Deep-tissue photoacoustic tomography of a genetically encoded near-infrared fluorescent probe

NRhFluors: Quantitative Revealing the Interaction between Protein Homeostasis and Mitochondria Dysfunction via Fluorescence Lifetime Imaging

Degenerative diseases are closely related to the changes of protein conformation beyond the steady state. The development of feasible tools for quantitative detection of changes in the cellular environment is crucial for investigating the process of protein conformational variations. Here, we have developed a near-infrared AIE probe based on the rhodamine fluorophore, which exhibits dual responses of fluorescence intensity and lifetime to local viscosity changes. Notably, computational analysis reveals that NRhFluors fluorescence activation is due to inhibition of the RACI mechanism in viscous environment. In the chemical regulation of rhodamine fluorophores, we found that variations of electron density distribution can effectively regulate CI states and achieve fluorescence sensitivity of NRhFluors. In addition, combined with the AggTag method, the lifetime of probe A9-Halo exhibits a positive correlation with viscosity changes. This analytical capacity allows us to quantitatively monitor protein conformational changes using fluorescence lifetime imaging (FLIM) and demonstrate that mitochondrial dysfunction leads to reduced protein expression in HEK293 cells. In summary, this work developed a set of near-infrared AIE probes activated by the RACI mechanism, which can quantitatively detect cell viscosity and protein aggregation formation, providing a versatile tool for exploring disease-related biological processes and therapeutic approaches.

Biomedical Photoacoustic Imaging for Molecular Detection and Disease Diagnosis: "Always-On" and "Turn-On" Probes

Photoacoustic (PA) imaging is a nonionizing, noninvasive imaging technique that combines optical and ultrasonic imaging modalities to provide images with excellent contrast, spatial resolution, and penetration depth. Exogenous PA contrast agents are created to increase the sensitivity and specificity of PA imaging and to offer diagnostic information for illnesses. The existing PA contrast agents are categorized into two groups in this review: "always-on" and "turn-on," based on their ability to be triggered by target molecules. The present state of these probes, their merits and limitations, and their future development, is explored.

Segmentation and Quantitative Analysis of Photoacoustic Imaging: A Review

Photoacoustic imaging is an emerging biomedical imaging technique that combines optical contrast and ultrasound resolution to create unprecedented light absorption contrast in deep tissue. Thanks to its fusional imaging advantages, photoacoustic imaging can provide multiple structural and functional insights into biological tissues such as blood vasculatures and tumors and monitor the kinetic movements of hemoglobin and lipids. To better visualize and analyze the regions of interest, segmentation and quantitative analyses were used to extract several biological factors, such as the intensity level changes, diameter, and tortuosity of the tissues. Over the past 10 years, classical segmentation methods and advances in deep learning approaches have been utilized in research investigations. In this review, we provide a comprehensive review of segmentation and quantitative methods that have been developed to process photoacoustic imaging in preclinical and clinical experiments. We focus on the parametric reliability of quantitative analysis for semantic and instance-level segmentation. We also introduce the similarities and alternatives of deep learning models in qualitative measurements using classical segmentation methods for photoacoustic imaging.

Photomedicine based on heme-derived compounds

Photoimaging and phototherapy have become major platforms for the diagnosis and treatment of various health complications. These applications require a photosensitizer (PS) that is capable of absorbing light from a source and converting it into other energy forms for detection and therapy. While synthetic inorganic materials such as quantum dots and gold nanorods have been widely explored for their medical diagnosis and photodynamic (PDT) and photothermal (PTT) therapy capabilities, translation of these technologies has lagged, primarily owing to potential cytotoxicity and immunogenicity issues. Of the various photoreactive molecules, the naturally occurring endogenous compound heme, a constituent of red blood cells, and its derivatives, porphyrin, biliverdin and bilirubin, have shown immense potential as noteworthy candidates for clinically translatable photoreactive agents, as evidenced by previous reports. While porphyrin-based photomedicines have attracted significant attention and are well documented, research on photomedicines based on two other heme-derived compounds, biliverdin and bilirubin, has been relatively lacking. In this review, we summarize the unique photoproperties of heme-derived compounds and outline recent efforts to use them in biomedical imaging and phototherapy applications.

Multiscale Photoacoustic Tomography of a Genetically Encoded Near-Infrared FRET Biosensor

Photoacoustic tomography (PAT) with genetically encoded near-infrared probes enables visualization of specific cell populations in vivo at high resolution deeply in biological tissues. However, because of a lack of proper probes, PAT of cellular dynamics remains unexplored. Here, the authors report a near-infrared Forster resonance energy transfer (FRET) biosensor based on a miRFP670-iRFP720 pair of the near-infrared fluorescent proteins, which enables dynamic functional imaging of active biological processes in deep tissues. By photoacoustically detecting the changes in the optical absorption of the miRFP670 FRET-donor, they monitored cell apoptosis in deep tissue at high spatiotemporal resolution using PAT. Specifically, they detected apoptosis in single cells at a resolution of ≈3 µm in a mouse ear tumor, and in deep brain tumors (>3 mm beneath the scalp) of living mice at a spatial resolution of ≈150 µm with a 20 Hz frame rate. These results open the way for high-resolution photoacoustic imaging of dynamic biological processes in deep tissues using NIR biosensors and PAT.

New contrast agents for photoacoustic imaging and theranostics: Recent 5-year overview on phthalocyanine/naphthalocyanine-based nanoparticles

The phthalocyanine (Pc) and naphthalocyanine (Nc) nanoagents have drawn much attention as contrast agents for photoacoustic (PA) imaging due to their large extinction coefficients and long absorption wavelengths in the near-infrared region. Many investigations have been conducted to enhance Pc/Ncs' photophysical properties and address their poor solubility in an aqueous solution. Many diverse strategies have been adopted, including centric metal chelation, structure modification, and peripheral substitution. This review highlights recent advances on Pc/Nc-based PA agents and their extended use for multiplexed biomedical imaging, multimodal diagnostic imaging, and image-guided phototherapy.

A practical guide to photoswitching optoacoustics tomography

Photochromic proteins and photoswitching optoacoustics (OA) are a promising combination, that allows OA imaging of even small numbers of cells in whole live animals and thus can facilitate a more wide-spread use of OA in life-science and preclinical research. The concept relies on exploiting the modulation achieved by the photoswitching to discriminate the agents' signal from the non-modulating background. Here we share our analysis approaches that can be readily used on data generated with commercial OA tomography imaging instrumentation allowing-depending on the used photoswitching agent and sample-routine visualizations of as little as several hundreds of transgene labeled cells per imaging volume in the live animal.

Alkaline phosphatase-triggered self-assembly of near-infrared nanoparticles for the enhanced photoacoustic imaging of tumors

In this chapter, we discuss the need for the development of enzyme-activatable probes in the field of tumor-targeted photoacoustic (PA) imaging, then we give a brief description of the innovation of designing alkaline phosphatase (ALP)-activatable probes for PA imaging. After that, we provide detailed protocols for the syntheses and characterizations of a near-infrared photoacoustic imaging probe, 1P, developed in our research group. With this tool, 1P could form nanoparticles 1-NPs under the catalysis of ALP and thus could be used to enhance PA imaging both in vitro and in vivo.

Recent Advances in Photoacoustic Tomography

Photoacoustic tomography (PAT) that integrates the molecular contrast of optical imaging with the high spatial resolution of ultrasound imaging in deep tissue has widespread applications in basic biological science, preclinical research, and clinical trials. Recently, tremendous progress has been made in PAT regarding technical innovations, preclinical applications, and clinical translations. Here, we selectively review the recent progresses and advances in PAT, including the development of advanced PAT systems for small-animal and human imaging, newly engineered optical probes for molecular imaging, broad-spectrum PAT for label-free imaging of biological tissues, high-throughput snapshot photoacoustic topography, and integration of machine learning for image reconstruction and processing. We envision that PAT will have further technical developments and more impactful applications in biomedicine.

Photoacoustic Neuroimaging - Perspectives on a Maturing Imaging Technique and its Applications in Neuroscience

A prominent goal of neuroscience is to improve our understanding of how brain structure and activity interact to produce perception, emotion, behavior, and cognition. The brain's network activity is inherently organized in distinct spatiotemporal patterns that span scales from nanometer-sized synapses to meter-long nerve fibers and millisecond intervals between electrical signals to decades of memory storage. There is currently no single imaging method that alone can provide all the relevant information, but intelligent combinations of complementary techniques can be effective. Here, we thus present the latest advances in biomedical and biological engineering on photoacoustic neuroimaging in the context of complementary imaging techniques. A particular focus is placed on recent advances in whole-brain photoacoustic imaging in rodent models and its influential role in bridging the gap between fluorescence microscopy and more non-invasive techniques such as magnetic resonance imaging (MRI). We consider current strategies to address persistent challenges, particularly in developing molecular contrast agents, and conclude with an overview of potential future directions for photoacoustic neuroimaging to provide deeper insights into healthy and pathological brain processes.

iRFP (near-infrared fluorescent protein) imaging of subcutaneous and deep tissue tumours in mice highlights differences between imaging platforms

BACKGROUND

In vivo imaging using fluorescence is used in cancer biology for the detection, measurement and monitoring of tumours. This can be achieved with the expression of fluorescent proteins such as iRFP, which emits light at a wavelength less attenuated in biological tissues compared to light emitted by other fluorescent proteins such as GFP or RFP. Imaging platforms capable of detecting fluorescent tumours in small animals have been developed but studies comparing the performance of these platforms are scarce.

RESULTS

Through access to three platforms from Xenogen, Bruker and Li-Cor, we compared their ability to detect iRFP-expressing subcutaneous tumours as well as tumours localised deeper within the body of female NSG mice. Each platform was paired with proprietary software for image analyse, but the output depends on subjective decisions from the user. To more objectively compare platforms, we developed an 'in house' software-based approach which results in lower measured variability between mice.

CONCLUSIONS

Our comparisons showed that all three platforms allowed for reliable detection and monitoring of subcutaneous iRFP tumour growth. The biggest differences between platforms became apparent when imaging deeper tumours with the Li-Cor platform detecting most tumours and showing the highest dynamic range.

Photoacoustic Tomography Opening New Paradigms in Biomedical Imaging

After the emergence of the ultrasound, X-ray CT, PET, and MRI, photoacoustic tomography (PAT) is now in the phase of its exponential growth, with its expected full maturation being another form of mainstream clinical imaging modality. By combining the high contrast benefit of optical imaging and the high-resolution deep imaging capability of ultrasound, PAT can provide unprecedented anatomical image contrasts at clinically relevant depths as well as enable the use of a variety of functional and molecular imaging information, which is not possible with conventional imaging modalities. With these strengths, PAT has achieved numerous breakthroughs in various biomedical applications and also provided new technical platforms that may be able to resolve unmet issues in clinics. In this chapter, we provide an overview of the development of PAT technology for several major biomedical applications and provide an approximate projection of the future of PAT.

Sound Out the Deep Colors: Photoacoustic Molecular Imaging at New Depths

Photoacoustic tomography (PAT) has become increasingly popular for molecular imaging due to its unique optical absorption contrast, high spatial resolution, deep imaging depth, and high imaging speed. Yet, the strong optical attenuation of biological tissues has traditionally prevented PAT from penetrating more than a few centimeters and limited its application for studying deeply seated targets. A variety of PAT technologies have been developed to extend the imaging depth, including employing deep-penetrating microwaves and X-ray photons as excitation sources, delivering the light to the inside of the organ, reshaping the light wavefront to better focus into scattering medium, as well as improving the sensitivity of ultrasonic transducers. At the same time, novel optical fluence mapping algorithms and image reconstruction methods have been developed to improve the quantitative accuracy of PAT, which is crucial to recover weak molecular signals at larger depths. The development of highly-absorbing near-infrared PA molecular probes has also flourished to provide high sensitivity and specificity in studying cellular processes. This review aims to introduce the recent developments in deep PA molecular imaging, including novel imaging systems, image processing methods and molecular probes, as well as their representative biomedical applications. Existing challenges and future directions are also discussed.

Rhodamine Conjugated Gelatin Methacryloyl Nanoparticles for Stable Cell Imaging

Fluorescent nanomaterials have been widely used in biological imaging due to their selectivity, sensitivity, and noninvasive nature. These characteristics make the materials suitable for real-time and in situ imaging. However, further development of highly biocompatible nanosystems with long-lasting fluorescent intensity and photostability is needed for advanced bioimaging. We have used electrospraying to generate gelatin methacryloyl (GelMA)-based fluorescent nanoparticles (NPs) with chemically conjugated rhodamine B (RB). The extent of conjugation can be controlled by varying the mass ratio of RB and GelMA precursors to obtain RB-conjugated GelMA (RB-GelMA) NPs with optimal fluorescent properties and particle size. These NPs exhibited superior biocompatibility when compared with pure RB in in vitro cell viability and proliferation assays using multiple cell types. Moreover, RB-GelMA NPs showed enhanced cell internalization and improved brightness compared with unconjugated RB. Our experiments demonstrate that engineered RB-GelMA NPs can be used as a biocompatible fluorescent label for bioimaging.

From Light to Sound: Photoacoustic and Ultrasound Imaging in Fundamental Research of Alzheimer's Disease

Alzheimer's disease (AD) causes severe cognitive dysfunction and has long been studied for the underlining physiological and pathological mechanisms. Several biomedical imaging modalities have been applied, including MRI, PET, and high-resolution optical microscopy, for research purposes. However, there is still a strong need for imaging tools that can provide high spatiotemporal resolutions with relatively deep penetration to enhance our understanding of AD pathology and monitor treatment progress in fundamental research. Photoacoustic (PA) imaging and ultrasound (US) imaging can potentially address these unmet needs in AD research. PA imaging provides functional information with endogenous and/or exogenous contrast, while US imaging provides structural information. Recent studies have demonstrated the ability to monitor physiological parameters in small-animal brains with PA and US imaging as well as the feasibility of using US imaging as a therapeutic tool for AD. This concise review aims to introduce recent advances in AD research using PA and US imaging, provide the fundamentals, and discuss the potentials and challenges for future advances.

In vivo photoacoustic imaging of a nonfluorescent E2 crimson genetic reporter in mammalian tissues

SIGNIFICANCE

Green-fluorescent protein (GFP)-like fluorescent proteins are used extensively as genetic reporters in fluorescence imaging due to their distinctive ability to form chromophores independent of external enzymes or cofactors. However, their use for photoacoustic (PA) imaging has not been demonstrated in mammalian tissues because they possess low PA signal generation efficiency in their native state. By engineering them to become nonfluorescent (NF), their PA generation efficiency was increased. This enabled the generation of in vivo contrast in mice, making it possible for GFP-like proteins to be used as PA genetic reporters in mammalian tissues.

AIM

The aim was to develop a darkened GFP-like protein reporter by modifying E2 crimson fluorescent protein (FP) in order to generate NF mutant proteins with high PA signal generation efficiency for in vivo imaging.

APPROACH

The absorbance, fluorescence, and PA amplitude spectra of purified protein solutions of the FP and engineered NF mutants were measured in order to identify the mutant with the highest PA signal generation efficiency. This mutant, referred to as NFA, and the native FP were then stably expressed in LS174T human colorectal tumor cells using a retroviral vector and tested for photostability under continuous pulsed illumination. To demonstrate the improvement in PA signal generation in vivo, cells expressing the FP and NFA mutant were injected subcutaneously in mice and imaged using a Fabry-Perot based PA scanner.

RESULTS

The NF mutants of E2 crimson exhibited fluorescence that was 2 orders of magnitude lower than the FP and a higher PA signal generation efficiency; the NFA-generated PA signal was approximately three times higher than the FP. Tumor cells expressing the NFA mutant provided sufficient image contrast to be visualized in vivo against a background of strong vascular contrast, whereas the FP-expressing cells did not generate visible contrast.

CONCLUSION

A GFP-like protein has been demonstrated as a genetic reporter for PA imaging in mammalian tissue for the first time. This was achieved by a mutation, which darkened the FP and increased the PA signal generation efficiency. The approach taken suggests that GFP-like proteins could be a promising addition to the current cohort of genetic reporters available for in vivo PA imaging.

Spatial heterogeneity of nanomedicine investigated by multiscale imaging of the drug, the nanoparticle and the tumour environment

Genetic and phenotypic tumour heterogeneity is an important cause of therapy resistance. Moreover, non-uniform spatial drug distribution in cancer treatment may cause pseudo-resistance, meaning that a treatment is ineffective because the drug does not reach its target at sufficient concentrations. Together with tumour heterogeneity, non-uniform drug distribution causes “therapy heterogeneity”: a spatially heterogeneous treatment effect. Spatial heterogeneity in drug distribution occurs on all scales ranging from interpatient differences to intratumour differences on tissue or cellular scale. Nanomedicine aims to improve the balance between efficacy and safety of drugs by targeting drug-loaded nanoparticles specifically to tumours. Spatial heterogeneity in nanoparticle and payload distribution could be an important factor that limits their efficacy in patients. Therefore, imaging spatial nanoparticle distribution and imaging the tumour environment giving rise to this distribution could help understand (lack of) clinical success of nanomedicine. Imaging the nanoparticle, drug and tumour environment can lead to improvements of new nanotherapies, increase understanding of underlying mechanisms of heterogeneous distribution, facilitate patient selection for nanotherapies and help assess the effect of treatments that aim to reduce heterogeneity in nanoparticle distribution.

In this review, we discuss three groups of imaging modalities applied in nanomedicine research: non-invasive clinical imaging methods (nuclear imaging, MRI, CT, ultrasound), optical imaging and mass spectrometry imaging. Because each imaging modality provides information at a different scale and has its own strengths and weaknesses, choosing wisely and combining modalities will lead to a wealth of information that will help bring nanomedicine forward.

Structure-Based Mutagenesis of Phycobiliprotein smURFP for Optoacoustic Imaging

Photo- or optoacoustics (OA) imaging is increasingly being used as a non-invasive imaging method that can simultaneously reveal structure and function in deep tissue. However, the most frequent transgenic OA labels are current fluorescent proteins that are not optimized for OA imaging. Thus, they lack OA signal strength, and their absorption maxima are positioned at short wavelengths, thus giving small penetration depths and strong background signals. Here, we apply insights from our recent determination of the structure of the fluorescent phycobiliprotein smURFP to mutate a range of residues to promote the nonradiative decay pathway that generates the OA signal. We identified hydrophobic and aromatic substitutions within the chromophore-binding pocket that substantially increase the intensity of the OA signal and red-shift the absorption. Our results demonstrate the feasibility of structure-based mutagenesis to repurpose fluorescent probes for OA imaging, and they may provide structure-function insights for de novo engineering of transgenic OA probes.

Monitoring Tuberculosis Drug Activity in Live Animals by Near-Infrared Fluorescence Imaging

Worldwide, tuberculosis (TB) is the leading cause of death due to infection with a single pathogenic agent, Mycobacterium tuberculosis In the absence of an effective vaccine, new, more powerful antibiotics are required to halt the growing spread of multidrug-resistant strains and to shorten the duration of TB treatment. However, assessing drug efficacy at the preclinical stage remains a long and fastidious procedure that delays progression of drugs down the pipeline and towards the clinic. In this investigation, we report the construction, optimization and characterization of genetically engineered near-infrared (NIR) fluorescent reporter strains of the pathogens Mycobacterium marinum and Mycobacterium tuberculosis that enable direct visualization of bacteria in infected zebrafish and mice, respectively. Fluorescence could be measured precisely in infected immunodeficient mice, while its intensity appeared to be below the limit of detection in immunocompetent mice, probably because of the lower bacterial load obtained in these animals. Furthermore, we show that the fluorescence level accurately reflects the bacterial load, as determined by colony forming unit (CFU) enumeration, thus enabling the efficacy of antibiotic treatment to be assessed in live animals in real time. The NIR fluorescent imaging system disclosed here is a valuable resource for TB research and can serve to accelerate drug development.

Enabling biodegradable functional biomaterials for the management of neurological disorders

An increasing number of patients are being diagnosed with neurological diseases, but are rarely cured because of the lack of curative therapeutic approaches. This situation creates an urgent clinical need to develop effective diagnosis and treatment strategies for repair and regeneration of injured or diseased neural tissues. In this regard, biodegradable functional biomaterials provide promising solutions to meet this demand owing to their unique responsiveness to external stimulation fields, which enable neuro-imaging, neuro-sensing, specific targeting, hyperthermia treatment, controlled drug delivery, and nerve regeneration. This review discusses recent progress in the research and development of biodegradable functional biomaterials including electroactive biomaterials, magnetic materials and photoactive biomaterials for the management of neurological disorders with emphasis on their applications in bioimaging (photoacoustic imaging, MRI and fluorescence imaging), biosensing (electrochemical sensing, magnetic sensing and opical sensing), and therapy strategies (drug delivery, hyperthermia treatment, and tissue engineering). It is expected that this review will provide an insightful discussion on the roles of biodegradable functional biomaterials in the diagnosis and treatment of neurological diseases, and lead to innovations for the design and development of the next generation biodegradable functional biomaterials.

Feature coupling photoacoustic computed tomography for joint reconstruction of initial pressure and sound speed in vivo

Photoacoustic imaging relies on diffused photons for optical contrast and diffracted ultrasound for high resolution. As a tomographic imaging modality, often an inverse problem of acoustic diffraction needs to be solved to reconstruct a photoacoustic image. The inverse problem is complicated by the fact that the acoustic properties, including the speed of sound distribution, in the image field of view are unknown. During reconstruction, subtle changes of the speed of sound in the acoustic ray path may accumulate and give rise to noticeable blurring in the image. Thus, in addition to the ultrasound detection bandwidth, inaccurate acoustic modeling, especially the unawareness of the speed of sound, defines the image resolution and influences image quantification. Here, we proposed a method termed feature coupling to jointly reconstruct the speed of sound distribution and a photoacoustic image with improved sharpness, at no additional hardware cost. Simulations, phantom studies, and in vivo experiments demonstrated the effectiveness and reliability of our method.

Near-Infrared Fluorescent Proteins and Their Applications

High transparency, low light-scattering, and low autofluorescence of mammalian tissues in the near-infrared (NIR) spectral range (~650-900 nm) open a possibility for in vivo imaging of biological processes at the micro- and macroscales to address basic and applied problems in biology and biomedicine. Recently, probes that absorb and fluoresce in the NIR optical range have been engineered using bacterial phytochromes - natural NIR light-absorbing photoreceptors that regulate metabolism in bacteria. Since the chromophore in all these proteins is biliverdin, a natural product of heme catabolism in mammalian cells, they can be used as genetically encoded fluorescent probes, similarly to GFP-like fluorescent proteins. In this review, we discuss photophysical and biochemical properties of NIR fluorescent proteins, reporters, and biosensors and analyze their characteristics required for expression of these molecules in mammalian cells. Structural features and molecular engineering of NIR fluorescent probes are discussed. Applications of NIR fluorescent proteins and biosensors for studies of molecular processes in cells, as well as for tissue and organ visualization in whole-body imaging in vivo, are described. We specifically focus on the use of NIR fluorescent probes in advanced imaging technologies that combine fluorescence and bioluminescence methods with photoacoustic tomography.

Cardiovascular optoacoustics: From mice to men - A review

Imaging has become an indispensable tool in the research and clinical management of cardiovascular disease (CVD). An array of imaging technologies is considered for CVD diagnostics and therapeutic assessment, ranging from ultrasonography, X-ray computed tomography and magnetic resonance imaging to nuclear and optical imaging methods. Each method has different operational characteristics and assesses different aspects of CVD pathophysiology; nevertheless, more information is desirable for achieving a comprehensive view of the disease. Optoacoustic (photoacoustic) imaging is an emerging modality promising to offer novel information on CVD parameters by allowing high-resolution imaging of optical contrast several centimeters deep inside tissue. Implemented with illumination at several wavelengths, multi-spectral optoacoustic tomography (MSOT) in particular, is sensitive to oxygenated and deoxygenated hemoglobin, water and lipids allowing imaging of the vasculature, tissue oxygen saturation and metabolic or inflammatory parameters. Progress with fast-tuning lasers, parallel detection and advanced image reconstruction and data-processing algorithms have recently transformed optoacoustics from a laboratory tool to a promising modality for small animal and clinical imaging. We review progress with optoacoustic CVD imaging, highlight the research and diagnostic potential and current applications and discuss the advantages, limitations and possibilities for integration into clinical routine.

Optoacoustic mesoscopy for biomedicine

Fuelled by innovation, optical microscopy plays a critical role in the life sciences and medicine, from basic discovery to clinical diagnostics. However, optical microscopy is limited by typical penetration depths of a few hundred micrometres for in vivo interrogations in the visible spectrum. Optoacoustic microscopy complements optical microscopy by imaging the absorption of light, but it is similarly limited by penetration depth. In this Review, we summarize progress in the development and applicability of optoacoustic mesoscopy (OPAM); that is, optoacoustic imaging with acoustic resolution and wide-bandwidth ultrasound detection. OPAM extends the capabilities of optical imaging beyond the depths accessible to optical and optoacoustic microscopy, and thus enables new applications. We explain the operational principles of OPAM, its placement as a bridge between optoacoustic microscopy and optoacoustic macroscopy, and its performance in the label-free visualization of tissue pathophysiology, such as inflammation, oxygenation, vascularization and angiogenesis. We also review emerging applications of OPAM in clinical and biological imaging.

Photocontrollable Proteins for Optoacoustic Imaging

Photocontrollable proteins revolutionized life-science imaging due to their contribution to subdiffraction-resolution optical microscopy. They might have yet another lasting impact on photo- or optoacoustic imaging (OA). OA combines optical contrast with ultrasound detection enabling high-resolution real-time in vivo imaging well-beyond the typical penetration depth of optical methods. While OA already showed numerous applications relying on endogenous contrast from blood hemoglobin or lipids, its application in the life-science was limited by a lack of labels overcoming the strong signal from the aforementioned endogenous absorbers. Here, a number of recent studies showed that photocontrollable proteins provide the means to overcome this barrier eventually enabling OA to image small cell numbers in a complete organism in vivo. In this Feature article, we introduce the key photocontrollable proteins, explain the basic concepts, and highlight achievements that have been already made.

Whole-Cell Photoacoustic Sensor Based on Pigment Relocalization

Photoacoustic (optoacoustic) imaging can extract molecular information with deeper tissue penetration than possible by fluorescence microscopy techniques. However, there is currently still a lack of robust genetically controlled contrast agents and molecular sensors that can dynamically detect biological analytes of interest with photoacoustics. In a biomimetic approach, we took inspiration from cuttlefish who can change their color by relocalizing pigment-filled organelles in so-called chromatophore cells under neurohumoral control. Analogously, we tested the use of melanophore cells from Xenopus laevis, containing compartments (melanosomes) filled with strongly absorbing melanin, as whole-cell sensors for optoacoustic imaging. Our results show that pigment relocalization in these cells, which is dependent on binding of a ligand of interest to a specific G protein-coupled receptor (GPCR), can be monitored in vitro and in vivo using photoacoustic mesoscopy. In addition to changes in the photoacoustic signal amplitudes, we could furthermore detect the melanosome aggregation process by a change in the frequency content of the photoacoustic signals. Using bioinspired engineering, we thus introduce a photoacoustic pigment relocalization sensor (PaPiReS) for molecular photoacoustic imaging of GPCR-mediated signaling molecules.

Combining near-infrared fluorescence with Brainbow to visualize expression of specific genes within a multicolor context

Fluorescent proteins are a powerful experimental tool, allowing the visualization of gene expression and cellular behaviors in a variety of systems. Multicolor combinations of fluorescent proteins, such as Brainbow, have expanded the range of possible research questions and are useful for distinguishing and tracking cells. The addition of a separately driven color, however, would allow researchers to report expression of a manipulated gene within the multicolor context to investigate mechanistic effects. A far-red or near-infrared protein could be particularly suitable in this context, as these can be distinguished spectrally from Brainbow. We investigated five far-red/near-infrared proteins in zebrafish: TagRFP657, mCardinal, miRFP670, iRFP670, and mIFP. Our results show that both mCardinal and iRFP670 are useful fluorescent proteins for zebrafish expression. We also introduce a new transgenic zebrafish line that expresses Brainbow under the control of the neuroD promoter. We demonstrate that mCardinal can be used to track the expression of a manipulated bone morphogenetic protein receptor within the Brainbow context. The overlay of near-infrared fluorescence onto a Brainbow background defines a clear strategy for future research questions that aim to manipulate or track the effects of specific genes within a population of cells that are delineated using multicolor approaches.

Alkaline Phosphatase-Triggered Self-Assembly of Near-Infrared Nanoparticles for the Enhanced Photoacoustic Imaging of Tumors

Photoacoustic (PA) imaging is advantageous for the diagnosis of superficial cancer with high spatial resolution. However, to the best of our knowledge, using an alkaline phosphatase (ALP)-activatable probe for the enhanced PA imaging of tumors has not been reported. In this work, we rationally designed a NIR probe IR775-Phe-Phe-Tyr(H₂PO₃)-OH (1P) for PA imaging ALP activity in vitro and in tumor. Under the catalysis of ALP, 1P was efficiently converted to IR775-Phe-Phe-Tyr-OH (1), which self-assembled into the nanoparticles 1-NPs. The formation of 1-NPs induced a 6.4-fold enhancement of the 795 nm PA signal of 1P. In vivo tumor PA imaging results indicated that, compared to that in the ALP inhibitor-treated control group, PA contrast in the experimental group enhanced 2.3 folds at 4 h after 1P injection. By replacing the Phe-Phe-Tyr(H₂PO₃)-OH motif in 1P with other enzyme-cleavable ones, we hope that more PA probes could be developed for the precise diagnoses of their corresponding cancers in the near future.

Organic Semiconducting Agents for Deep-Tissue Molecular Imaging: Second Near-Infrared Fluorescence, Self-Luminescence, and Photoacoustics

Optical imaging has played a pivotal role in biology and medicine, but it faces challenges of relatively low tissue penetration and poor signal-to-background ratio due to light scattering and tissue autofluorescence. To overcome these issues, second near-infrared fluorescence, self-luminescence, and photoacoustic imaging have recently emerged, which utilize an optical region with reduced light-tissue interactions, eliminate real-time light excitation, and detect acoustic signals with negligible attenuation, respectively. Because there are only a few endogenous molecules absorbing or emitting above the visible region, development of contrast agents is essential for those deep-tissue optical imaging modalities. Organic semiconducting agents with π-conjugated frameworks can be synthesized to meet different optical imaging requirements due to their easy chemical modification and legible structure-property relation. Herein, the deep-tissue optical imaging applications of organic semiconducting agents including small-molecule agents and nanoparticle derivatives are summarized. In particular, the molecular engineering and nanoformulation approaches to further improve the tissue penetration and detection sensitivity of these optical imaging modalities are highlighted. Finally, current challenges and potential opportunities in this emerging subfield of biomedical imaging are discussed.

Small Molecule Optoacoustic Contrast Agents: An Unexplored Avenue for Enhancing In Vivo Imaging

Almost every variety of medical imaging technique relies heavily on exogenous contrast agents to generate high-resolution images of biological structures. Organic small molecule contrast agents, in particular, are well suited for biomedical imaging applications due to their favorable biocompatibility and amenability to structural modification. PET/SPECT, MRI, and fluorescence imaging all have a large host of small molecule contrast agents developed for them, and there exists an academic understanding of how these compounds can be developed. Optoacoustic imaging is a relatively newer imaging technique and, as such, lacks well-established small molecule contrast agents; many of the contrast agents used are the same ones which have found use in fluorescence imaging applications. Many commonly-used fluorescent dyes have found successful application in optoacoustic imaging, but others generate no detectable signal. Moreover, the structural features that either enable a molecule to generate a detectable optoacoustic signal or prevent it from doing so are poorly understood, so design of new contrast agents lacks direction. This review aims to compile the small molecule optoacoustic contrast agents that have been successfully employed in the literature to bridge the information gap between molecular design and optoacoustic signal generation. The information contained within will help to provide direction for the future synthesis of optoacoustic contrast agents.

Engineering molecular imaging strategies for regenerative medicine

The reshaping of the world's aging population has created an urgent need for therapies for chronic diseases. Regenerative medicine offers a ray of hope, and its complex solutions include material, cellular, or tissue systems. We review basics of regenerative medicine/stem cells and describe how the field of molecular imaging, which is based on quantitative, noninvasive, imaging of biological events in living subjects, can be applied to regenerative medicine in order to interrogate tissues in innovative, informative, and personalized ways. We consider aspects of regenerative medicine for which molecular imaging will benefit. Next, genetic and nanoparticle-based cell imaging strategies are discussed in detail, with modalities like magnetic resonance imaging, optical imaging (near infra-red, bioluminescence), raman microscopy, and photoacoustic microscopy), ultrasound, computed tomography, single-photon computed tomography, and positron emission tomography. We conclude with a discussion of "next generation" molecular imaging strategies, including imaging host tissues prior to cell/tissue transplantation.

In vivo photoacoustic difference-spectra imaging of bacteria using photoswitchable chromoproteins

Photoacoustic (PA) imaging offers great promise for deep molecular imaging of optical reporters but has difficulties in imaging multiple molecular probes simultaneously in a strong blood background. Photoswitchable chromoproteins like BphP1 have recently allowed for sensitive PA detection by reducing high-blood background signals but lack multiplexing capabilities. We propose a method known as difference-spectra demixing for multiplexing multiple photoswitchable chromoproteins and introduce a second photoswitchable chromoprotein, sGPC2. sGPC2 has a far-red and orange state with peaks at 700 and 630 nm, respectively. It is roughly one-tenth the size of BphP1 and photoswitches four times as fast (2.4% per mJ  /  cm2). We simultaneously image Escherichia coli expressing sGPC2 and BphP1 injected in mice in vivo. Difference-spectra demixing obtained successful multiplexed images of photoswitchable molecular probes, resulting in a 21.6-fold increase in contrast-to-noise ratio in vivo over traditional PA imaging and an 8% to 40% reduction in erroneously demixed signals in comparison with traditional spectral demixing. PA imaging and characterization were conducted using a custom-built photoswitching PA imaging system.

Ingestible roasted barley for contrast-enhanced photoacoustic imaging in animal and human subjects

Photoacoustic computed tomography (PACT) is an emerging imaging modality. While many contrast agents have been developed for PACT, these typically cannot immediately be used in humans due to the lengthy regulatory process. We screened two hundred types of ingestible foodstuff samples for photoacoustic contrast with 1064 nm pulse laser excitation, and identified roasted barley as a promising candidate. Twenty brands of roasted barley were further screened to identify the one with the strongest contrast, presumably based on complex chemical modifications incurred during the roasting process. Individual roasted barley particles could be detected through 3.5 cm of chicken-breast tissue and through the whole hand of healthy human volunteers. With PACT, but not ultrasound imaging, a single grain of roasted barley was detected in a field of hundreds of non-roasted particles. Upon oral administration, roasted barley enabled imaging of the gut and peristalsis in mice. Prepared roasted barley tea could be detected through 2.5 cm chicken breast tissue. When barley tea was administered to humans, photoacoustic imaging visualized swallowing dynamics in healthy volunteers. Thus, roasted barley represents an edible foodstuff that should be considered for photoacoustic contrast imaging of swallowing and gut processes, with immediate potential for clinical translation.

Near-Infrared Fluorescent Proteins: Multiplexing and Optogenetics across Scales

Since mammalian tissue is relatively transparent to near-infrared (NIR) light, NIR fluorescent proteins (FPs) engineered from bacterial phytochromes have become widely used probes for non-invasive in vivo imaging. Recently, these genetically encoded NIR probes have been substantially improved, enabling imaging experiments that were not possible previously. Here, we discuss the use of monomeric NIR FPs and NIR biosensors for multiplexed imaging with common visible GFP-based probes and blue light-activatable optogenetic tools. These NIR probes are suitable for visualization of functional activities from molecular to organismal levels. In combination with advanced imaging techniques, such as two-photon microscopy with adaptive optics, photoacoustic tomography and its recent modification reversibly switchable photoacoustic computed tomography, NIR probes allow subcellular resolution at millimeter depths.

Multimodal cell tracking from systemic administration to tumour growth by combining gold nanorods and reporter genes

Understanding the fate of exogenous cells after implantation is important for clinical applications. Preclinical studies allow imaging of cell location and survival. Labelling with nanoparticles enables high sensitivity detection, but cell division and cell death cause signal dilution and false positives. By contrast, genetic reporter signals are amplified by cell division. Here, we characterise lentivirus-based bi-cistronic reporter gene vectors and silica-coated gold nanorods (GNRs) as synergistic tools for cell labelling and tracking. Co-expression of the bioluminescence reporter luciferase and the optoacoustic reporter near-infrared fluorescent protein iRFP720 enabled cell tracking over time in mice. Multispectral optoacoustic tomography (MSOT) showed immediate biodistribution of GNR-labelled cells after intracardiac injection and successive clearance of GNRs (day 1–15) with high resolution, while optoacoustic iRFP720 detection indicated tumour growth (day 10–40). This multimodal cell tracking approach could be applied widely for cancer and regenerative medicine research to monitor short- and long-term biodistribution, tumour formation and metastasis.

Many scientists are studying the possibility of using human cells to treat diseases. For example, using stem cells to regenerate damaged body parts or genetically engineered immune cells to destroy cancer. Scientists need new tools to track what happens to these cells once they have been injected into a laboratory animal. This will help them understand how they work and make sure these potential treatments are safe. One concern with using cells as a treatment is that they might form cancerous tumors.

To track these cells in a laboratory animal, scientists need two things: a way to distinguish the treatment cells from the animal’s normal cells and an imaging tool that allows them to see where the cells are in a living animal. One way to differentiate treatment cells from normal cells is to genetically engineer them to make a fluorescent protein called iRFP720. Another way is to fill the cells with gold nanorods. Both, the fluorescent protein and the gold nanorods, absorb light in the infrared range. Scientists can use a technique called multispectral optoacoustic tomography, which transforms infrared light into ultrasound signals to create an image, to see where these markers are in the body.

Now, Comenge et al. showed that the gold nanorods and multispectral optoacoustic tomography track the cells immediately after injection into the blood stream of a mouse. Most of the injected cells die within a few days, and the nanorods are progressively eliminated from the body through the liver. But some of the injected cells live on, multiply, and form tumors within a month. This was expected because the cells they used were chosen for their ability to sometimes form tumors. Using multispectral optoacoustic tomography to track the cells making iRFP720, Comenge et al. were able to see exactly where the tumors are deep inside the body.

Together, gold nanorods and iRFP720 could allow scientists to track where the cell-based therapies for cancer or other diseases go in the short and long term. This may help them prove whether these treatments work, and whether they have harmful effects. Comenge et al. are helping other scientists to use these techniques by distributing their tool for making iRFP720-producing cells.

Imaging Biomaterial-Tissue Interactions

Modern biomedical imaging has revolutionized life science by providing anatomical, functional, and molecular information of biological species with high spatial resolution, deep penetration, enhanced temporal responsiveness, and improved chemical specificity. In recent years, these imaging techniques have been increasingly tailored for characterizing biomaterials and probing their interactions with biological tissues. This in turn has spurred substantial advances in engineering material properties to accommodate different imaging modalities that was previously unattainable. Here, we review advances in engineering both imaging modalities and material properties with improved contrast, providing a timely practical guide to better assess biomaterial-tissue interactions both in vitro and in vivo.

Towards optimized naphthalocyanines as sonochromes for photoacoustic imaging in vivo

In this paper we establish a methodology to predict photoacoustic imaging capabilities from the structure of absorber molecules (sonochromes). The comparative in vitro and in vivo screening of naphthalocyanines and cyanine dyes has shown a substitution pattern dependent shift in photoacoustic excitation wavelength, with distal substitution producing the preferred maximum around 800 nm. Central ion change showed variable production of photoacoustic signals, as well as singlet oxygen photoproduction and fluorescence with the optimum for photoacoustic imaging being nickel(II). Our approach paves the way for the design, evaluation and realization of optimized sonochromes as photoacoustic contrast agents.

Multispectral Optoacoustic Tomography of Brown Adipose Tissue

MSOT has revolutionized biomedical imaging because it allows anatomical, functional, and molecular imaging of deep tissues in vivo in an entirely noninvasive, label-free, and real-time manner. This imaging modality works by pulsing light onto tissue, triggering the production of acoustic waves, which can be collected and reconstructed to provide high-resolution images of features as deep as several centimeters below the body surface. Advances in hardware and software continue to bring MSOT closer to clinical translation. Most recently, a clinical handheld MSOT system has been used to image brown fat tissue (BAT) and its metabolic activity by directly resolving the spectral signatures of hemoglobin and lipids. This opens up new possibilities for studying BAT physiology and its role in metabolic disease without the need to inject animals or humans with contrast agents. In this chapter, we overview how MSOT works and how it has been implemented in preclinical and clinical contexts. We focus on our recent work using MSOT to image BAT in resting and activated states both in mice and humans.

Semiconducting Polymer Nanoparticles for Centimeters-Deep Photoacoustic Imaging in the Second Near-Infrared Window

Thienoisoindigo-based semiconducting polymer with a strong near-infrared absorbance is synthesized and its water-dispersed nanoparticles (TSPNs) are investigated as a contrast agent for photoacoustic (PA) imaging in the second near-infrared (NIR-II) window (1000-1350 nm). The TSPNs generate a strong PA signal in the NIR-II optical window, where background signals from endogenous contrast agents, including blood and lipid, are at the local minima. By embedding a TSPN-containing tube in chicken-breast tissue, an imaging depth of more than 5 cm at 1064 nm excitation is achieved with a contrast-agent concentration as low as 40 µg mL^-1 . The TSPNs under the skin or in the tumor are clearly visualized at 1100 and 1300 nm, with negligible interference from the tissue background. TSPN as a PA contrast in the NIR-II window opens new opportunities for biomedical imaging of deep tissues with improved contrast.

Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging

Several series of near-infrared (NIR) fluorescent proteins (FPs) were recently engineered from bacterial phytochromes but were not systematically compared in neurons. To fluoresce, NIR FPs utilize an enzymatic derivative of heme, the linear tetrapyrrole biliverdin, as a chromophore whose level in neurons is poorly studied. Here, we evaluated NIR FPs of the iRFP protein family, which were reported to be the brightest in non-neuronal mammalian cells, in primary neuronal culture, in brain slices of mouse and monkey, and in mouse brain in vivo. We applied several fluorescence imaging modes, such as wide-field and confocal one-photon and two-photon microscopy, to compare photochemical and biophysical properties of various iRFPs. The iRFP682 and iRFP670 proteins exhibited the highest brightness and photostability under one-photon and two-photon excitation modes, respectively. All studied iRFPs exhibited efficient binding of the endogenous biliverdin chromophore in cultured neurons and in the mammalian brain and can be readily applied to neuroimaging.

Bacterial Phytochromes, Cyanobacteriochromes and Allophycocyanins as a Source of Near-Infrared Fluorescent Probes

Bacterial photoreceptors absorb light energy and transform it into intracellular signals that regulate metabolism. Bacterial phytochrome photoreceptors (BphPs), some cyanobacteriochromes (CBCRs) and allophycocyanins (APCs) possess the near-infrared (NIR) absorbance spectra that make them promising molecular templates to design NIR fluorescent proteins (FPs) and biosensors for studies in mammalian cells and whole animals. Here, we review structures, photochemical properties and molecular functions of several families of bacterial photoreceptors. We next analyze molecular evolution approaches to develop NIR FPs and biosensors. We then discuss phenotypes of current BphP-based NIR FPs and compare them with FPs derived from CBCRs and APCs. Lastly, we overview imaging applications of NIR FPs in live cells and in vivo. Our review provides guidelines for selection of existing NIR FPs, as well as engineering approaches to develop NIR FPs from the novel natural templates such as CBCRs.

Photoacoustic imaging using genetically encoded reporters: a review

Genetically encoded contrast in photoacoustic imaging (PAI) is complementary to the intrinsic contrast provided by endogenous absorbing chromophores such as hemoglobin. The use of reporter genes expressing absorbing proteins opens the possibility of visualizing dynamic cellular and molecular processes. This is an enticing prospect but brings with it challenges and limitations associated with generating and detecting different types of reporters. The purpose of this review is to compare existing PAI reporters and signal detection strategies, thereby offering a practical guide, particularly for the nonbiologist, to choosing the most appropriate reporter for maximum sensitivity in the biological and technological system of interest.

Near-infrared fluorescent protein iRFP713 as a reporter protein for optogenetic vectors, a transgenic Cre-reporter rat, and other neuronal studies

BACKGROUND

The use of genetically-encoded fluorescent reporters is essential for the identification and observation of cells that express transgenic modulatory proteins. Near-infrared (NIR) fluorescent proteins have superior light penetration through biological tissue, but are not yet widely adopted.

NEW METHOD

Using the near-infrared fluorescent protein, iRFP713, improves the imaging resolution in thick tissue sections or the intact brain due to the reduced light-scattering at the longer, NIR wavelengths used to image the protein. Additionally, iRFP713 can be used to identify transgenic cells without photobleaching other fluorescent reporters or affecting opsin function. We have generated a set of adeno-associated vectors in which iRFP713 has been fused to optogenetic channels, and can be expressed constitutively or Cre-dependently.

RESULTS

iRFP713 is detectable when expressed in neurons both in vitro and in vivo without exogenously supplied chromophore biliverdin. Neuronally-expressed iRFP713 has similar properties to GFP-like fluorescent proteins, including the ability to be translationally fused to channelrhodopsin or halorhodopsin, however, it shows superior photostability compared to EYFP. Furthermore, electrophysiological recordings from iRFP713-labeled cells compared to cells labeled with mCherry suggest that iRFP713 cells are healthier and therefore more stable and reliable in an ex vivo preparation. Lastly, we have generated a transgenic rat that expresses iRFP713 in a Cre-dependent manner.

CONCLUSIONS

Overall, we have demonstrated that iRFP713 can be used as a reporter in neurons without the use of exogenous biliverdin, with minimal impact on viability and function thereby making it feasible to extend the capabilities for imaging genetically-tagged neurons in slices and in vivo.