area (VTA) neurons play roles in reward and aversion. We recently discovered that the VTA has neurons that co-transmit glutamate and GABA (glutamate-GABA co-transmitting neurons), transmit glutamate without GABA (glutamate-transmitting neurons), or transmit GABA without glutamate (GABA-transmitting neurons). However, the functions of these VTA cell types in motivated behavior are unclear. To identify the functions of these VTA cell types, we combine recombinase mouse lines with INTRSECT2.0 vectors to selectively target these neurons. We find that VTA cell types have unique signaling patterns for reward, aversion, and learned cues. Whereas VTA glutamate-transmitting neurons signal cues predicting reward, VTA GABA-transmitting neurons signal cues predicting the absence of reward, and glutamate-GABA co-transmitting neurons signal rewarding and aversive outcomes without signaling learned cues related to those outcomes. Thus, we demonstrate that genetically defined subclasses of VTA glutamate and GABA neurons signal different aspects of motivated behavior.

    View details for DOI 10.1016/j.celrep.2020.108094

    View details for PubMedID 32877676

  • Deep brain optogenetics without intracranial surgery. Nature biotechnology Chen, R. n., Gore, F. n., Nguyen, Q. A., Ramakrishnan, C. n., Patel, S. n., Kim, S. H., Raffiee, M. n., Kim, Y. S., Hsueh, B. n., Krook-Magnusson, E. n., Soltesz, I. n., Deisseroth, K. n. 2020

    Abstract

    Achieving temporally precise, noninvasive control over specific neural cell types in the deep brain would advance the study of nervous system function. Here we use the potent channelrhodopsin ChRmine to achieve transcranial photoactivation of defined neural circuits, including midbrain and brainstem structures, at unprecedented depths of up to 7 mm with millisecond precision. Using systemic viral delivery of ChRmine, we demonstrate behavioral modulation without surgery, enabling implant-free deep brain optogenetics.

    View details for DOI 10.1038/s41587-020-0679-9

    View details for PubMedID 33020604

  • Excitation of diverse classes of cholecystokinin interneurons in the basolateral amygdala facilitates fear extinction. eNeuro Rovira-Esteban, L., Gunduz-Cinar, O., Bukalo, O., Limoges, A., Brockway, E., Muller, K., Fenno, L., Kim, Y. S., Ramakrishnan, C., Andrasi, T., Deisseroth, K., Holmes, A., Hajos, N. 2019

    Abstract

    There is growing evidence that interneurons orchestrate neural activity and plasticity in corticoamygdala circuits to regulate fear behaviors. However, defining the precise role of cholecystokinin-expressing interneurons (CCK INs) remains elusive due to the technical challenge of parsing this population from CCK-expressing principal neurons (CCK PNs). Here we used an intersectional genetic strategy in CCK-Cre;Dlx5/6-Flpe double-transgenic mice to study the anatomical, molecular and electrophysiological properties of CCK INs in the basal amygdala (BA) and optogenetically manipulate these cells in fear extinction. Electrophysiological recordings confirmed that this strategy targeted GABAergic cells and that a significant proportion expressed functional cannabinoid CB1 receptors; a defining characteristic of CCK-expressing basket cells. However, immunostaining showed that subsets of the genetically-targeted cells expressed either neuropeptide Y (NPY) (29%) or parvalbumin (PV) (17%), but not somatostatin (SOM) or CaMKII-alpha. Further morphological and electrophysiological analyses showed that four interneuron types could be identified among the EYFP-expressing cells: CCK/CB1R-expressing basket cells, neurogliaform cells, PV+ basket and PV+ axo-axonic cells. At the behavioral level, in vivo optogenetic photostimulation of the targeted population during extinction acquisition led to reduced freezing on a light-free extinction retrieval test, indicating extinction memory facilitation; whereas photosilencing was without effect. Conversely, non-selective (i.e., inclusive of INs and PNs) photostimulation or photosilencing of CCK-targeted cells, using CCK-Cre single-transgenic mice, impaired extinction. These data reveal an unexpectedly high degree of phenotypic complexity in a unique population of extinction-modulating BA INs.Significance statement Distinct types of interneurons in the basolateral amygdala (BA) are known to control principal cell activity, allowing complex behaviors. Despite their importance, the role of cholecystokinin (CCK)-expressing inhibitory cells remains unknown. In this work, we could specifically alter the function of CCK-expressing interneurons in the BA by using an INTRSECT viral strategy. Using a combination of anatomical and electrophysiological methods, we found that CCK+ interneurons in the BA are comprised of CB1R-expressing basket cells, neurogliaform cells, parvalbumin-expressing basket as well as axo-axonic cells. Importantly, we provided the first direct evidence that CCK-expressing interneurons in the BA can modulate fear extinction learning. Our data thus show that CCK is expressed in functionally diverse interneuron populations, positioned to impact amygdala operation.

    View details for DOI 10.1523/ENEURO.0220-19.2019

    View details for PubMedID 31636080

  • Mapping Brain-Wide Afferent Inputs of Parvalbumin-Expressing GABAergic Neurons in Barrel Cortex Reveals Local and Long-Range Circuit Motifs. Cell reports Hafner, G., Witte, M., Guy, J., Subhashini, N., Fenno, L. E., Ramakrishnan, C., Kim, Y. S., Deisseroth, K., Callaway, E. M., Oberhuber, M., Conzelmann, K., Staiger, J. F. 2019; 28 (13): 3450

    Abstract

    Parvalbumin (PV)-expressing GABAergic neurons are the largest class of inhibitory neocortical cells. We visualize brain-wide, monosynaptic inputs to PV neurons in mouse barrel cortex. We develop intersectional rabies virus tracing to specifically target GABAergic PV cells and exclude a small fraction of excitatory PV cells from our starter population. Local inputs are mainly from layer (L) IV and excitatory cells. A small number of inhibitory inputs originate from LI neurons, which connect to LII/III PV neurons. Long-range inputs originate mainly from other sensory cortices and the thalamus. In visual cortex, most transsynaptically labeled neurons are located in LIV, which contains a molecularly mixed population of projection neurons with putative functional similarity to LIII neurons. This study expands our knowledge of the brain-wide circuits in which PV neurons are embedded and introduces intersectional rabies virus tracing as an applicable tool to dissect the circuitry of more clearly defined cell types.

    View details for DOI 10.1016/j.celrep.2019.08.064

    View details for PubMedID 31553913