Probing the brain with molecular fMRI

Elucidating hemodynamics and neuro-glio-vascular signaling using rodent fMRI

Despite extensive functional mapping studies using rodent functional magnetic resonance imaging (fMRI), interpreting the fMRI signals in relation to their neuronal origins remains challenging due to the hemodynamic nature of the response. Ultra high-resolution rodent fMRI, beyond merely enhancing spatial specificity, has revealed vessel-specific hemodynamic responses, highlighting the distinct contributions of intracortical arterioles and venules to fMRI signals. This 'single-vessel' fMRI approach shifts the paradigm of rodent fMRI, enabling its integration with other neuroimaging modalities to investigate neuro-glio-vascular (NGV) signaling underlying a variety of brain dynamics. Here, we review the emerging trend of combining multimodal fMRI with opto/chemogenetic neuromodulation and genetically encoded biosensors for cellular and circuit-specific recording, offering unprecedented opportunities for cross-scale brain dynamic mapping in rodent models.

Direct observation of NMR transverse relaxation in nanopatterned clusters of iron oxide particles

PURPOSE

We aim to verify predictions showing T2 relaxation rate of nanoparticle clusters and its dependence on spacing, size, geometry, and pulse sequence.

METHODS

We performed a laboratory validation study using nanopatterned arrays of iron oxide nanoparticles to precisely control cluster geometry and image diverse samples using a 4.7T MRI scanner with a T2 -weighted fast spin-echo multislice sequence. We applied denoising and normalization to regions of interest and estimated relative R2 for each relevant nanoparticle array or nanocluster array. We determined significance using an unpaired two-tailed t-test or one-way analysis of variance and performed curve fitting.

RESULTS

We measured a density-dependent T2 effect (p = 8.9976 × 10-20 , one-way analysis of variance) and insignificant effect of cluster anisotropy (p = 0.5924, unpaired t-test) on T2 relaxation. We found negative quadratic relationships (-0.0045[log τD ]2 -0.0655[log τD ]-2.7800) for single nanoparticles of varying sizes and for clusters (-0.0045[log τD ]2 -0.0827[log τD ]-2.3249) for diffusional correlation time τD  = rp 2 /D. Clusters show positive quadratic relationships for large (3.8615 × 10-6 [dpp /rp ]2 -9.3853 × 10-5 [dpp /rp ]-2.0393) and exponential relationships for small (-2.0050[dpp /rp ]0.0010 ) clusters. Calculated R2 peak values also align well with in silico predictions (7.85 × 10-4  ms compared with 1.47 × 10-4 , 4.23 × 10-4 , and 5.02 × 10-4  ms for single iron oxide nanoparticles, 7.88 × 10-4  ms compared with 5.24 × 10-4  ms for nanoparticle clusters).

CONCLUSION

Our verification affirms longstanding in silico predictions and demonstrates aggregation-dependent behavior in agreement with previous Monte Carlo simulation studies.

Mapping light distribution in tissue by using MRI-detectable photosensitive liposomes

Characterizing sources and targets of illumination in living tissue is challenging. Here we show that spatial distributions of light in tissue can be mapped by using magnetic resonance imaging (MRI) in the presence of photosensitive nanoparticle probes. Each probe consists of a reservoir of paramagnetic molecules enclosed by a liposomal membrane incorporating photosensitive lipids. Incident light causes the photoisomerization of the lipids and alters hydrodynamic exchange across the membrane, thereby affecting longitudinal relaxation-weighted contrast in MRI. We injected the nanoparticles into the brains of live rats and used MRI to map responses to illumination profiles characteristic of widely used applications of photostimulation, photometry and phototherapy. The responses deviated from simple photon propagation models and revealed signatures of light scattering and nonlinear responsiveness. Paramagnetic liposomal nanoparticles may enable MRI to map a broad range of optical phenomena in deep tissue and other opaque environments.

Simultaneous Functional Magnetic Resonance and Optoacoustic Imaging of Brain-Wide Sensory Responses in Mice

Functional magnetic resonance imaging (fMRI) has massively contributed to the understanding of mammalian brain function. However, the origin and interpretation of the blood oxygen level-dependent (BOLD) signals retrieved by fMRI remain highly disputed. This article reports on the development of a fully hybridized system enabling concurrent functional magnetic resonance optoacoustic tomography (MROT) measurements of stimulus-evoked brain-wide sensory responses in mice. The highly complementary angiographic and soft tissue contrasts of both modalities along with simultaneous multi-parametric readings of stimulus-evoked hemodynamic responses are leveraged in order to establish unequivocal links between the various counteracting physiological and metabolic processes in the brain. The results indicate that the BOLD signals are highly correlated, both spatially and temporally, with the total hemoglobin readings resolved with volumetric multi-spectral optoacoustic tomography. Furthermore, the differential oxygenated and deoxygenated hemoglobin optoacoustic readings exhibit superior sensitivity as compared to the BOLD signals when detecting stimulus-evoked hemodynamic responses. The fully hybridized MROT approach greatly expands the neuroimaging toolset to comprehensively study neurovascular and neurometabolic coupling mechanisms and related diseases.

Probing nitric oxide signaling using molecular MRI

Wide field measurements of nitric oxide (NO) signaling could help understand and diagnose the many physiological processes in which NO plays a key role. Magnetic resonance imaging (MRI) can support particularly powerful approaches for this purpose if equipped with molecular probes sensitized to NO and NO-associated targets. In this review, we discuss the development of MRI-detectable probes that could enable studies of nitrergic signaling in animals and potentially human subjects. Major families of probes include contrast agents designed to capture and report integrated NO levels directly, as well as molecules that respond to or emulate the activity of nitric oxide synthase enzymes. For each group, we outline the relevant molecular mechanisms and discuss results that have been obtained in vitro and in animals. The most promising in vivo data described to date have been acquired using NO capture-based relaxation agents and using engineered nitric oxide synthases that provide hemodynamic readouts of NO signaling pathway activation. These advances establish a beachhead for ongoing efforts to improve the sensitivity, specificity, and clinical applicability of NO-related molecular MRI technology.

In-cell NMR: Why and how?

NMR spectroscopy has been applied to cells and tissues analysis since its beginnings, as early as 1950. We have attempted to gather here in a didactic fashion the broad diversity of data and ideas that emerged from NMR investigations on living cells. Covering a large proportion of the periodic table, NMR spectroscopy permits scrutiny of a great variety of atomic nuclei in all living organisms non-invasively. It has thus provided quantitative information on cellular atoms and their chemical environment, dynamics, or interactions. We will show that NMR studies have generated valuable knowledge on a vast array of cellular molecules and events, from water, salts, metabolites, cell walls, proteins, nucleic acids, drugs and drug targets, to pH, redox equilibria and chemical reactions. The characterization of such a multitude of objects at the atomic scale has thus shaped our mental representation of cellular life at multiple levels, together with major techniques like mass-spectrometry or microscopies. NMR studies on cells has accompanied the developments of MRI and metabolomics, and various subfields have flourished, coined with appealing names: fluxomics, foodomics, MRI and MRS (i.e. imaging and localized spectroscopy of living tissues, respectively), whole-cell NMR, on-cell ligand-based NMR, systems NMR, cellular structural biology, in-cell NMR… All these have not grown separately, but rather by reinforcing each other like a braided trunk. Hence, we try here to provide an analytical account of a large ensemble of intricately linked approaches, whose integration has been and will be key to their success. We present extensive overviews, firstly on the various types of information provided by NMR in a cellular environment (the "why", oriented towards a broad readership), and secondly on the employed NMR techniques and setups (the "how", where we discuss the past, current and future methods). Each subsection is constructed as a historical anthology, showing how the intrinsic properties of NMR spectroscopy and its developments structured the accessible knowledge on cellular phenomena. Using this systematic approach, we sought i) to make this review accessible to the broadest audience and ii) to highlight some early techniques that may find renewed interest. Finally, we present a brief discussion on what may be potential and desirable developments in the context of integrative studies in biology.

Reporter Genes for Brain Imaging Using MRI, SPECT and PET

The use of molecular imaging technologies for brain imaging can not only play an important supporting role in disease diagnosis and treatment but can also be used to deeply study brain functions. Recently, with the support of reporter gene technology, optical imaging has achieved a breakthrough in brain function studies at the molecular level. Reporter gene technology based on traditional clinical imaging modalities is also expanding. By benefiting from the deeper imaging depths and wider imaging ranges now possible, these methods have led to breakthroughs in preclinical and clinical research. This article focuses on the applications of magnetic resonance imaging (MRI), single-photon emission computed tomography (SPECT), and positron emission tomography (PET) reporter gene technologies for use in brain imaging. The tracking of cell therapies and gene therapies is the most successful and widely used application of these techniques. Meanwhile, breakthroughs have been achieved in the research and development of reporter genes and their imaging probe pairs with respect to brain function research. This paper introduces the imaging principles and classifications of the reporter gene technologies of these imaging modalities, lists the relevant brain imaging applications, reviews their characteristics, and discusses the opportunities and challenges faced by clinical imaging modalities based on reporter gene technology. The conclusion is provided in the last section.

Pushing the frontiers: tools for monitoring neurotransmitters and neuromodulators

Neurotransmitters and neuromodulators have a wide range of key roles throughout the nervous system. However, their dynamics in both health and disease have been challenging to assess, owing to the lack of in vivo tools to track them with high spatiotemporal resolution. Thus, developing a platform that enables minimally invasive, large-scale and long-term monitoring of neurotransmitters and neuromodulators with high sensitivity, high molecular specificity and high spatiotemporal resolution has been essential. Here, we review the methods available for monitoring the dynamics of neurotransmitters and neuromodulators. Following a brief summary of non-genetically encoded methods, we focus on recent developments in genetically encoded fluorescent indicators, highlighting how these novel indicators have facilitated advances in our understanding of the functional roles of neurotransmitters and neuromodulators in the nervous system. These studies present a promising outlook for the future development and use of tools to monitor neurotransmitters and neuromodulators.

Molecular fMRI of neurochemical signaling

Magnetic resonance imaging (MRI) is the most widely applied technique for brain-wide measurement of neural function in humans and animals. In conventional functional MRI (fMRI), brain signaling is detected indirectly, via localized activity-dependent changes in regional blood flow, oxygenation, and volume, to which MRI contrast can be readily sensitized. Although such hemodynamic fMRI methods are powerful tools for analysis of brain activity, they lack specificity for the many molecules and cell types that play functionally distinct roles in neural processing. A suite of techniques collectively known to as "molecular fMRI," addresses this limitation by permitting MRI-based detection of specific molecular processes in deep brain tissue. This review discusses how molecular fMRI is coming to be used in the study of neurochemical dynamics that mediate intercellular communication in the brain. Neurochemical molecular fMRI is a potentially powerful approach for mechanistic analysis of brain-wide function, but the techniques are still in early stages of development. Here we provide an overview of the major advances and results that have been achieved to date, as well as directions for further development.

Emerging imaging methods to study whole-brain function in rodent models

In the past decade, the idea that single populations of neurons support cognition and behavior has gradually given way to the realization that connectivity matters and that complex behavior results from interactions between remote yet anatomically connected areas that form specialized networks. In parallel, innovation in brain imaging techniques has led to the availability of a broad set of imaging tools to characterize the functional organization of complex networks. However, each of these tools poses significant technical challenges and faces limitations, which require careful consideration of their underlying anatomical, physiological, and physical specificity. In this review, we focus on emerging methods for measuring spontaneous or evoked activity in the brain. We discuss methods that can measure large-scale brain activity (directly or indirectly) with a relatively high temporal resolution, from milliseconds to seconds. We further focus on methods designed for studying the mammalian brain in preclinical models, specifically in mice and rats. This field has seen a great deal of innovation in recent years, facilitated by concomitant innovation in gene-editing techniques and the possibility of more invasive recordings. This review aims to give an overview of currently available preclinical imaging methods and an outlook on future developments. This information is suitable for educational purposes and for assisting scientists in choosing the appropriate method for their own research question.

Calcium-responsive contrast agents for functional magnetic resonance imaging

Calcium ions represent one of the key second messengers accompanying neural activity and synaptic signaling. Accordingly, dynamic imaging of calcium fluctuations in living organisms represents a cornerstone technology for discovering neural mechanisms that underlie memory, determine behavior, and modulate emotional states as well as how these mechanisms are perturbed by neurological disease and brain injury. While optical technologies are well established for high resolution imaging of calcium dynamics, physical limits on light penetration hinder their application for whole-brain imaging in intact vertebrates. Unlike optics, magnetic resonance imaging (MRI) enables noninvasive large-scale imaging across vertebrates of all sizes. This has motivated the development of several sensors that leverage innovative physicochemical mechanisms to sensitize MRI contrast to intracellular and extracellular changes in calcium. Here, we review the current state-of-the-art in MRI-based calcium sensors, focusing on fundamental aspects of sensor performance, in vivo applications, and challenges related to sensitivity. We also highlight how innovations at the intersection of reporter gene technology and gene delivery open potential opportunities for mapping calcium activity in genetically targeted cells, complementing the benefits of small molecule probes and nanoparticle sensors.

Emerging Frontier of Peripheral Nerve and Organ Interfaces

The development of new tools to interface with the nervous system, empowered by advances in electronics and materials science, has transformed neuroscience and is informing therapies for neurological and mental conditions. Although the vast majority of neural engineering research has focused on advancing tools to study the brain, understanding the peripheral nervous system and other organs can similarly benefit from these technologies. To realize this vision, the neural interface technologies need to address the biophysical, mechanical, and chemical challenges posed by the peripheral nerves and organs. In this Perspective, we discuss design considerations and recent technological advances to modulate electrical signaling outside the central nervous system. The innovations in bioelectronics borne out of interdisciplinary collaborations between biologists and physical scientists may not only advance fundamental study of peripheral (neuro)physiology but also empower clinical interventions for conditions including neurological, gastrointestinal, and immune dysfunction.

Imaging Neurotransmitter and Neuromodulator Dynamics In Vivo with Genetically Encoded Indicators

The actions of neuromodulation are thought to mediate the ability of the mammalian brain to dynamically adjust its functional state in response to changes in the environment. Altered neurotransmitter (NT) and neuromodulator (NM) signaling is central to the pathogenesis or treatment of many human neurological and psychiatric disorders, including Parkinson's disease, schizophrenia, depression, and addiction. To reveal the precise mechanisms by which these neurochemicals regulate healthy and diseased neural circuitry, one needs to measure their spatiotemporal dynamics in the living brain with great precision. Here, we discuss recent development, optimization, and applications of optical approaches to measure the spatial and temporal profiles of NT and NM release in the brain using genetically encoded sensors for in vivo studies.

Ultrasound Technologies for Imaging and Modulating Neural Activity

Visualizing and perturbing neural activity on a brain-wide scale in model animals and humans is a major goal of neuroscience technology development. Established electrical and optical techniques typically break down at this scale due to inherent physical limitations. In contrast, ultrasound readily permeates the brain, and in some cases the skull, and interacts with tissue with a fundamental resolution on the order of 100 μm and 1 ms. This basic ability has motivated major efforts to harness ultrasound as a modality for large-scale brain imaging and modulation. These efforts have resulted in already-useful neuroscience tools, including high-resolution hemodynamic functional imaging, focused ultrasound neuromodulation, and local drug delivery. Furthermore, recent breakthroughs promise to connect ultrasound to neurons at the genetic level for biomolecular imaging and sonogenetic control. In this article, we review the state of the art and ongoing developments in ultrasonic neurotechnology, building from fundamental principles to current utility, open questions, and future potential.

Linking the nature and functions of sleep: insights from multimodal imaging of the sleeping brain

Sleep and wakefulness are traditionally considered as two mutually exclusive states with contrasting behavioural manifestations and complementary neurobiological functions. However, the discoveries of local sleep in global wakefulness and local wakefulness in global sleep have challenged this classical view and raised questions about the nature and functions of sleep. Here, we review the contributions from recent multimodal imaging studies of human sleep towards understanding the relationship between the nature and functions of sleep. Through simultaneous tracking of brain state and mapping of brain activity, these studies revealed that the sleeping brain can carry out covert cognitive processing that was thought to be wake-specific (wake-like function in the sleeping brain). Conversely, the awake brain can perform housekeeping functions through local sleep of neural populations (sleep-like function in the awake brain). We discuss how the blurred boundary between sleep and wakefulness highlights the need to radically rethink the definition of brain states, and how the recently discovered fMRI signatures of global and local sleep can help to address these outstanding questions.

Target-responsive vasoactive probes for ultrasensitive molecular imaging

The ability to monitor molecules volumetrically throughout the body could provide valuable biomarkers for studies of healthy function and disease, but noninvasive detection of molecular targets in living subjects often suffers from poor sensitivity or selectivity. Here we describe a family of potent imaging probes that can be activated by molecules of interest in deep tissue, providing a basis for mapping nanomolar-scale analytes without the radiation or heavy metal content associated with traditional molecular imaging agents. The probes are reversibly caged vasodilators that induce responses detectable by hemodynamic imaging; they are constructed by combining vasoactive peptides with synthetic chemical appendages and protein blocking domains. We use this architecture to create ultrasensitive biotin-responsive imaging agents, which we apply for wide-field mapping of targets in rat brains using functional magnetic resonance imaging. We also adapt the sensor design for detecting the neurotransmitter dopamine, illustrating versatility of this approach for addressing biologically important molecules.

The impact of neuroimaging advancement on neurocognitive evaluation in pediatric brain tumor survivors: A review

Pediatric brain tumors are a type of tumors that are commonly present in children and young adults. With the improvement of treatment, the quality of life, especially the cognitive functioning, is gaining increasingly more attention. Apart from cognitive evaluations, neuroimaging studies begin to play an important part in neurocognitive functioning investigation. In this way, the brain tissue changes caused by tumor variables (including tumor location and tumor size) and treatment variables (including surgery, chemotherapy and radiotherapy) can be detected by neuroimaging. Recent advancement of neuroimaging techniques, such as functional-MRI (fMRI) and diffusion tensor imaging (DTI), made great contributions to understanding cognitive dysfunction and quantifying the effects of tumor variables and treatment variables. In recent years, laminar-fMRI provided a potentially valuable tool for examining the exact origins of neural activity and cognitive function. On the other hand, molecular fMRI might guide diagnosis and treatment of brain disease in the future by using new biomarkers, and DTI can detect white matter changes and obtain some anatomically specific information.

Early detection and monitoring of cerebral ischemia using calcium-responsive MRI probes

Cerebral ischemia is one of the leading causes of mortality and disability in infants and adults and its timely diagnosis is essential for an efficient treatment. We present a methodology for fast detection and real-time monitoring of fluctuations of calcium ions associated with focal ischemia using a molecular functional MRI approach. We used a dinuclear paramagnetic gadolinium(III) complex chelate that changes MR image contrast through its reversible interaction with extracellular calcium ions, while applying a remote transient middle cerebral artery occlusion as a model for ischemic stroke. Our method sensitively recognizes the onset and follows the dynamics of the ischemic core and penumbra with submillimeter spatial and second-scale temporal resolution, thus paving the way for noninvasive monitoring and development of targeted treatment strategies for cerebral ischemia.

Neurotransmitter-Responsive Nanosensors for T2-Weighted Magnetic Resonance Imaging

Neurotransmitter-sensitive contrast agents for magnetic resonance imaging (MRI) have recently been used for mapping signaling dynamics in live animal brains, but paramagnetic sensors for T₁-weighted MRI are usually effective only at micromolar concentrations that themselves perturb neurochemistry. Here we present an alternative molecular architecture for detecting neurotransmitters, using superparamagnetic iron oxide nanoparticles conjugated to tethered neurotransmitter analogs and engineered neurotransmitter binding proteins. Interactions between the nanoparticle conjugates result in clustering that is reversibly disrupted in the presence of neurotransmitter analytes, thus altering T₂-weighted MRI signals. We demonstrate this principle using tethered dopamine and serotonin analogs, together with proteins selected for their ability to competitively bind either the analogs or the neurotransmitters themselves. Corresponding sensors for dopamine and serotonin exhibit target-selective relaxivity changes of up to 20%, while also operating below endogenous neurotransmitter concentrations. Semisynthetic magnetic particle sensors thus represent a promising path for minimally perturbative studies of neurochemical analytes.

MRI-guided robotic arm drives optogenetic fMRI with concurrent Ca2+ recording

Optical fiber-mediated optogenetic activation and neuronal Ca2+ recording in combination with fMRI provide a multi-modal fMRI platform. Here, we developed an MRI-guided robotic arm (MgRA) as a flexible positioning system with high precision to real-time assist optical fiber brain intervention for multi-modal animal fMRI. Besides the ex vivo precision evaluation, we present the highly reliable brain activity patterns in the projected basal forebrain regions upon MgRA-driven optogenetic stimulation in the lateral hypothalamus. Also, we show the step-wise optical fiber targeting thalamic nuclei and map the region-specific functional connectivity with whole-brain fMRI accompanied by simultaneous calcium recordings to specify its circuit-specificity. The MgRA also guides the real-time microinjection to specific deep brain nuclei, which is demonstrated by an Mn-enhanced MRI method. The MgRA represents a clear advantage over the standard stereotaxic-based fiber implantation and opens a broad avenue to investigate the circuit-specific functional brain mapping with the multi-modal fMRI platform.

Sensing intracellular calcium ions using a manganese-based MRI contrast agent

Calcium ions are essential to signal transduction in virtually all cells, where they coordinate processes ranging from embryogenesis to neural function. Although optical probes for intracellular calcium imaging have been available for decades, the development of probes for noninvasive detection of intracellular calcium signaling in deep tissue and intact organisms remains a challenge. To address this problem, we synthesized a manganese-based paramagnetic contrast agent, ManICS1-AM, designed to permeate cells, undergo esterase cleavage, and allow intracellular calcium levels to be monitored by magnetic resonance imaging (MRI). Cells loaded with ManICS1-AM show changes in MRI contrast when stimulated with pharmacological agents or optogenetic tools; responses directly parallel the signals obtained using fluorescent calcium indicators. Introduction of ManICS1-AM into rodent brains furthermore permits MRI-based measurement of neural activation in optically inaccessible brain regions. These results thus validate ManICS1-AM as a calcium sensor compatible with the extensive penetration depth and field of view afforded by MRI.

Multi-Modal Nano Particle Labeling of Neurons

The development of imaging methodologies for single cell measurements over extended timescales of up to weeks, in the intact animal, will depend on signal strength, stability, validity and specificity of labeling. Whereas light-microscopy can achieve these with genetically-encoded probes or dyes, this modality does not allow mesoscale imaging of entire intact tissues. Non-invasive imaging techniques, such as magnetic resonance imaging (MRI), outperform light microscopy in field of view and depth of imaging, but do not offer cellular resolution and specificity, suffer from low signal-to-noise ratio and, in some instances, low temporal resolution. In addition, the origins of the signals measured by MRI are either indirect to the process of interest or hard to validate. It is therefore highly warranted to find means to enhance MRI signals to allow increases in resolution and cellular-specificity. To this end, cell-selective bi-functional magneto-fluorescent contrast agents can provide an elegant solution. Fluorescence provides means for identification of labeled cells and particles location after MRI acquisition, and it can be used to facilitate the design of cell-selective labeling of defined targets. Here we briefly review recent available designs of magneto-fluorescent markers and elaborate on key differences between them with respect to durability and relevant cellular highlighting approaches. We further focus on the potential of intracellular labeling and basic functional sensing MRI, with assays that enable imaging cells at microscopic and mesoscopic scales. Finally, we illustrate the qualities and limitations of the available imaging markers and discuss prospects for in vivo neural imaging and large-scale brain mapping.