1
|
Sosa M, Plitt MH, Giocomo LM. Hippocampal sequences span experience relative to rewards. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.27.573490. [PMID: 38234842 PMCID: PMC10793396 DOI: 10.1101/2023.12.27.573490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Hippocampal place cells fire in sequences that span spatial environments and non-spatial modalities, suggesting that hippocampal activity can anchor to the most behaviorally salient aspects of experience. As reward is a highly salient event, we hypothesized that sequences of hippocampal activity can anchor to rewards. To test this, we performed two-photon imaging of hippocampal CA1 neurons as mice navigated virtual environments with changing hidden reward locations. When the reward moved, the firing fields of a subpopulation of cells moved to the same relative position with respect to reward, constructing a sequence of reward-relative cells that spanned the entire task structure. The density of these reward-relative sequences increased with task experience as additional neurons were recruited to the reward-relative population. Conversely, a largely separate subpopulation maintained a spatially-based place code. These findings thus reveal separate hippocampal ensembles can flexibly encode multiple behaviorally salient reference frames, reflecting the structure of the experience.
Collapse
Affiliation(s)
- Marielena Sosa
- Department of Neurobiology, Stanford University School of Medicine; Stanford, CA, USA
| | - Mark H. Plitt
- Department of Neurobiology, Stanford University School of Medicine; Stanford, CA, USA
- Present address: Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA, USA
| | - Lisa M. Giocomo
- Department of Neurobiology, Stanford University School of Medicine; Stanford, CA, USA
| |
Collapse
|
2
|
Aoun A, Shetler O, Raghuraman R, Rodriguez GA, Hussaini SA. Beyond correlation: optimal transport metrics for characterizing representational stability and remapping in neurons encoding spatial memory. Front Cell Neurosci 2024; 17:1273283. [PMID: 38303974 PMCID: PMC10831886 DOI: 10.3389/fncel.2023.1273283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 12/05/2023] [Indexed: 02/03/2024] Open
Abstract
Introduction Spatial representations in the entorhinal cortex (EC) and hippocampus (HPC) are fundamental to cognitive functions like navigation and memory. These representations, embodied in spatial field maps, dynamically remap in response to environmental changes. However, current methods, such as Pearson's correlation coefficient, struggle to capture the complexity of these remapping events, especially when fields do not overlap, or transformations are non-linear. This limitation hinders our understanding and quantification of remapping, a key aspect of spatial memory function. Methods We propose a family of metrics based on the Earth Mover's Distance (EMD) as a versatile framework for characterizing remapping. Results The EMD provides a granular, noise-resistant, and rate-robust description of remapping. This approach enables the identification of specific cell types and the characterization of remapping in various scenarios, including disease models. Furthermore, the EMD's properties can be manipulated to identify spatially tuned cell types and to explore remapping as it relates to alternate information forms such as spatiotemporal coding. Discussion We present a feasible, lightweight approach that complements traditional methods. Our findings underscore the potential of the EMD as a powerful tool for enhancing our understanding of remapping in the brain and its implications for spatial navigation, memory studies and beyond.
Collapse
Affiliation(s)
- Andrew Aoun
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Oliver Shetler
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Radha Raghuraman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - Gustavo A. Rodriguez
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| | - S. Abid Hussaini
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University Medical Center, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, United States
| |
Collapse
|
3
|
Grieves RM. Estimating neuronal firing density: A quantitative analysis of firing rate map algorithms. PLoS Comput Biol 2023; 19:e1011763. [PMID: 38150481 PMCID: PMC10775984 DOI: 10.1371/journal.pcbi.1011763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 01/09/2024] [Accepted: 12/15/2023] [Indexed: 12/29/2023] Open
Abstract
The analysis of neurons that exhibit receptive fields dependent on an organism's spatial location, such as grid, place or boundary cells typically begins by mapping their activity in space using firing rate maps. However, mapping approaches are varied and depend on multiple tuning parameters that are usually chosen qualitatively by the experimenter and thus vary significantly across studies. Small changes in parameters such as these can impact results significantly, yet, to date a quantitative investigation of firing rate maps has not been attempted. Using simulated datasets, we examined how tuning parameters, recording duration and firing field size affect the accuracy of spatial maps generated using the most widely used approaches. For each approach we found a clear subset of parameters which yielded low-error firing rate maps and isolated the parameters yielding 1) the least error possible and 2) the Pareto-optimal parameter set which balanced error, computation time, place field detection accuracy and the extrapolation of missing values. Smoothed bivariate histograms and averaged shifted histograms were consistently associated with the fastest computation times while still providing accurate maps. Adaptive smoothing and binning approaches were found to compensate for low positional sampling the most effectively. Kernel smoothed density estimation also compensated for low sampling well and resulted in accurate maps, but it was also among the slowest methods tested. Overall, the bivariate histogram, coupled with spatial smoothing, is likely the most desirable method in the majority of cases.
Collapse
Affiliation(s)
- Roddy M. Grieves
- Department of Psychological and Brain Sciences, Dartmouth College, Hanover, New Hampshire, United States of America
| |
Collapse
|
4
|
Aoun A, Shetler O, Raghuraman R, Rodriguez GA, Hussaini SA. Beyond Correlation: Optimal Transport Metrics For Characterizing Representational Stability and Remapping in Neurons Encoding Spatial Memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548592. [PMID: 37503011 PMCID: PMC10369988 DOI: 10.1101/2023.07.11.548592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Spatial representations in the entorhinal cortex (EC) and hippocampus (HPC) are fundamental to cognitive functions like navigation and memory. These representations, embodied in spatial field maps, dynamically remap in response to environmental changes. However, current methods, such as Pearson's correlation coefficient, struggle to capture the complexity of these remapping events, especially when fields do not overlap, or transformations are non-linear. This limitation hinders our understanding and quantification of remapping, a key aspect of spatial memory function. To address this, we propose a family of metrics based on the Earth Mover's Distance (EMD) as a versatile framework for characterizing remapping. Applied to both normalized and unnormalized distributions, the EMD provides a granular, noise-resistant, and rate-robust description of remapping. This approach enables the identification of specific cell types and the characterization of remapping in various scenarios, including disease models. Furthermore, the EMD's properties can be manipulated to identify spatially tuned cell types and to explore remapping as it relates to alternate information forms such as spatiotemporal coding. By employing approximations of the EMD, we present a feasible, lightweight approach that complements traditional methods. Our findings underscore the potential of the EMD as a powerful tool for enhancing our understanding of remapping in the brain and its implications for spatial navigation, memory studies and beyond.
Collapse
Affiliation(s)
- Andrew Aoun
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Co-first author
| | - Oliver Shetler
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Co-first author
| | - Radha Raghuraman
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Gustavo A. Rodriguez
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - S. Abid Hussaini
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, Columbia University Medical Center, New York, NY 10032, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| |
Collapse
|
5
|
Bonnar O, Shaw K, Anderle S, Grijseels DM, Clarke D, Bell L, King SL, Hall CN. APOE4 expression confers a mild, persistent reduction in neurovascular function in the visual cortex and hippocampus of awake mice. J Cereb Blood Flow Metab 2023; 43:1826-1841. [PMID: 37350319 PMCID: PMC10676141 DOI: 10.1177/0271678x231172842] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 06/24/2023]
Abstract
Vascular factors are known to be early and important players in Alzheimer's disease (AD) development, however the role of the ε4 allele of the Apolipoprotein (APOE) gene (a risk factor for developing AD) remains unclear. APOE4 genotype is associated with early and severe neocortical vascular deficits in anaesthetised mice, but in humans, vascular and cognitive dysfunction are focused on the hippocampal formation and appear later. How APOE4 might interact with the vasculature to confer AD risk during the preclinical phase represents a gap in existing knowledge. To avoid potential confounds of anaesthesia and to explore regions most relevant for human disease, we studied the visual cortex and hippocampus of awake APOE3 and APOE4-TR mice using 2-photon microscopy of neurons and blood vessels. We found mild vascular deficits: vascular density and functional hyperaemia were unaffected in APOE4 mice, and neuronal or vascular function did not decrease up to late middle-age. Instead, vascular responsiveness was lower, arteriole vasomotion was reduced and neuronal calcium signals during visual stimulation were increased. This suggests that, alone, APOE4 expression is not catastrophic but stably alters neurovascular physiology. We suggest this state makes APOE4 carriers more sensitive to subsequent insults such as injury or beta amyloid accumulation.
Collapse
Affiliation(s)
| | | | - Silvia Anderle
- School of Psychology and Sussex Neuroscience, University of Sussex, Falmer, Brighton, East Sussex, UK
| | - Dori M Grijseels
- School of Psychology and Sussex Neuroscience, University of Sussex, Falmer, Brighton, East Sussex, UK
| | - Devin Clarke
- School of Psychology and Sussex Neuroscience, University of Sussex, Falmer, Brighton, East Sussex, UK
| | - Laura Bell
- School of Psychology and Sussex Neuroscience, University of Sussex, Falmer, Brighton, East Sussex, UK
| | - Sarah L King
- School of Psychology and Sussex Neuroscience, University of Sussex, Falmer, Brighton, East Sussex, UK
| | - Catherine N Hall
- School of Psychology and Sussex Neuroscience, University of Sussex, Falmer, Brighton, East Sussex, UK
| |
Collapse
|
6
|
Madar A, Dong C, Sheffield M. BTSP, not STDP, Drives Shifts in Hippocampal Representations During Familiarization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562791. [PMID: 37904999 PMCID: PMC10614909 DOI: 10.1101/2023.10.17.562791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Synaptic plasticity is widely thought to support memory storage in the brain, but the rules determining impactful synaptic changes in-vivo are not known. We considered the trial-by-trial shifting dynamics of hippocampal place fields (PFs) as an indicator of ongoing plasticity during memory formation. By implementing different plasticity rules in computational models of spiking place cells and comparing to experimentally measured PFs from mice navigating familiar and novel environments, we found that Behavioral-Timescale-Synaptic-Plasticity (BTSP), rather than Hebbian Spike-Timing-Dependent-Plasticity, is the principal mechanism governing PF shifting dynamics. BTSP-triggering events are rare, but more frequent during novel experiences. During exploration, their probability is dynamic: it decays after PF onset, but continually drives a population-level representational drift. Finally, our results show that BTSP occurs in CA3 but is less frequent and phenomenologically different than in CA1. Overall, our study provides a new framework to understand how synaptic plasticity shapes neuronal representations during learning.
Collapse
Affiliation(s)
- A.D. Madar
- Department of Neurobiology, Neuroscience Institute, University of Chicago
| | - C. Dong
- Department of Neurobiology, Neuroscience Institute, University of Chicago
- current affiliation: Department of Neurobiology, Stanford University School of Medicine
| | - M.E.J. Sheffield
- Department of Neurobiology, Neuroscience Institute, University of Chicago
| |
Collapse
|
7
|
Johnston KG, Grieco SF, Zhang H, Jin S, Xu X, Nie Q. Tracking longitudinal population dynamics of single neuronal calcium signal using SCOUT. CELL REPORTS METHODS 2022; 2:100207. [PMID: 35637911 PMCID: PMC9142684 DOI: 10.1016/j.crmeth.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/06/2022] [Accepted: 04/08/2022] [Indexed: 11/07/2022]
Abstract
In vivo calcium imaging enables simultaneous recording of large neuronal ensembles engaged in complex operations. Many experiments require monitoring and identification of cell populations across multiple sessions. Population cell tracking across multiple sessions is complicated by non-rigid transformations induced by cell movement and imaging field shifts. We introduce SCOUT (Single-Cell spatiOtemporal longitUdinal Tracking), a fast, robust cell-tracking method utilizing multiple cell-cell similarity metrics, probabilistic inference, and an adaptive clustering methodology, to perform cell identification across multiple sessions. By comparing SCOUT with earlier cell-tracking algorithms on simulated, 1-photon, and 2-photon recordings, we show that our approach significantly improves cell-tracking quality, particularly when recordings exhibit spatial footprint movement between sessions or sub-optimal neural extraction quality.
Collapse
Affiliation(s)
- Kevin G. Johnston
- Department of Mathematics and the NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
| | - Steven F. Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Hai Zhang
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Suoqin Jin
- Department of Mathematics and the NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
- Department of Computer Science, University of California, Irvine, CA 92697, USA
- The Center for the Neurobiology of Learning and Memory, University of California, Irvine, CA 92697, USA
- The Center for Neural Circuit Mapping, University of California, Irvine, CA 92697, USA
| | - Qing Nie
- Department of Mathematics and the NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, CA 92697, USA
- Department of Developmental and Cell Biology, University of California, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
- The Center for Neural Circuit Mapping, University of California, Irvine, CA 92697, USA
| |
Collapse
|
8
|
Sotskov VP, Pospelov NA, Plusnin VV, Anokhin KV. Calcium Imaging Reveals Fast Tuning Dynamics of Hippocampal Place Cells and CA1 Population Activity during Free Exploration Task in Mice. Int J Mol Sci 2022; 23:ijms23020638. [PMID: 35054826 PMCID: PMC8775446 DOI: 10.3390/ijms23020638] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/01/2022] [Accepted: 01/04/2022] [Indexed: 02/06/2023] Open
Abstract
Hippocampal place cells are a well-known object in neuroscience, but their place field formation in the first moments of navigating in a novel environment remains an ill-defined process. To address these dynamics, we performed in vivo imaging of neuronal activity in the CA1 field of the mouse hippocampus using genetically encoded green calcium indicators, including the novel NCaMP7 and FGCaMP7, designed specifically for in vivo calcium imaging. Mice were injected with a viral vector encoding calcium sensor, head-mounted with an NVista HD miniscope, and allowed to explore a completely novel environment (circular track surrounded by visual cues) without any reinforcement stimuli, in order to avoid potential interference from reward-related behavior. First, we calculated the average time required for each CA1 cell to acquire its place field. We found that 25% of CA1 place fields were formed at the first arrival in the corresponding place, while the average tuning latency for all place fields in a novel environment equaled 247 s. After 24 h, when the environment was familiar to the animals, place fields formed faster, independent of retention of cognitive maps during this session. No cumulation of selectivity score was observed between these two sessions. Using dimensionality reduction, we demonstrated that the population activity of rapidly tuned CA1 place cells allowed the reconstruction of the geometry of the navigated circular maze; the distribution of reconstruction error between the mice was consistent with the distribution of the average place field selectivity score in them. Our data thus show that neuronal activity recorded with genetically encoded calcium sensors revealed fast behavior-dependent plasticity in the mouse hippocampus, resulting in the rapid formation of place fields and population activity that allowed the reconstruction of the geometry of the navigated maze.
Collapse
Affiliation(s)
- Vladimir P. Sotskov
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Correspondence: (V.P.S.); (K.V.A.)
| | - Nikita A. Pospelov
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, 119991 Moscow, Russia;
| | - Viktor V. Plusnin
- National Research Center “Kurchatov Institute”, 123098 Moscow, Russia;
- Moscow Institute of Physics and Technology, 141700 Dolgoprudny, Russia
| | - Konstantin V. Anokhin
- Institute for Advanced Brain Studies, Lomonosov Moscow State University, 119991 Moscow, Russia;
- P.K. Anokhin Institute of Normal Physiology RAS, 125315 Moscow, Russia
- Correspondence: (V.P.S.); (K.V.A.)
| |
Collapse
|