1
|
Sylwestrak EL, Jo Y, Vesuna S, Wang X, Holcomb B, Tien RH, Kim DK, Fenno L, Ramakrishnan C, Allen WE, Chen R, Shenoy KV, Sussillo D, Deisseroth K. Cell-type-specific population dynamics of diverse reward computations. Cell 2022; 185:3568-3587.e27. [PMID: 36113428 PMCID: PMC10387374 DOI: 10.1016/j.cell.2022.08.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 06/16/2022] [Accepted: 08/17/2022] [Indexed: 01/26/2023]
Abstract
Computational analysis of cellular activity has developed largely independently of modern transcriptomic cell typology, but integrating these approaches may be essential for full insight into cellular-level mechanisms underlying brain function and dysfunction. Applying this approach to the habenula (a structure with diverse, intermingled molecular, anatomical, and computational features), we identified encoding of reward-predictive cues and reward outcomes in distinct genetically defined neural populations, including TH+ cells and Tac1+ cells. Data from genetically targeted recordings were used to train an optimized nonlinear dynamical systems model and revealed activity dynamics consistent with a line attractor. High-density, cell-type-specific electrophysiological recordings and optogenetic perturbation provided supporting evidence for this model. Reverse-engineering predicted how Tac1+ cells might integrate reward history, which was complemented by in vivo experimentation. This integrated approach describes a process by which data-driven computational models of population activity can generate and frame actionable hypotheses for cell-type-specific investigation in biological systems.
Collapse
Affiliation(s)
- Emily L Sylwestrak
- Department of Biology, University of Oregon, Eugene, OR 97403, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA.
| | - YoungJu Jo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Xiao Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Blake Holcomb
- Institute of Neuroscience, University of Oregon, Eugene, OR 97403, USA
| | - Rebecca H Tien
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Doo Kyung Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lief Fenno
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - William E Allen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Neurosciences Interdepartmental Program, Stanford University, Stanford, CA 94303, USA
| | - Ritchie Chen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Krishna V Shenoy
- Department of Neurobiology, Stanford University, Stanford, CA 94303, USA; Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - David Sussillo
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
2
|
Vesuna S, Bharmal M, Cohoon T, Suppogu N, Ranasinghe S, Vu T, Hagopian G, Keleshian V, Kim C, Lee A. PROFOUND VERAPAMIL INTOLERANCE WITH NEAR HEMODYNAMIC COLLAPSE; AN UNUSUAL CASE OF CARDIOGENIC SHOCK IN HYPERTROPHIC CARDIOMYOPATHY. J Am Coll Cardiol 2022. [DOI: 10.1016/s0735-1097(22)03645-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
3
|
Trautmann EM, O'Shea DJ, Sun X, Marshel JH, Crow A, Hsueh B, Vesuna S, Cofer L, Bohner G, Allen W, Kauvar I, Quirin S, MacDougall M, Chen Y, Whitmire MP, Ramakrishnan C, Sahani M, Seidemann E, Ryu SI, Deisseroth K, Shenoy KV. Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface. Nat Commun 2021; 12:3689. [PMID: 34140486 PMCID: PMC8211867 DOI: 10.1038/s41467-021-23884-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 05/19/2021] [Indexed: 02/05/2023] Open
Abstract
Calcium imaging is a powerful tool for recording from large populations of neurons in vivo. Imaging in rhesus macaque motor cortex can enable the discovery of fundamental principles of motor cortical function and can inform the design of next generation brain-computer interfaces (BCIs). Surface two-photon imaging, however, cannot presently access somatic calcium signals of neurons from all layers of macaque motor cortex due to photon scattering. Here, we demonstrate an implant and imaging system capable of chronic, motion-stabilized two-photon imaging of neuronal calcium signals from macaques engaged in a motor task. By imaging apical dendrites, we achieved optical access to large populations of deep and superficial cortical neurons across dorsal premotor (PMd) and gyral primary motor (M1) cortices. Dendritic signals from individual neurons displayed tuning for different directions of arm movement. Combining several technical advances, we developed an optical BCI (oBCI) driven by these dendritic signalswhich successfully decoded movement direction online. By fusing two-photon functional imaging with CLARITY volumetric imaging, we verified that many imaged dendrites which contributed to oBCI decoding originated from layer 5 output neurons, including a putative Betz cell. This approach establishes new opportunities for studying motor control and designing BCIs via two photon imaging.
Collapse
Affiliation(s)
- Eric M Trautmann
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
| | - Daniel J O'Shea
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
| | - Xulu Sun
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - James H Marshel
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Ailey Crow
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Brian Hsueh
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Lucas Cofer
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Gergő Bohner
- Gatsby Computational Neuroscience Unit, University College London, London, UK
| | - Will Allen
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA
| | - Isaac Kauvar
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA
| | - Sean Quirin
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | | | - Yuzhi Chen
- Center for Perceptual Systems, University of Texas, Austin, TX, USA
- Department of Psychology, University of Texas, Austin, TX, USA
- Department of Neuroscience, University of Texas, Austin, TX, USA
| | - Matthew P Whitmire
- Center for Perceptual Systems, University of Texas, Austin, TX, USA
- Department of Psychology, University of Texas, Austin, TX, USA
- Department of Neuroscience, University of Texas, Austin, TX, USA
| | | | - Maneesh Sahani
- Gatsby Computational Neuroscience Unit, University College London, London, UK
| | - Eyal Seidemann
- Center for Perceptual Systems, University of Texas, Austin, TX, USA
- Department of Psychology, University of Texas, Austin, TX, USA
- Department of Neuroscience, University of Texas, Austin, TX, USA
| | - Stephen I Ryu
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Palo Alto Medical Foundation, Palo Alto, CA, USA
| | - Karl Deisseroth
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Department of Psychiatry and Behavioral Science, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, USA.
| | - Krishna V Shenoy
- Neurosciences Graduate Program, Stanford University, Stanford, CA, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA.
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Wu Tsai Neuroscience Institute, Stanford University, Stanford, CA, USA.
- Department of Neurobiology, Stanford University, Stanford, CA, USA.
| |
Collapse
|
4
|
Vesuna S, Kauvar IV, Richman E, Gore F, Oskotsky T, Sava-Segal C, Luo L, Malenka RC, Henderson JM, Nuyujukian P, Parvizi J, Deisseroth K. Deep posteromedial cortical rhythm in dissociation. Nature 2020; 586:87-94. [PMID: 32939091 PMCID: PMC7553818 DOI: 10.1038/s41586-020-2731-9] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 08/20/2020] [Indexed: 12/12/2022]
Abstract
Advanced imaging methods now allow cell-type-specific recording of neural activity across the mammalian brain, potentially enabling the exploration of how brain-wide dynamical patterns give rise to complex behavioural states1-12. Dissociation is an altered behavioural state in which the integrity of experience is disrupted, resulting in reproducible cognitive phenomena including the dissociation of stimulus detection from stimulus-related affective responses. Dissociation can occur as a result of trauma, epilepsy or dissociative drug use13,14, but despite its substantial basic and clinical importance, the underlying neurophysiology of this state is unknown. Here we establish such a dissociation-like state in mice, induced by precisely-dosed administration of ketamine or phencyclidine. Large-scale imaging of neural activity revealed that these dissociative agents elicited a 1-3-Hz rhythm in layer 5 neurons of the retrosplenial cortex. Electrophysiological recording with four simultaneously deployed high-density probes revealed rhythmic coupling of the retrosplenial cortex with anatomically connected components of thalamus circuitry, but uncoupling from most other brain regions was observed-including a notable inverse correlation with frontally projecting thalamic nuclei. In testing for causal significance, we found that rhythmic optogenetic activation of retrosplenial cortex layer 5 neurons recapitulated dissociation-like behavioural effects. Local retrosplenial hyperpolarization-activated cyclic-nucleotide-gated potassium channel 1 (HCN1) pacemakers were required for systemic ketamine to induce this rhythm and to elicit dissociation-like behavioural effects. In a patient with focal epilepsy, simultaneous intracranial stereoencephalography recordings from across the brain revealed a similarly localized rhythm in the homologous deep posteromedial cortex that was temporally correlated with pre-seizure self-reported dissociation, and local brief electrical stimulation of this region elicited dissociative experiences. These results identify the molecular, cellular and physiological properties of a conserved deep posteromedial cortical rhythm that underlies states of dissociation.
Collapse
Affiliation(s)
- Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Isaac V Kauvar
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
| | - Ethan Richman
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Felicity Gore
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Tomiko Oskotsky
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Clara Sava-Segal
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Liqun Luo
- Department of Biology, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Robert C Malenka
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | | | - Paul Nuyujukian
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, USA
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - Josef Parvizi
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
| |
Collapse
|
5
|
Fenno LE, Ramakrishnan C, Kim YS, Evans KE, Lo M, Vesuna S, Inoue M, Cheung KYM, Yuen E, Pichamoorthy N, Hong ASO, Deisseroth K. Comprehensive Dual- and Triple-Feature Intersectional Single-Vector Delivery of Diverse Functional Payloads to Cells of Behaving Mammals. Neuron 2020; 107:836-853.e11. [PMID: 32574559 PMCID: PMC7687746 DOI: 10.1016/j.neuron.2020.06.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/08/2020] [Accepted: 05/29/2020] [Indexed: 01/12/2023]
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.
Collapse
Affiliation(s)
- Lief E Fenno
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Yoon Seok Kim
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathryn E Evans
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Maisie Lo
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Masatoshi Inoue
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathy Y M Cheung
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Elle Yuen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Alice S O Hong
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
6
|
Wang X, Allen WE, Wright MA, Sylwestrak EL, Samusik N, Vesuna S, Evans K, Liu C, Ramakrishnan C, Liu J, Nolan GP, Bava FA, Deisseroth K. Three-dimensional intact-tissue sequencing of single-cell transcriptional states. Science 2018; 361:science.aat5691. [PMID: 29930089 PMCID: PMC6339868 DOI: 10.1126/science.aat5691] [Citation(s) in RCA: 658] [Impact Index Per Article: 109.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/01/2018] [Accepted: 06/13/2018] [Indexed: 12/12/2022]
Abstract
Retrieving high-content gene-expression information while retaining three-dimensional (3D) positional anatomy at cellular resolution has been difficult, limiting integrative understanding of structure and function in complex biological tissues. We developed and applied a technology for 3D intact-tissue RNA sequencing, termed STARmap (spatially-resolved transcript amplicon readout mapping), which integrates hydrogel-tissue chemistry, targeted signal amplification, and in situ sequencing. The capabilities of STARmap were tested by mapping 160 to 1020 genes simultaneously in sections of mouse brain at single-cell resolution with high efficiency, accuracy, and reproducibility. Moving to thick tissue blocks, we observed a molecularly defined gradient distribution of excitatory-neuron subtypes across cubic millimeter-scale volumes (>30,000 cells) and a short-range 3D self-clustering in many inhibitory-neuron subtypes that could be identified and described with 3D STARmap.
Collapse
Affiliation(s)
- Xiao Wang
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - William E Allen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Neuroscience Program, Stanford University, CA 94305, USA
| | - Matthew A Wright
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Psychiatry and Behavioral Sciences, Stanford University, CA 94305, USA
| | - Emily L Sylwestrak
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Nikolay Samusik
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kathryn Evans
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Cindy Liu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jia Liu
- Department of Chemical Engineering, Stanford University, CA 94305, USA
| | - Garry P Nolan
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
| | - Felice-Alessio Bava
- Baxter Laboratory, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA.
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA. .,Department of Psychiatry and Behavioral Sciences, Stanford University, CA 94305, USA.,Howard Hughes Medical Institute, Stanford University, CA 94305, USA
| |
Collapse
|
7
|
Christensen AJ, Iyer SM, François A, Vyas S, Ramakrishnan C, Vesuna S, Deisseroth K, Scherrer G, Delp SL. In Vivo Interrogation of Spinal Mechanosensory Circuits. Cell Rep 2017; 17:1699-1710. [PMID: 27806306 DOI: 10.1016/j.celrep.2016.10.010] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Revised: 08/22/2016] [Accepted: 10/03/2016] [Indexed: 11/26/2022] Open
Abstract
Spinal dorsal horn circuits receive, process, and transmit somatosensory information. To understand how specific components of these circuits contribute to behavior, it is critical to be able to directly modulate their activity in unanesthetized in vivo conditions. Here, we develop experimental tools that enable optogenetic control of spinal circuitry in freely moving mice using commonly available materials. We use these tools to examine mechanosensory processing in the spinal cord and observe that optogenetic activation of somatostatin-positive interneurons facilitates both mechanosensory and itch-related behavior, while reversible chemogenetic inhibition of these neurons suppresses mechanosensation. These results extend recent findings regarding the processing of mechanosensory information in the spinal cord and indicate the potential for activity-induced release of the somatostatin neuropeptide to affect processing of itch. The spinal implant approach we describe here is likely to enable a wide range of studies to elucidate spinal circuits underlying pain, touch, itch, and movement.
Collapse
Affiliation(s)
- Amelia J Christensen
- Department of Electrical Engineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Shrivats M Iyer
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Amaury François
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Saurabh Vyas
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Sam Vesuna
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA
| | - Grégory Scherrer
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Molecular and Cellular Physiology, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Neurosurgery, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Stanford Neurosciences Institute, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.
| | - Scott L Delp
- Department of Bioengineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA; Department of Mechanical Engineering, Stanford University, 318 Campus Drive, Stanford, CA 94305, USA.
| |
Collapse
|
8
|
Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods 2017; 14:959-962. [PMID: 28846090 PMCID: PMC5623106 DOI: 10.1038/nmeth.4396] [Citation(s) in RCA: 1203] [Impact Index Per Article: 171.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 12/16/2022]
Abstract
We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.
Collapse
Affiliation(s)
- M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexandro E Trevino
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA
| | - Emily G Hamilton
- Program in Cancer Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Program in Biomedical Informatics, Stanford University School of Medicine, Stanford, California, USA
| | | | - Sam Vesuna
- Department of Bioengineering, Stanford University School of Medicine and School of Engineering, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Adam J Rubin
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Kathleen S Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Beijing Wu
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Arwa Kathiria
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ava C Carter
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Maya Kasowski
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Lisa A Orloff
- Department of Otolaryngology Head and Neck Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Viviana I Risca
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Computer Science, Stanford University, Stanford, California, USA
| | - Paul A Khavari
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| | - Thomas J Montine
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
- Department of Dermatology, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|
9
|
Iyer SM, Vesuna S, Ramakrishnan C, Huynh K, Young S, Berndt A, Lee SY, Gorini CJ, Deisseroth K, Delp SL. Optogenetic and chemogenetic strategies for sustained inhibition of pain. Sci Rep 2016; 6:30570. [PMID: 27484850 PMCID: PMC4971509 DOI: 10.1038/srep30570] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/04/2016] [Indexed: 01/02/2023] Open
Abstract
Spatially targeted, genetically-specific strategies for sustained inhibition of nociceptors may help transform pain science and clinical management. Previous optogenetic strategies to inhibit pain have required constant illumination, and chemogenetic approaches in the periphery have not been shown to inhibit pain. Here, we show that the step-function inhibitory channelrhodopsin, SwiChR, can be used to persistently inhibit pain for long periods of time through infrequent transdermally delivered light pulses, reducing required light exposure by >98% and resolving a long-standing limitation in optogenetic inhibition. We demonstrate that the viral expression of the hM4D receptor in small-diameter primary afferent nociceptor enables chemogenetic inhibition of mechanical and thermal nociception thresholds. Finally, we develop optoPAIN, an optogenetic platform to non-invasively assess changes in pain sensitivity, and use this technique to examine pharmacological and chemogenetic inhibition of pain.
Collapse
Affiliation(s)
| | - Sam Vesuna
- Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Karen Huynh
- Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Stephanie Young
- Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Andre Berndt
- Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Soo Yeun Lee
- Bioengineering, Stanford University, Stanford, CA 94305, USA
| | | | - Karl Deisseroth
- Bioengineering, Stanford University, Stanford, CA 94305, USA
- Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Scott L. Delp
- Bioengineering, Stanford University, Stanford, CA 94305, USA
- Mechanical Engineering, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
10
|
Calle EA, Vesuna S, Dimitrievska S, Zhou K, Huang A, Zhao L, Niklason LE, Levene MJ. The use of optical clearing and multiphoton microscopy for investigation of three-dimensional tissue-engineered constructs. Tissue Eng Part C Methods 2014; 20:570-7. [PMID: 24251630 PMCID: PMC4074743 DOI: 10.1089/ten.tec.2013.0538] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Accepted: 11/05/2013] [Indexed: 01/14/2023] Open
Abstract
Recent advances in three-dimensional (3D) tissue engineering have concomitantly generated a need for new methods to visualize and assess the tissue. In particular, methods for imaging intact volumes of whole tissue, rather than a single plane, are required. Herein, we describe the use of multiphoton microscopy, combined with optical clearing, to noninvasively probe decellularized lung extracellular matrix scaffolds and decellularized, tissue-engineered blood vessels. We also evaluate recellularized lung tissue scaffolds. In addition to nondestructive imaging of tissue volumes greater than 4 mm(3), the lung tissue can be visualized using three distinct signals, combined or singly, that allow for simple separation of cells and different components of the extracellular matrix. Because the 3D volumes are not reconstructions, they do not require registration algorithms to generate digital volumes, and maintenance of isotropic resolution is not required when acquiring stacks of images. Once a virtual volume of tissue is generated, structures that have innate 3D features, such as the lumens of vessels and airways, are easily animated and explored in all dimensions. In blood vessels, individual collagen fibers can be visualized at the micron scale and their alignment assessed at various depths through the tissue, potentially providing some nondestructive measure of vessel integrity and mechanics. Finally, both the lungs and vessels assayed here were optically cleared, imaged, and visualized in a matter of hours, such that the added benefits of these techniques can be achieved with little more hassle or processing time than that associated with traditional histological methods.
Collapse
Affiliation(s)
- Elizabeth A. Calle
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Sam Vesuna
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Sashka Dimitrievska
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Kevin Zhou
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Angela Huang
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Liping Zhao
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Laura E. Niklason
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
- Department of Anesthesiology, Yale University, New Haven, Connecticut
| | - Michael J. Levene
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| |
Collapse
|
11
|
Abstract
CONTEXT Despite continuing advances in tissue processing automation, traditional embedding, cutting, and staining methods limit our ability for rapid, comprehensive visual examination. These limitations are particularly relevant to biopsies for which immediate therapeutic decisions are most necessary, faster feedback to the patient is desired, and preservation of tissue for ancillary studies is most important. The recent development of improved tissue clearing techniques has made it possible to consider use of multiphoton microscopy (MPM) tools in clinical settings, which could address difficulties of established methods. OBJECTIVE To demonstrate the potential of MPM of cleared tissue for the evaluation of unembedded and uncut pathology samples. DESIGN Human prostate, liver, breast, and kidney specimens were fixed and dehydrated by using traditional histologic techniques, with or without incorporation of nucleic acid fluorescent stains into dehydration steps. A benzyl alcohol/benzyl benzoate clearing protocol was substituted for xylene. Multiphoton microscopy was performed on a home-built system. RESULTS Excellent morphologic detail was achievable with MPM at depths greater than 500 μm. Pseudocoloring produced images analogous to hematoxylin-eosin-stained images. Concurrent second-harmonic generation detection allowed mapping of collagen. Subsequent traditional section staining with hematoxylin-eosin did not reveal any detrimental morphologic effects. Sample immunostains on renal tissue showed preservation of normal reactivity. Complete reconstructions of 1-mm cubic samples elucidated 3-dimensional architectural organization. CONCLUSIONS Multiphoton microscopy on cleared, unembedded, uncut biopsy specimens shows potential as a practical clinical tool with significant advantages over traditional histology while maintaining compatibility with gold standard techniques. Further investigation to address remaining implementation barriers is warranted.
Collapse
Affiliation(s)
- Richard Torres
- From the Departments of Laboratory Medicine (Dr Torres) and Neurology (Dr Levene), Yale University School of Medicine, New Haven, Connecticut; and the Department of Biomedical Engineering, Yale University School of Engineering and Applied Science, New Haven, Connecticut (Drs Torres and Levene and Mr Vesuna)
| | | | | |
Collapse
|
12
|
Vesuna S, Torres R, Levene MJ. Multiphoton fluorescence, second harmonic generation, and fluorescence lifetime imaging of whole cleared mouse organs. J Biomed Opt 2011; 16:106009. [PMID: 22029356 DOI: 10.1117/1.3641992] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Multiphoton microscopy of cleared tissue has previously been demonstrated to generate large three-dimensional (3D) volumetric image data on entire intact mouse organs using intrinsic tissue fluorescence. This technique holds great promise for performing 3D virtual biopsies, providing unique information on tissue morphology, and guidance for subsequent traditional slicing and staining. Here, we demonstrate the use of fluorescence lifetime imaging in cleared organs for achieving molecular contrast that can reveal morphologically distinct structures, even in the absence of knowledge of the underlying molecular source. In addition, we demonstrate the power of multimodal imaging, combining multiphoton fluorescence, second harmonic generation, and lifetime imaging to reveal exceptional morphological detail in an optically cleared mouse knee.
Collapse
Affiliation(s)
- Sam Vesuna
- Yale University, Department of Biomedical Engineering, 55 Prospect St., New Haven, Connecticut 06511, USA
| | | | | |
Collapse
|