Inhibitory interneuron diversity is a central feature of cortical circuits. The IN-CODE consortium seeks to combine large-scale recordings of interneuron types with machine-learning tools to identify the role of their physiological features, connectivity motifs, and cooperativity in cognitive functions.

The medial prefrontal cortex (mPFC) is thought to support cognitive flexibility by forming and maintaining generalized representations of abstract tasks. The formation of these representations as well as their relation to preexisting representations of contextual or spatial information is incompletely understood. In this study, we analyzed longitudinal one-photon calcium recordings in mice performing an olfaction-guided spatial memory task over an 8-week period that included habituation, training, and sleep epochs. Our results reveal that, while a minority of neurons initially conveyed significant information about the behavior of the animal, the bulk of task-related activity only emerged after the animals reached proficient performance. Although goal arm information is robustly represented at both the single-cell and network levels both during learning and in task-proficient mice, it undergoes significant remapping throughout the learning process. Additionally, we identified the establishment of recurring sequences during learning and their replay at reward locations, with no evidence of them existing during odor sampling phase, during sleep, or before training. Conversely, during odor sampling, information about odor identity is robustly available in the rate coactivation patterns, even before animals reached task proficiency. These findings suggest that the mPFC predominantly establishes generalized task representations de novo during learning, relying only minimally on preexisting spatial representations and that sub-second neural sequences in the mPFC are more likely involved in evaluating behavioral outcomes rather than planning future actions.

To select appropriate behaviour, individuals must rely on encoding of relevant features within their environment in the context of current and past experiences. This function has been linked to goal-associated activity patterns of hippocampal principal cells. Using single-unit recordings from optogenetically identified somatostatin-expressing interneurons (SOMIs) in the dentate gyrus of head-fixed mice trained in a spatial goal-oriented reward-learning task in virtual realities, we show that SOMI activity temporally precedes reward-locations in expert mice characterized by goal-anticipatory behaviour. Predictive goal-encoding by SOMIs is lost after translocation of learned goals to novel previously unrewarded sites leading to rapid reductions in anticipatory behaviour and fast reconfiguration of SOMI activity to times after reward onset in association with reward consumption at novel goal-sites. Chemogenetic silencing of SOMIs caused a loss of memory that trained goal-sites were no longer available. Thus, our data reveal the ability of SOMIs to flexibly encode goal-locations depending on current and past experiences to bias behavioral outcomes.

The phenomenon of representational drift (i.e., changing neuronal tuning during repeated exposure to the same stimuli), is a fundamental paradox in neuroscience that raises the question how stable behaviour can emerge from unstable neural representations. Place cells in CA1 of the hippocampus are crucial for spatial navigation and memories but show gradual changes in their preferred firing location over time when exposed to the same environment. This drift occurs despite the fact that the animal maintains the ability to navigate and to perform spatial tasks, suggesting a complex relationship between neural activity and behaviour. Here, we show that while the spatial tuning functions of individual CA1 neurons drift over time, stable space coding prevails at the population level: Representational drift is not random but can be described as a translation and rotation in population state space, which preserves the internal geometry of population activity over time. Compensating for the coordinated translation and rotation allows for drift correction and a recovery of spatial tuning on future days. Moreover, the preserved internal geometry stabilises downstream readout under noisy conditions. We propose that the conserved population geometry might serve as a mechanism by which downstream reader networks achieve effective drift correction and, thus, ameliorate the readout of stable information. ### Competing Interest Statement The authors have declared no competing interest.

Neurons in the medial prefrontal cortex (mPFC) are spatially tuned. Trajectory-specific firing with distinct spatial tuning on different paths to reward sites as well as generalized spatial tuning with similar responses on separate trajectories have been described. However, it is unclear whether such distinct populations contribute differently to the encoding of task space. Here, we find coexisting populations of neurons with trajectory-specific and generalized tuning profiles in an olfaction-guided spatial memory task in mice. Neurons with generalized representation show stable spatial tuning within and across days, allow accurate predictions of the animal's position, and preferentially emerge upon task learning. In contrast, cells with trajectory-specific spatial tuning display dynamically changing tuning functions, are less informative about the current position, and can be identified at a larger proportion early in task learning. These results highlight a role for neurons with generalized tuning in the efficient and stable representation of task space.

To select appropriate behaviour, individuals need to rely on the encoding of relevant features within their environment in the context of current and past experiences. This function has so far been related to goal-associated activity patterns of hippocampal principal cells. By applying single unit recordings of optogenetically identified somatostatin-expressing interneurons (SOMIs) in the hippocampal dentate gyrus of head-fixed mice trained on a spatial goal-oriented reward-learning task in a virtual reality, we show that in expert mice characterized by goal anticipatory behaviour, SOMIs activity temporally precedes reward-locations. Predictive goal-coding by SOMIs is lost after translocation of learned goals to novel previously unrewarded sides resulted in rapid reduction of anticipatory behaviour, and rapid reconfiguration of SOMI activity to times after reward onset in association with reward consumption at novel goal-sides. Chemogenetic silencing of SOMIs caused a loss in memorizing that trained goal-sides are no longer available. Thus, our data show a so far unrecognized ability of SOMIs to flexibly encode goal-locations depending on current and past experiences to bias behavioral outcomes.

Intense threat elicits action in the form of active and passive coping. The medial prefrontal cortex (mPFC) executes top-level control over the selection of threat coping strategies, but the dynamics of mPFC activity upon continuing threat encounters remain unexplored. Here, we used 1-photon calcium imaging in mice to probe the activity of prefrontal pyramidal cells during repeated exposure to intense threat in a tail suspension (TS) paradigm. A subset of prefrontal neurons displayed selective activation during TS, which was stably maintained over days. During threat, neurons showed specific tuning to active or passive coping. These responses were unrelated to general motion tuning and persisted over days. Moreover, the neural manifold traversed by low-dimensional population activity remained stable over subsequent days of TS exposure and was preserved across individuals. These data thus reveal a specific, temporally, and interindividually conserved repertoire of prefrontal tuning to behavioral responses under threat.

Behavior can be remarkably consistent, even over extended time periods, yet whether this is reflected in stable or 'drifting' neuronal responses to task features remains controversial. Here, we find a persistently active ensemble of neurons in the medial prefrontal cortex (mPFC) of mice that reliably maintains trajectory-specific tuning over several weeks while performing an olfaction-guided spatial memory task. This task-specific reference frame is stabilized during learning, upon which repeatedly active neurons show little representational drift and maintain their trajectory-specific tuning across long pauses in task exposure and across repeated changes in cue-target location pairings. These data thus suggest a 'core ensemble' of prefrontal neurons forming a reference frame of task-relevant space for the performance of consistent behavior over extended periods of time.

Experience-driven alterations in neuronal activity are followed by structural-functional modifications allowing cells to adapt to these activity changes. Structural plasticity has been observed for cortical principal cells. However, how GABAergic interneurons respond to experience-dependent network activity changes is not well understood. We show that parvalbumin-expressing interneurons (PVIs) of the dentate gyrus (DG) possess dendritic spines, which undergo behaviorally induced structural dynamics. Glutamatergic inputs at PVI spines evoke signals with high spatial compartmentalization defined by neck length. Mice experiencing novel contexts form more PVI spines with elongated necks and exhibit enhanced network and PVI activity and cFOS expression. Enhanced green fluorescent protein reconstitution across synaptic partner-mediated synapse labeling shows that experience-driven PVI spine growth boosts targeting of PVI spines over shafts by glutamatergic synapses. Our findings propose a role for PVI spine dynamics in regulating PVI excitation by their inputs, which may allow PVIs to dynamically adjust their functional integration in the DG microcircuitry in relation to network computational demands.

Abstract Parvalbumin-positive interneurons (PVIs) in the dentate gyrus (DG) possess dendritic spines, but their functional properties and structural dynamics remain uncharted. Using in vitro 2-Photon imaging, we show that glutamatergic synapses at PVI dendritic spines evoke AMPA and NMDA receptor-mediated calcium signals with high spatial compartmentalization defined by their neck length. Ex vivo morphological analysis shows that DREADD-mediated in vivo PVI excitation increases spine density and length, whereas recruitment of glutamatergic inputs causes spine head enlargement. These spine dynamics could be reproduced in mice experiencing novel contexts. By using dual-eGRASP-mediated input labeling we provide evidence that experience-driven PVI spine growth and input density boosts synaptic targeting of PVI spines over shafts, a mechanism supporting functional isolation of postsynaptic signals from parent dendrites. We propose that experience-related PVI spine dynamics echo excitation levels of the DG network allowing PVIs to dynamically adjust their microcircuit integration in relation to the networks’ computational demands.

The prefrontal cortex (PFC) enables a staggering variety of complex behaviors, such as planning actions, solving problems, and adapting to new situations according to external information and internal states. These higher-order abilities, collectively defined as adaptive cognitive behavior, require cellular ensembles that coordinate the tradeoff between the stability and flexibility of neural representations. While the mechanisms underlying the function of cellular ensembles are still unclear, recent experimental and theoretical studies suggest that temporal coordination dynamically binds prefrontal neurons into functional ensembles. A so far largely separate stream of research has investigated the prefrontal efferent and afferent connectivity. These two research streams have recently converged on the hypothesis that prefrontal connectivity patterns influence ensemble formation and the function of neurons within ensembles. Here, we propose a unitary concept that, leveraging a cross-species definition of prefrontal regions, explains how prefrontal ensembles adaptively regulate and efficiently coordinate multiple processes in distinct cognitive behaviors.

Respiration-rhythmic oscillations in the local field potential emerge in the mPFC, a cortical region with a key role in the regulation of cognitive and emotional behavior. Respiration-driven rhythms coordinate local activity by entraining fast γ oscillations as well as single-unit discharges. To what extent respiration entrainment differently engages the mPFC network in a behavioral state-dependent manner, however, is not known. Here, we compared the respiration entrainment of mouse PFC local field potential and spiking activity (23 male and 2 female mice) across distinct behavioral states: during awake immobility in the home cage (HC), during passive coping in response to inescapable stress under tail suspension (TS), and during reward consumption (Rew). Respiration-driven rhythms emerged during all three states. However, prefrontal γ oscillations were more strongly entrained by respiration during HC than TS or Rew. Moreover, neuronal spikes of putative pyramidal cells and putative interneurons showed significant respiration phase-coupling throughout behaviors with characteristic phase preferences depending on the behavioral state. Finally, while phase-coupling dominated in deep layers in HC and Rew conditions, TS resulted in the recruitment of superficial layer neurons to respiration. These results jointly suggest that respiration dynamically entrains prefrontal neuronal activity depending on the behavioral state.SIGNIFICANCE STATEMENT The mPFC, through its extensive connections (e.g., to the amygdala, the striatum, serotoninergic and dopaminergic nuclei), flexibly regulates cognitive behaviors. Impairment of prefrontal functions can lead to disease states, such as depression, addiction, or anxiety disorders. Deciphering the complex regulation of PFC activity during defined behavioral states is thus an essential challenge. Here, we investigated the role of a prefrontal slow oscillation that has recently attracted rising interest, the respiration rhythm, in modulating prefrontal neurons during distinct behavioral states. We show that prefrontal neuronal activity is differently entrained by the respiration rhythm in a cell type- and behavior-dependent manner. These results provide first insight into the complex modulation of prefrontal activity patterns by rhythmic breathing.

Spatial tuning of neocortical pyramidal cells has been observed in diverse cortical regions and is thought to rely primarily on input from the hippocampal formation. Despite the well-studied hippocampal place code, many properties of the neocortical spatial tuning system are still insufficiently understood. In particular, it has remained unclear how the topography of direct anatomical connections from hippocampus to neocortex affects spatial tuning depth, and whether the dynamics of spatial coding in the hippocampal output region CA1, such as remapping in novel environments, is transmitted to the neocortex. Using mice navigating through virtual environments, we addressed these questions in the mouse medial prefrontal cortex, which receives direct input from the hippocampus. We found a rapidly emerging prefrontal representation of space in the absence of task rules, which discriminates familiar from novel environments and is reinstated upon reexposure to the same familiar environment. Topographical analysis revealed a dorsoventral gradient in the representation of the own position, which runs opposite to the innervation density of hippocampal inputs. Jointly, these results reveal a dynamically emerging and topographically organized prefrontal place code during spontaneous locomotion.

Nasal breathing affects cognitive functions, but it has remained largely unclear how respiration-driven inputs shape information processing in neuronal circuits. Current theories emphasize the role of neuronal assemblies, coalitions of transiently active pyramidal cells, as the core unit of cortical network computations. Here, we show that the phase of respiration-related oscillations (RROs) influences the likelihood of activation of a subset of neuronal assemblies in the medial prefrontal cortex of awake mice. RROs bias the activation of neuronal assemblies more efficiently than that of individual neurons by entraining the coactivity of assembly neurons. Moreover, the activation of assemblies is moderately biased towards the descending phase of RROs. Despite the enriched activation of assemblies during descending RRO, the overlap between individual assemblies remains constant across RRO phases. Putative GABAergic interneurons are shown to coactivate with assemblies and receive enhanced excitatory drive from assembly neurons during descending RRO, suggesting that the phase-specific recruitment of putative interneurons might help to keep the activation of different assemblies separated from each other during times of preferred assembly activation. Our results thus identify respiration-synchronized brain rhythms as drivers of neuronal assemblies and point to a role of RROs in defining time windows of enhanced yet segregated assembly activity. KEY POINTS: Activation of neuronal assemblies is phase-coupled to ongoing respiration-related oscillations (RROs) in the medial prefrontal cortex of mice. The phase coupling strength of assemblies exceeds that of individual neurons. Assemblies preferentially activate during the descending phase of RRO. Despite higher assembly frequency during descending RRO, overlap between active assemblies remains constant across RRO phase. Putative GABAergic interneurons are preferentially recruited by assembly neurons during descending RRO, suggesting that interneurons might contribute to the segregation of active assemblies during the descending phase of RRO.

LIM homeobox domain transcription factor 6 (Lhx6) is crucial for the prenatal specification and differentiation of hippocampal GABAergic interneuron precursors. Interestingly, Lhx6 remains to be expressed in parvalbumin-positive hippocampal interneurons (PVIs) long after specification and differentiation have been completed, the functional implications of which remain elusive. We addressed the role of adult-expressed Lhx6 in the hippocampus by knocking down Lhx6 in adult mice (> 8 weeks old) using viral or transgenic expression of Cre-recombinase in Lhx6(loxP/loxP) mice. Late removal of Lhx6 did not affect the number of PVIs and had no impact on the morphological and physiological properties of PVIs. Furthermore, mice lacking Lhx6 in PVIs displayed normal cognitive behavior. Loss of Lhx6 only partially reduced the expression of Sox6 and Arx, downstream transcription factors that depend on Lhx6 during embryonic development of PVIs. Our data thus suggest that while Lhx6 is vitally important to drive interneuron transcriptional networks during early development, it becomes uncoupled from downstream effectors during postnatal life.

We interrogated prefrontal circuit function in mice lacking Disrupted-in-schizophrenia-1 (Disc1-mutant mice), a risk factor for psychiatric disorders. Single-unit recordings in awake mice revealed reduced average firing rates of fast-spiking interneurons (INTs), including optogenetically identified parvalbumin-positive cells, and a lower proportion of INTs phase-coupled to ongoing gamma oscillations. Moreover, we observed decreased spike transmission efficacy at local pyramidal cell (PYR)-INT connections in vivo, suggesting a reduced excitatory effect of local glutamatergic inputs as a potential mechanism of lower INT rates. On the network level, impaired INT function resulted in altered activation of PYR assemblies: While assembly activations defined as coactivations within 25 ms were observed equally often, the expression strength of individual assembly patterns was significantly higher in Disc1-mutant mice. Our data, thus, reveal a role of Disc1 in shaping the properties of prefrontal assembly patterns by setting INT responsiveness to glutamatergic drive.

Data and analysis code for "Disrupted-in-Schizophrenia-1 is required for normal pyramidal cell-interneuron communication and assembly dynamics in the prefrontal cortex", 2022, eLife.

Alzheimer's disease (AD) is characterized by the accumulation of amyloid-β (Aβ) which ultimately forms plaques. These Aβ deposits can be induced in APP transgenic mouse models by prion-like seeding. It has been widely accepted that anosmia and hyposmia occur during the early stages of AD, even before cognitive deficits are present. In order to determine the impact of seed-induced Aβ deposits on olfaction, we performed intracerebral injections of seed-competent brain homogenate into the olfactory bulb of young pre-depositing APP transgenic mice. Remarkably, we observed a dramatic olfactory impairment in those mice. Furthermore, the number of newborn neurons as well as the activity of cells in the mitral cell layer was decreased. Notably, exposure to an enriched environment reduced Aβ seeding, vivified neurogenesis and most importantly reversed olfactory deficits. Based on our findings, we conclude that altered neuronal function as a result of induced Aβ pathology might contribute to olfactory dysfunction in AD.