Gaining insight into the neural basis of resting-state fMRI signal

Disparity in temporal and spatial relationships between resting-state electrophysiological and fMRI signals

Resting-state brain networks (RSNs) have been widely applied in health and disease, but the interpretation of RSNs in terms of the underlying neural activity is unclear. To address this fundamental question, we conducted simultaneous recordings of whole-brain resting-state functional magnetic resonance imaging (rsfMRI) and electrophysiology signals in two separate brain regions of rats. Our data reveal that for both recording sites, spatial maps derived from band-specific local field potential (LFP) power can account for up to 90% of the spatial variability in RSNs derived from rsfMRI signals. Surprisingly, the time series of LFP band power can only explain to a maximum of 35% of the temporal variance of the local rsfMRI time course from the same site. In addition, regressing out time series of LFP power from rsfMRI signals has minimal impact on the spatial patterns of rsfMRI-based RSNs. This disparity in the spatial and temporal relationships between resting-state electrophysiology and rsfMRI signals suggests that electrophysiological activity alone does not fully explain the effects observed in the rsfMRI signal, implying the existence of an rsfMRI component contributed by "electrophysiology-invisible" signals. These findings offer a novel perspective on our understanding of RSN interpretation.

The human hypothalamus coordinates switching between different survival actions

Comparative research suggests that the hypothalamus is critical in switching between survival behaviors, yet it is unclear if this is the case in humans. Here, we investigate the role of the human hypothalamus in survival switching by introducing a paradigm where volunteers switch between hunting and escape in response to encounters with a virtual predator or prey. Given the small size and low tissue contrast of the hypothalamus, we used deep learning-based segmentation to identify the individual-specific hypothalamus and its subnuclei as well as an imaging sequence optimized for hypothalamic signal acquisition. Across 2 experiments, we employed computational models with identical structures to explain internal movement generation processes associated with hunting and escaping. Despite the shared structure, the models exhibited significantly different parameter values where escaping or hunting were accurately decodable just by computing the parameters of internal movement generation processes. In experiment 2, multi-voxel pattern analyses (MVPA) showed that the hypothalamus, hippocampus, and periaqueductal gray encode switching of survival behaviors while not encoding simple motor switching outside of the survival context. Furthermore, multi-voxel connectivity analyses revealed a network including the hypothalamus as encoding survival switching and how the hypothalamus is connected to other regions in this network. Finally, model-based fMRI analyses showed that a strong hypothalamic multi-voxel pattern of switching is predictive of optimal behavioral coordination after switching, especially when this signal was synchronized with the multi-voxel pattern of switching in the amygdala. Our study is the first to identify the role of the human hypothalamus in switching between survival behaviors and action organization after switching.

Perturbing cortical networks: in vivo electrophysiological consequences of pan-neuronal chemogenetic manipulations using deschloroclozapine

Introduction

Chemogenetic techniques, specifically the use of Designer Receptors Exclusively Activated by Designer Drugs (DREADDs), have become invaluable tools in neuroscience research. Yet, the understanding of how Gq- and Gicoupled DREADDs alter local field potential (LFP) oscillations in vivo remains incomplete.

Methods

This study investigates the in vivo electrophysiological effects of DREADD actuation by deschloroclozapine, on spontaneous firing rate and LFP oscillations recorded from the anterior cingulate cortex in lightly anesthetized male rats.

Results

Unexpectedly, in response to the administration of deschloroclozapine, we observed inhibitory effects with pan-neuronal hM3D(Gq) stimulation, and excitatory effects with pan-neuronal hM4D(Gi) stimulation in a significant portion of neurons. These results emphasize the need to account for indirect perturbation effects at the local neuronal network level in vivo, particularly when not all neurons express the chemogenetic receptors uniformly. In the current study, for instance, the majority of cells that were transduced with both hM3D(Gq) and hM4D(Gi) were GABAergic. Moreover, we found that panneuronal cortical chemogenetic modulation can profoundly alter oscillatory neuronal activity, presenting a potential research tool or therapeutic strategy in several neuropsychiatric models and diseases.

Discussion

These findings help to optimize the use of chemogenetic techniques in neuroscience research and open new possibilities for novel therapeutic strategies.

Where do we stand on fMRI in awake mice?

Imaging awake animals is quickly gaining traction in neuroscience as it offers a means to eliminate the confounding effects of anesthesia, difficulties of inter-species translation (when humans are typically imaged while awake), and the inability to investigate the full range of brain and behavioral states in unconscious animals. In this systematic review, we focus on the development of awake mouse blood oxygen level dependent functional magnetic resonance imaging (fMRI). Mice are widely used in research due to their fast-breeding cycle, genetic malleability, and low cost. Functional MRI yields whole-brain coverage and can be performed on both humans and animal models making it an ideal modality for comparing study findings across species. We provide an analysis of 30 articles (years 2011-2022) identified through a systematic literature search. Our conclusions include that head-posts are favorable, acclimation training for 10-14 d is likely ample under certain conditions, stress has been poorly characterized, and more standardization is needed to accelerate progress. For context, an overview of awake rat fMRI studies is also included. We make recommendations that will benefit a wide range of neuroscience applications.

Multimodal measures of spontaneous brain activity reveal both common and divergent patterns of cortical functional organization

Large-scale functional networks have been characterized in both rodent and human brains, typically by analyzing fMRI-BOLD signals. However, the relationship between fMRI-BOLD and underlying neural activity is complex and incompletely understood, which poses challenges to interpreting network organization obtained using this technique. Additionally, most work has assumed a disjoint functional network organization (i.e., brain regions belong to one and only one network). Here, we employ wide-field Ca2+ imaging simultaneously with fMRI-BOLD in mice expressing GCaMP6f in excitatory neurons. We determine cortical networks discovered by each modality using a mixed-membership algorithm to test the hypothesis that functional networks exhibit overlapping organization. We find that there is considerable network overlap (both modalities) in addition to disjoint organization. Our results show that multiple BOLD networks are detected via Ca2+ signals, and networks determined by low-frequency Ca2+ signals are only modestly more similar to BOLD networks. In addition, the principal gradient of functional connectivity is nearly identical for BOLD and Ca2+ signals. Despite similarities, important differences are also detected across modalities, such as in measures of functional connectivity strength and diversity. In conclusion, Ca2+ imaging uncovers overlapping functional cortical organization in the mouse that reflects several, but not all, properties observed with fMRI-BOLD signals.

Mapping and comparing fMRI connectivity networks across species

Technical advances in neuroimaging, notably in fMRI, have allowed distributed patterns of functional connectivity to be mapped in the human brain with increasing spatiotemporal resolution. Recent years have seen a growing interest in extending this approach to rodents and non-human primates to understand the mechanism of fMRI connectivity and complement human investigations of the functional connectome. Here, we discuss current challenges and opportunities of fMRI connectivity mapping across species. We underscore the critical importance of physiologically decoding neuroimaging measures of brain (dys)connectivity via multiscale mechanistic investigations in animals. We next highlight a set of general principles governing the organization of mammalian connectivity networks across species. These include the presence of evolutionarily conserved network systems, a dominant cortical axis of functional connectivity, and a common repertoire of topographically conserved fMRI spatiotemporal modes. We finally describe emerging approaches allowing comparisons and extrapolations of fMRI connectivity findings across species. As neuroscientists gain access to increasingly sophisticated perturbational, computational and recording tools, cross-species fMRI offers novel opportunities to investigate the large-scale organization of the mammalian brain in health and disease.

Resting-state functional connectivity changes in older adults with sleep disturbance and the role of amyloid burden

Sleep and related disorders could lead to changes in various brain networks, but little is known about the role of amyloid β (Aβ) burden-a key Alzheimer's disease (AD) biomarker-in the relationship between sleep disturbance and altered resting state functional connectivity (rsFC) in older adults. This cross-sectional study examined the association between sleep disturbance, Aβ burden, and rsFC using a large-scale dataset from the Alzheimer's Disease Neuroimaging Initiative (ADNI). Sample included 489 individuals (53.6% cognitively normal, 32.5% mild cognitive impairment, and 13.9% AD) who had completed sleep measures (Neuropsychiatric Inventory), PET Aβ data, and resting-state fMRI scans at baseline. Within and between rsFC of the Salience (SN), the Default Mode (DMN) and the Frontal Parietal network (FPN) were compared between participants with sleep disturbance versus without sleep disturbance. The interaction between Aβ positivity and sleep disturbance was evaluated using the linear regressions, controlling for age, diagnosis status, gender, sedatives and hypnotics use, and hypertension. Although no significant main effect of sleep disturbance was found on rsFC, a significant interaction term emerged between sleep disturbance and Aβ burden on rsFC of SN (β = 0.11, P = 0.006). Specifically, sleep disturbance was associated with SN hyperconnectivity, only with the presence of Aβ burden. Sleep disturbance may lead to altered connectivity in the SN when Aβ is accumulated in the brain. Individuals with AD pathology may be at increased risk for sleep-related aberrant rsFC; therefore, identifying and treating sleep problems in these individuals may help prevent further disease progression.

Acute alcohol induces greater dose-dependent increase in the lateral cortical network functional connectivity in adult than adolescent rats

Alcohol misuse and, particularly adolescent drinking, is a major public health concern. While evidence suggests that adolescent alcohol use affects frontal brain regions that are important for cognitive control over behavior little is known about how acute alcohol exposure alters large-scale brain networks and how sex and age may moderate such effects. Here, we employ a recently developed functional magnetic resonance imaging (fMRI) protocol to acquire rat brain functional connectivity data and use an established analytical pipeline to examine the effect of sex, age, and alcohol dose on connectivity within and between three major rodent brain networks: defaul mode, salience, and lateral cortical network. We identify the intra- and inter-network connectivity differences and establish moderation models to reveal significant influences of age on acute alcohol-induced lateral cortical network connectivity. Through this work, we make brain-wide isotropic fMRI data with acute alcohol challenge publicly available, with the hope to facilitate future discovery of brain regions/circuits that are causally relevant to the impact of acute alcohol use.

Sex differences in resting-state functional networks in awake rats

Sex-related differences can be found in many brain disorders and psychophysiological traits, highlighting the importance to systematically understand the sex differences in brain function in humans and animal models. Despite emerging effort to address sex differences in behaviors and disease models in rodents, how brain-wide functional connectivity (FC) patterns differ between male and female rats remains largely unknown. Here, we used resting-state functional magnetic resonance imaging (rsfMRI) to investigate regional and systems-level differences between female and male rats. Our data show that female rats display stronger hypothalamus connectivity, whereas male rats exhibit more prominent striatum-related connectivity. At the global scale, female rats demonstrate stronger segregation within the cortical and subcortical systems, while male rats display more prominent cortico-subcortical interactions, particularly between the cortex and striatum. Taken together, these data provide a comprehensive framework of sex differences in resting-state connectivity patterns in the awake rat brain, and offer a reference for studies aiming to reveal sex-related FC differences in different animal models of brain disorders.

Odor-evoked layer-specific fMRI activities in the awake mouse olfactory bulb

Awake rodent fMRI is increasingly common over the use of anesthesia since it permits behavioral paradigms and does not confound normal brain function or neurovascular coupling. It is well established that adequate acclimation to the loud fMRI environment and head fixation reduces stress in the rodents and allows for whole brain imaging with little contamination from motion. However, it is unknown whether high-resolution fMRI with increased susceptibility to motion and lower sensitivity can measure small, but spatially discrete, activations in awake mice. To examine this, we used contrast-enhanced cerebral blood volume-weighted (CBVw) fMRI in the mouse olfactory bulb for its enhanced sensitivity and neural specificity. We determined that activation patterns in the glomerular layer to four different odors were spatially distinct and were consistent with previously established histological patterns. In addition, odor-evoked laminar activations were greatest in superficial layers that decreased with laminar depth, similar to previous observations. Interestingly, the fMRI response strengths in the granule cell layer were greater in awake mice than our previous anesthetized rat studies, suggesting that feedback neural activities were intact with wakefulness. We finally determined that fMRI signal changes to repeated odor exposure (i.e., olfactory adaptation) attenuated relatively more in the feedback granule cell layer compared to the input glomerular layer, which is consistent with prior observations. We, therefore, conclude that high-resolution CBVw fMRI can measure odor-specific activation patterns and distinguish changes in laminar activity of head and body restrained awake mice.

Effects of repetitive transcranial magnetic stimulation and their underlying neural mechanisms evaluated with magnetic resonance imaging-based brain connectivity network analyses

Repetitive transcranial magnetic stimulation (rTMS) is a noninvasive brain modulation and rehabilitation technique used in patients with neuropsychiatric diseases. rTMS can structurally remodel or functionally induce activities of specific cortical regions and has developed to an important therapeutic method in such patients. Magnetic resonance imaging (MRI) provides brain data that can be used as an explanation tool for the neural mechanisms underlying rTMS effects; brain alterations related to different functions or structures may be reflected in changes in the interaction and influence of brain connections within intrinsic specific networks. In this review, we discuss the technical details of rTMS and the biological interpretation of brain networks identified with MRI analyses, comprehensively summarize the neurobiological effects in rTMS-modulated individuals, and elaborate on changes in the brain network in patients with various neuropsychiatric diseases receiving rehabilitation treatment with rTMS. We conclude that brain connectivity network analysis based on MRI can reflect alterations in functional and structural connectivity networks comprising adjacent and separated brain regions related to stimulation sites, thus reflecting the occurrence of intrinsic functional integration and neuroplasticity. Therefore, MRI is a valuable tool for understanding the neural mechanisms of rTMS and practically tailoring treatment plans for patients with neuropsychiatric diseases.

Intrinsic activity development unfolds along a sensorimotor-association cortical axis in youth

Animal studies of neurodevelopment have shown that recordings of intrinsic cortical activity evolve from synchronized and high amplitude to sparse and low amplitude as plasticity declines and the cortex matures. Leveraging resting-state functional MRI (fMRI) data from 1,033 youths (ages 8-23 years), we find that this stereotyped refinement of intrinsic activity occurs during human development and provides evidence for a cortical gradient of neurodevelopmental change. Declines in the amplitude of intrinsic fMRI activity were initiated heterochronously across regions and were coupled to the maturation of intracortical myelin, a developmental plasticity regulator. Spatiotemporal variability in regional developmental trajectories was organized along a hierarchical, sensorimotor-association cortical axis from ages 8 to 18. The sensorimotor-association axis furthermore captured variation in associations between youths' neighborhood environments and intrinsic fMRI activity; associations suggest that the effects of environmental disadvantage on the maturing brain diverge most across this axis during midadolescence. These results uncover a hierarchical neurodevelopmental axis and offer insight into the progression of cortical plasticity in humans.

Sex differences in resting-state functional networks in awake rats

Sex-related differences can be found in many brain disorders and psychophysiological traits, highlighting the importance to systematically understand the sex differences in brain function in humans and animal models. Despite emerging effort to address sex differences in behaviors and disease models in rodents, how brain-wide functional connectivity (FC) patterns differ between male and female rats remains largely unknown. Here we used resting-state functional magnetic resonance imaging (rsfMRI) to investigate regional and systems-level differences between female and male rats. Our data show that female rats display stronger hypothalamus connectivity, whereas male rats exhibit more prominent striatum-related connectivity. At the global scale, female rats demonstrate stronger segregation within the cortical and subcortical systems, while male rats display more prominent cortico-subcortical interactions, particularly between the cortex and striatum. Taken together, these data provide a comprehensive framework of sex differences in resting-state connectivity patterns in the awake rat brain, and offer a reference for studies aiming to reveal sex-related FC differences in different animal models of brain disorders.

Deriving causal relationships in resting-state functional connectivity using SSFO-based optogenetic fMRI

Objective.The brain network has been extensively studied as a collection of brain regions that are functionally inter-connected. However, the study of the causal relationship in brain-wide functional connectivity, which is critical to the brain function, remains challenging. We aim to examine the feasibility of using (SSFO)-based optogenetic functional magnetic resonance imaging to infer the causal relationship (i.e. directional information) in the brain network.Approach.We combined SSFO-based optogenetics with fMRI in a resting-state rodent model to study how a local increase of excitability affects brain-wide neural activity and resting-state functional connectivity (RSFC). We incorporated Pearson's correlation and partial correlation analyses in a graphic model to derive the directional information in connections exhibiting RSFC modulations.Main results. When the dentate gyrus (DG) was sensitized by SSFO activation, we found significantly changed activity and connectivity in several brain regions associated with the DG, particularly in the medial prefrontal cortex Our causal inference result shows an 84%-100% accuracy rate compared to the directional information based on anatomical tracing data.Significance.This study establishes a system to investigate the relationship between local region activity and RSFC modulation, and provides a way to analyze the underlying causal relationship between brain regions.

Brain activity studied with magnetic resonance imaging in awake rabbits

We reviewed fMRI experiments from our previous work in conscious rabbits, an experimental preparation that is advantageous for measuring brain activation that is free of anesthetic modulation and which can address questions in a variety of areas in sensory, cognitive, and pharmacological neuroscience research. Rabbits do not struggle or move for several hours while sitting with their heads restrained inside the horizontal bore of a magnet. This greatly reduces movement artifacts in magnetic resonance (MR) images in comparison to other experimental animals such as rodents, cats, and monkeys. We have been able to acquire high-resolution anatomic as well as functional images that are free of movement artifacts during several hours of restraint. Results from conscious rabbit fMRI studies with whisker stimulation are provided to illustrate the feasibility of this conscious animal model for functional MRI and the reproducibility of data gained with it.

Connecting the dots between cell populations, whole-brain activity, and behavior

Simultaneously manipulating and monitoring both microscopic and macroscopic brain activity in vivo and identifying the linkage to behavior are powerful tools in neuroscience research. These capabilities have been realized with the recent technical advances of optogenetics and its combination with fMRI, here termed "opto-fMRI." Opto-fMRI allows for targeted brain region-, cell-type-, or projection-specific manipulation and targeted Ca 2 + activity measurement to be linked with global brain signaling and behavior. We cover the history, technical advances, applications, and important considerations of opto-fMRI in anesthetized and awake rodents and the future directions of the combined techniques in neuroscience and neuroimaging.

Beyond correlation: functional OPTO-MAgnetic Integration Concept (OPTOMAIC) to reveal the brain-wide signature of local neuronal signals-of-interest

Significance: Due to the vascular origin of the fMRI signal, the spatiotemporally precise interpretation of the blood oxygen level-dependent (BOLD) response as brain-wide correlate of neuronal activity is limited. Optical fiber-based neuronal calcium recordings provide a specific and temporally highly resolved signal yet lacking brain-wide coverage. The cross-modal integration of both modalities holds the potential for unique synergies. Aim: The OPTO-MAgnetic Integration Concept (OPTOMAIC) extracts the very fraction of the BOLD response that reacts to optically recorded neuronal signals-of-interest. Approach and Results: First, OPTOMAIC identifies the trials containing neuronal signal-of-interest (SoI) in the optical recordings. The long duration of the BOLD response is considered by calculating and thresholding neuronal interevent intervals. The resulting optical regression vector is probed for a positive BOLD response with single-event and single-voxel resolution, generating a BOLD response matrix containing only those events and voxels with both a neuronal SoI and a positive fMRI signal increase. Last, the onset of the BOLD response is being quantified, representing the section of the BOLD response most reliably reporting at least components of the neuronal signal. Conclusions: The seven OPTOMAIC steps result in a brain-wide BOLD signature reflecting the underlying neuronal SoI with utmost cross-modal integration depth and taking full advantage of the specific strengths of each method.