Bioorthogonal chemical imaging of metabolic activities in live mammalian hippocampal tissues with stimulated Raman scattering

Synthetic Lipid Biology

Cells contain thousands of different lipids. Their rapid and redundant metabolism, dynamic movement, and many interactions with other biomolecules have justly earned lipids a reputation as a vexing class of molecules to understand. Further, as the cell's hydrophobic metabolites, lipids assemble into supramolecular structures─most commonly bilayers, or membranes─from which they carry out myriad biological functions. Motivated by this daunting complexity, researchers across disciplines are bringing order to the seeming chaos of biological lipids and membranes. Here, we formalize these efforts as "synthetic lipid biology". Inspired by the idea, central to synthetic biology, that our abilities to understand and build biological systems are intimately connected, we organize studies and approaches across numerous fields to create, manipulate, and analyze lipids and biomembranes. These include construction of lipids and membranes from scratch using chemical and chemoenzymatic synthesis, editing of pre-existing membranes using optogenetics and protein engineering, detection of lipid metabolism and transport using bioorthogonal chemistry, and probing of lipid-protein interactions and membrane biophysical properties. What emerges is a portrait of an incipient field where chemists, biologists, physicists, and engineers work together in proximity─like lipids themselves─to build a clearer description of the properties, behaviors, and functions of lipids and membranes.

Surface-Enhanced Raman Scattering Nanosensing and Imaging in Neuroscience

Monitoring neurochemicals and imaging the molecular content of brain tissues in vitro, ex vivo, and in vivo is essential for enhancing our understanding of neurochemistry and the causes of brain disorders. This review explores the potential applications of surface-enhanced Raman scattering (SERS) nanosensors in neurosciences, where their adoption could lead to significant progress in the field. These applications encompass detecting neurotransmitters or brain disorders biomarkers in biofluids with SERS nanosensors, and imaging normal and pathological brain tissues with SERS labeling. Specific studies highlighting in vitro, ex vivo, and in vivo analysis of brain disorders using fit-for-purpose SERS nanosensors will be detailed, with an emphasis on the ability of SERS to detect clinically pertinent levels of neurochemicals. Recent advancements in designing SERS-active nanomaterials, improving experimentation in biofluids, and increasing the usage of machine learning for interpreting SERS spectra will also be discussed. Furthermore, we will address the tagging of tissues presenting pathologies with nanoparticles for SERS imaging, a burgeoning domain of neuroscience that has been demonstrated to be effective in guiding tumor removal during brain surgery. The review also explores future research applications for SERS nanosensors in neuroscience, including monitoring neurochemistry in vivo with greater penetration using surface-enhanced spatially offset Raman scattering (SESORS), near-infrared lasers, and 2-photon techniques. The article concludes by discussing the potential of SERS for investigating the effectiveness of therapies for brain disorders and for integrating conventional neurochemistry techniques with SERS sensing.

Inspiring a convergent engineering approach to measure and model the tissue microenvironment

Understanding the molecular and physical complexity of the tissue microenvironment (TiME) in the context of its spatiotemporal organization has remained an enduring challenge. Recent advances in engineering and data science are now promising the ability to study the structure, functions, and dynamics of the TiME in unprecedented detail; however, many advances still occur in silos that rarely integrate information to study the TiME in its full detail. This review provides an integrative overview of the engineering principles underlying chemical, optical, electrical, mechanical, and computational science to probe, sense, model, and fabricate the TiME. In individual sections, we first summarize the underlying principles, capabilities, and scope of emerging technologies, the breakthrough discoveries enabled by each technology and recent, promising innovations. We provide perspectives on the potential of these advances in answering critical questions about the TiME and its role in various disease and developmental processes. Finally, we present an integrative view that appreciates the major scientific and educational aspects in the study of the TiME.

Fast Real-Time Brain Tumor Detection Based on Stimulated Raman Histology and Self-Supervised Deep Learning Model

In intraoperative brain cancer procedures, real-time diagnosis is essential for ensuring safe and effective care. The prevailing workflow, which relies on histological staining with hematoxylin and eosin (H&E) for tissue processing, is resource-intensive, time-consuming, and requires considerable labor. Recently, an innovative approach combining stimulated Raman histology (SRH) and deep convolutional neural networks (CNN) has emerged, creating a new avenue for real-time cancer diagnosis during surgery. While this approach exhibits potential, there exists an opportunity for refinement in the domain of feature extraction. In this study, we employ coherent Raman scattering imaging method and a self-supervised deep learning model (VQVAE2) to enhance the speed of SRH image acquisition and feature representation, thereby enhancing the capability of automated real-time bedside diagnosis. Specifically, we propose the VQSRS network, which integrates vector quantization with a proxy task based on patch annotation for analysis of brain tumor subtypes. Training on images collected from the SRS microscopy system, our VQSRS demonstrates a significant speed enhancement over traditional techniques (e.g., 20-30 min). Comparative studies in dimensionality reduction clustering confirm the diagnostic capacity of VQSRS rivals that of CNN. By learning a hierarchical structure of recognizable histological features, VQSRS classifies major tissue pathological categories in brain tumors. Additionally, an external semantic segmentation method is applied for identifying tumor-infiltrated regions in SRH images. Collectively, these findings indicate that this automated real-time prediction technique holds the potential to streamline intraoperative cancer diagnosis, providing assistance to pathologists in simplifying the process.

Raman microscopy reveals how cell inflammation activates glucose and lipid metabolism

Metabolism of endothelial cells (ECs) depends on the availability of the energy substrates. Since the endothelium is the first line of defence against inflammation in the cardiovascular system and its dysfunction can lead to the development of cardiovascular diseases, it is important to understand how glucose metabolism changes during inflammation. In this work, glucose uptake was studied in human microvascular endothelial cells (HMEC-1) in high glucose (HG), and additionally in an inflammatory state, using Raman imaging. HG state was induced by incubation of ECs with a deuterated glucose analogue, while the EC inflammation was caused by TNF-α pre-treatment. Spontaneous and stimulated Raman scattering spectroscopy provided comprehensive information on biochemical changes, including lipids and the extent of unsaturation induced by excess glucose in ECs., induced by excess glucose in ECs. In this work, we indicated spectroscopic markers of metabolic changes in ECs as a strong increase in the ratio of the intensity of lipids / (proteins + lipids) bands and an increase in the level of lipid unsaturation and mitochondrial changes. Inflamed ECs treated with HG, revealed enhanced glucose uptake, and intensified lipid production i.a. of unsaturated lipids. Additionally, increased cytochrome c signal in the mitochondrial region indicated higher mitochondrial activity and biogenesis. Raman spectroscopy is a powerful method for determining the metabolic markers of ED which will better inform understanding of disease onset, development, and treatment.

Stretching the Bisalkyne Raman Spectral Palette Reveals a New Electrophilic Covalent Motif

Small heteroaryl-diyne (Het-DY) tags with distinct vibrational frequencies, and physiologically relevant cLog P were designed for multiplexed bioorthogonal Raman imaging. Pd-Cu catalyzed coupling, combined with the use of Lei ligand, was shown to improve overall yields of the desired heterocoupled Het-DY tags, minimizing the production of homocoupled side-products. Spectral data were in agreement with the trends predicted by DFT calculations and systematic introduction of electron- rich/poor rings stretched the frequency limit of aryl-capped diynes (2209-2243 cm-1 ). The improved Log P of these Het-DY tags was evident from their diffuse distribution in cellular uptake studies and functionalizing tags with organelle markers allowed the acquisition of location-specific biological images. LC-MS- and NMR-based assays showed that some heteroaryl-capped internal alkynes are potential nucleophile traps with structure-dependent reactivity. These biocompatible Het-DY tags, equipped with covalent reactivity, open up new avenues for Raman bioorthogonal imaging.

3D Chemical Imaging by Fluorescence-detected Mid-Infrared Photothermal Fourier Light Field Microscopy

Three-dimensional molecular imaging of living organisms and cells plays a significant role in modern biology. Yet, current volumetric imaging modalities are largely fluorescence-based and thus lack chemical content information. Mid-infrared photothermal microscopy as a chemical imaging technology provides infrared spectroscopic information at submicrometer spatial resolution. Here, by harnessing thermosensitive fluorescent dyes to sense the mid-infrared photothermal effect, we demonstrate 3D fluorescence-detected mid-infrared photothermal Fourier light field (FMIP-FLF) microscopy at the speed of 8 volumes per second and submicron spatial resolution. Protein contents in bacteria and lipid droplets in living pancreatic cancer cells are visualized. Altered lipid metabolism in drug-resistant pancreatic cancer cells is observed with the FMIP-FLF microscope.

Raman Spectroscopy as a Tool to Study the Pathophysiology of Brain Diseases

The Raman phenomenon is based on the spontaneous inelastic scattering of light, which depends on the molecular characteristics of the dispersant. Therefore, Raman spectroscopy and imaging allow us to obtain direct information, in a label-free manner, from the chemical composition of the sample. Since it is well established that the development of many brain diseases is associated with biochemical alterations of the affected tissue, Raman spectroscopy and imaging have emerged as promising tools for the diagnosis of ailments. A combination of Raman spectroscopy and/or imaging with tagged molecules could also help in drug delivery and tracing for treatment of brain diseases. In this review, we first describe the basics of the Raman phenomenon and spectroscopy. Then, we delve into the Raman spectroscopy and imaging modes and the Raman-compatible tags. Finally, we center on the application of Raman in the study, diagnosis, and treatment of brain diseases, by focusing on traumatic brain injury and ischemia, neurodegenerative disorders, and brain cancer.

Raman Spectroscopy for Chemical Biology Research

In chemical biology research, various fluorescent probes have been developed and used to visualize target proteins or molecules in living cells and tissues, yet there are limitations to this technology, such as the limited number of colors that can be detected simultaneously. Recently, Raman spectroscopy has been applied in chemical biology to overcome such limitations. Raman spectroscopy detects the molecular vibrations reflecting the structures and chemical conditions of molecules in a sample and was originally used to directly visualize the chemical responses of endogenous molecules. However, our initial research to develop "Raman tags" opens a new avenue for the application of Raman spectroscopy in chemical biology. In this Perspective, we first introduce the label-free Raman imaging of biomolecules, illustrating the biological applications of Raman spectroscopy. Next, we highlight the application of Raman imaging of small molecules using Raman tags for chemical biology research. Finally, we discuss the development and potential of Raman probes, which represent the next-generation probes in chemical biology.

Towards Mapping Mouse Metabolic Tissue Atlas by Mid-Infrared Imaging with Heavy Water Labeling

Understanding metabolism is of great significance to decipher various physiological and pathogenic processes. While great progress has been made to profile gene expression, how to capture organ-, tissue-, and cell-type-specific metabolic profile (i.e., metabolic tissue atlas) in complex mammalian systems is lagging behind, largely owing to the lack of metabolic imaging tools with high resolution and high throughput. Here, the authors applied mid-infrared imaging coupled with heavy water (D2 O) metabolic labeling to a scope of mouse organs and tissues. The premise is that, as D2 O participates in the biosynthesis of various macromolecules, the resulting broad C-D vibrational spectrum should interrogate a wide range of metabolic pathways. Applying multivariate analysis to the C-D spectrum, the authors successfully identified both inter-organ and intra-tissue metabolic signatures of mice. A large-scale metabolic atlas map between different organs from the same mice is thus generated. Moreover, leveraging the power of unsupervised clustering methods, spatially-resolved metabolic signatures of brain tissues are discovered, revealing tissue and cell-type specific metabolic profile in situ. As a demonstration of this technique, the authors captured metabolic changes during brain development and characterized intratumoral metabolic heterogeneity of glioblastoma. Altogether, the integrated platform paves a way to map the metabolic tissue atlas for complex mammalian systems.

Raman Spectroscopy as a Neuromonitoring Tool in Traumatic Brain Injury: A Systematic Review and Clinical Perspectives

Traumatic brain injury (TBI) is a significant global health problem, for which no disease-modifying therapeutics are currently available to improve survival and outcomes. Current neuromonitoring modalities are unable to reflect the complex and changing pathophysiological processes of the acute changes that occur after TBI. Raman spectroscopy (RS) is a powerful, label-free, optical tool which can provide detailed biochemical data in vivo. A systematic review of the literature is presented of available evidence for the use of RS in TBI. Seven research studies met the inclusion/exclusion criteria with all studies being performed in pre-clinical models. None of the studies reported the in vivo application of RS, with spectral acquisition performed ex vivo and one performed in vitro. Four further studies were included that related to the use of RS in analogous brain injury models, and a further five utilised RS in ex vivo biofluid studies for diagnosis or monitoring of TBI. RS is identified as a potential means to identify injury severity and metabolic dysfunction which may hold translational value. In relation to the available evidence, the translational potentials and barriers are discussed. This systematic review supports the further translational development of RS in TBI to fully ascertain its potential for enhancing patient care.

Visualizing Lipid Dynamics Role in Infrared Neural Stimulation using Stimulated Raman Scattering

Infrared neural stimulation, or INS, uses pulsed infrared light to yield label-free neural stimulation with broad experimental and translational utility. Despite its robust demonstration, INS's mechanistic and biophysical underpinnings have been the subject of debate for more than a decade. The role of lipid membrane thermodynamics appears to play an important role in how fast IR-mediated heating nonspecifically drives action potential generation. Direct observation of lipid membrane dynamics during INS remains to be shown in a live neural model system. We used hyperspectral stimulated Raman scattering (hsSRS) microscopy to study biochemical signatures of high-speed vibrational dynamics underlying INS in a live neural cell culture model. Findings suggest that lipid bilayer structural changes are occurring during INS in vitro in NG108-15 neuroglioma cells. Lipid-specific signatures of cell SRS spectra varied with stimulation energy and radiant exposure. Spectroscopic observations agree with high-speed ratiometric fluorescence imaging of a conventional lipophilic membrane structure reporter, di-4-ANNEPS. Overall, the presented findings support the hypothesis that INS causes changes in the lipid membrane of neural cells by changing lipid membrane packing order. Furthermore, this work highlights the potential of hsSRS as a method to study biophysical and biochemical dynamics safely in live cells.

From Research to Diagnostic Application of Raman Spectroscopy in Neurosciences: Past and Perspectives

In recent years, Raman spectroscopy has been more and more frequently applied to address research questions in neuroscience. As a non-destructive technique based on inelastic scattering of photons, it can be used for a wide spectrum of applications including neurooncological tumor diagnostics or analysis of misfolded protein aggregates involved in neurodegenerative diseases. Progress in the technical development of this method allows for an increasingly detailed analysis of biological samples and may therefore open new fields of applications. The goal of our review is to provide an introduction into Raman scattering, its practical usage and also commonly associated pitfalls. Furthermore, intraoperative assessment of tumor recurrence using Raman based histology images as well as the search for non-invasive ways of diagnosis in neurodegenerative diseases are discussed. Some of the applications mentioned here may serve as a basis and possibly set the course for a future use of the technique in clinical practice. Covering a broad range of content, this overview can serve not only as a quick and accessible reference tool but also provide more in-depth information on a specific subtopic of interest.

Bioorthogonal Chemistry and Its Applications

Bioorthogonal chemistry is a set of methods using the chemistry of non-native functional groups to explore and understand biology in living organisms. In this review, we summarize the most common reactions used in bioorthogonal methods, their relative advantages and disadvantages, and their frequency of occurrence in the published literature. We also briefly discuss some of the less common but potentially useful methods. We then analyze the bioorthogonal-related publications in the CAS Content Collection to determine how often different types of biomolecules such as proteins, carbohydrates, glycans, and lipids have been studied using bioorthogonal chemistry. The most prevalent biological and chemical methods for attaching bioorthogonal functional groups to these biomolecules are elaborated. We also analyze the publication volume related to different types of bioorthogonal applications in the CAS Content Collection. The use of bioorthogonal chemistry for imaging, identifying, and characterizing biomolecules and for delivering drugs to treat disease is discussed at length. Bioorthogonal chemistry for the surface attachment of proteins and in the use of modified carbohydrates is briefly noted. Finally, we summarize the state of the art in bioorthogonal chemistry and its current limitations and promise for its future productive use in chemistry and biology.

From Raman to SESORRS: moving deeper into cancer detection and treatment monitoring

Raman spectroscopy is a non-invasive technique that allows specific chemical information to be obtained from various types of sample. The detailed molecular information that is present in Raman spectra permits monitoring of biochemical changes that occur in diseases, such as cancer, and can be used for the early detection and diagnosis of the disease, for monitoring treatment, and to distinguish between cancerous and non-cancerous biological samples. Several techniques have been developed to enhance the capabilities of Raman spectroscopy by improving detection sensitivity, reducing imaging times and increasing the potential applicability for in vivo analysis. The different Raman techniques each have their own advantages that can accommodate the alternative detection formats, allowing the techniques to be applied in several ways for the detection and diagnosis of cancer. This feature article discusses the various forms of Raman spectroscopy, how they have been applied for cancer detection, and the adaptation of the techniques towards their use for in vivo cancer detection and in clinical diagnostics. Despite the advances in Raman spectroscopy, the clinical application of the technique is still limited and certain challenges must be overcome to enable clinical translation. We provide an outlook on the future of the techniques in this area and what we believe is required to allow the potential of Raman spectroscopy to be achieved for clinical cancer diagnostics.

A decade of alkyne-tag Raman imaging (ATRI): applications in biological systems

Alkyne functional groups have Raman signatures in a region (1800 cm-1 to 2800 cm-1) that is free from interference from cell components, known as the "silent region", and alkyne signals in this region were first utilized a decade ago to visualize the nuclear localization of a thymidine analogue EdU. Since then, the strategy of Raman imaging of biological samples by using alkyne functional groups, called alkyne-tag Raman imaging (ATRI), has become widely used. This article reviews the applications of ATRI in biological samples ranging from organelles to whole animal models, and briefly discusses the prospects for this technique.

Advances in stimulated Raman scattering imaging for tissues and animals

Stimulated Raman scattering (SRS) microscopy has emerged in the last decade as a powerful optical imaging technology with high chemical selectivity, speed, and subcellular resolution. Since the invention of SRS microscopy, it has been extensively employed in life science to study composition, structure, metabolism, development, and disease in biological systems. Applications of SRS in research and the clinic have generated new insights in many fields including neurobiology, tumor biology, developmental biology, metabolomics, pharmacokinetics, and more. Herein we review the advances and applications of SRS microscopy imaging in tissues and animals, as well as envision future applications and development of SRS imaging in life science and medicine.

Label-free brain tumor imaging using Raman-based methods

INTRODUCTION

Label-free Raman-based imaging techniques create the possibility of bringing chemical and histologic data into the operation room. Relying on the intrinsic biochemical properties of tissues to generate image contrast and optical tissue sectioning, Raman-based imaging methods can be used to detect microscopic tumor infiltration and diagnose brain tumor subtypes.

METHODS

Here, we review the application of three Raman-based imaging methods to neurosurgical oncology: Raman spectroscopy, coherent anti-Stokes Raman scattering (CARS) microscopy, and stimulated Raman histology (SRH).

RESULTS

Raman spectroscopy allows for chemical characterization of tissue and can differentiate normal and tumor-infiltrated tissue based on variations in macromolecule content, both ex vivo and in vivo. To improve signal-to-noise ratio compared to conventional Raman spectroscopy, a second pulsed excitation laser can be used to coherently drive the vibrational frequency of specific Raman active chemical bonds (i.e. symmetric stretching of -CH₂ bonds). Coherent Raman imaging, including CARS and stimulated Raman scattering microscopy, has been shown to detect microscopic brain tumor infiltration in fresh brain tumor specimens with submicron image resolution. Advances in fiber-laser technology have allowed for the development of intraoperative SRH as well as artificial intelligence algorithms to facilitate interpretation of SRH images. With molecular diagnostics becoming an essential part of brain tumor classification, preliminary studies have demonstrated that Raman-based methods can be used to diagnose glioma molecular classes intraoperatively.

CONCLUSIONS

These results demonstrate how label-free Raman-based imaging methods can be used to improve the management of brain tumor patients by detecting tumor infiltration, guiding tumor biopsy/resection, and providing images for histopathologic and molecular diagnosis.

Stimulated Raman Microscopy Implemented by Three Femtosecond Laser Sources

In this work, the implementation of a femtosecond Stimulated Raman Scattering microscope, equipped with three femtosecond laser sources: a Titanium-Sapphire (Ti:Sa), an optical parametric oscillator (OPO), and a second harmonic generator (SHG); is presented. Our microscope is designed so that it can cover all the regions of Raman spectra, taking advantage of two possible laser combinations. The first, Ti:Sa and OPO laser beams, which cover the C-H region (>2800 cm-1 ) in stimulated Raman gain (SRG) modality, whereas the second, Ti:Sa and SHG laser beams, covering the C-H region and the fingerprint region in stimulated Raman losses (SRL) modality. The successful realization of the microscope is demonstrated, reporting images of polystyrene beads using both SRL and SRG modalities.

High-throughput screening for high-efficiency small-molecule biosynthesis

Systems metabolic engineering faces the formidable task of rewiring microbial metabolism to cost-effectively generate high-value molecules from a variety of inexpensive feedstocks for many different applications. Because these cellular systems are still too complex to model accurately, vast collections of engineered organism variants must be systematically created and evaluated through an enormous trial-and-error process in order to identify a manufacturing-ready strain. The high-throughput screening of strains to optimize their scalable manufacturing potential requires execution of many carefully controlled, parallel, miniature fermentations, followed by high-precision analysis of the resulting complex mixtures. This review discusses strategies for the design of high-throughput, small-scale fermentation models to predict improved strain performance at large commercial scale. Established and promising approaches from industrial and academic groups are presented for both cell culture and analysis, with primary focus on microplate- and microfluidics-based screening systems.

Metabolic labeling of glycerophospholipids via clickable analogs derivatized at the lipid headgroup

Metabolic labeling, in which substrate analogs containing diminutive tags can infiltrate biosynthetic pathways and generate labeled products in cells, has led to dramatic advancements in the means by which complex biomolecules can be detected and biological processes can be elucidated. Within this realm, metabolic labeling of lipid products, particularly in a manner that is headgroup-specific, brings about a number of technical challenges including the complexity of lipid metabolic pathways as well as the simplicity of biosynthetic precursors to headgroup functionality. As such, only a handful of strategies for metabolic labeling of lipids have thus far been reported. However, these approaches provide enticing examples of how strategic modifications to substrate structures, particularly by introducing clickable moieties, can enable the hijacking of lipid biosynthesis. Furthermore, early work in this field has led to an explosion in diverse applications by which these techniques have been exploited to answer key biological questions or detect and track various lipid-containing biological entities. In this article, we review these efforts and emphasize recent advancements in the development and application of lipid metabolic labeling strategies.

Imaging the invisible-Bioorthogonal Raman probes for imaging of cells and tissues

A revolutionary avenue for vibrational imaging with super-multiplexing capability can be seen in the recent development of Raman-active bioortogonal tags or labels. These tags and isotopic labels represent groups of chemically inert and small modifications, which can be introduced to any biomolecule of interest and then supplied to single cells or entire organisms. Recent developments in the field of spontaneous Raman spectroscopy and stimulated Raman spectroscopy in combination with targeted imaging of biomolecules within living systems are the main focus of this review. After having introduced common strategies for bioorthogonal labeling, we present applications thereof for profiling of resistance patterns in bacterial cells, investigations of pharmaceutical drug-cell interactions in eukaryotic cells and cancer diagnosis in whole tissue samples. Ultimately, this approach proves to be a flexible and robust tool for in vivo imaging on several length scales and provides comparable information as fluorescence-based imaging without the need of bulky fluorescent tags.

Current advances in in vitro models of central nervous system trauma

CNS trauma is a prominent cause of mortality and morbidity, and although much effort has focused on developing treatments for CNS trauma-related pathologies, little progress has been made. Pre-clinical models of TBI and SCI suffer from significant drawbacks, which result in substantial failures during clinical translation of promising pre-clinical therapies. Here, we review recent advances made in the development of in vitro models of CNS trauma, the promises and drawbacks of current in vitro CNS injury models, and the attributes necessary for future models to accurately mimic the trauma microenvironment and facilitate CNS trauma drug discovery. The goal is to provide insight for the development of future CNS injury models and to aid researchers in selecting effective models for pre-clinical research of trauma therapeutics.

Molecular imaging of extracellular vesicles in vitro via Raman metabolic labelling

Extracellular vesicles (EVs) are biologically-derived nanovectors important for intercellular communication and trafficking. As such, EVs show great promise as disease biomarkers and therapeutic drug delivery vehicles. However, despite the rapidly growing interest in EVs, understanding of the biological mechanisms that govern their biogenesis, secretion, and uptake remains poor. Advances in this field have been hampered by both the complex biological origins of EVs, which make them difficult to isolate and identify, and a lack of suitable imaging techniques to properly study their diverse biological roles. Here, we present a new strategy for simultaneous quantitative in vitro imaging and molecular characterisation of EVs in 2D and 3D based on Raman spectroscopy and metabolic labelling. Deuterium, in the form of deuterium oxide (D2O), deuterated choline chloride (d-Chol), or deuterated d-glucose (d-Gluc), is metabolically incorporated into EVs through the growth of parent cells on medium containing one of these compounds. Isolated EVs are thus labelled with deuterium, which acts as a bio-orthogonal Raman-active tag for direct Raman identification of EVs when introduced to unlabelled cell cultures. Metabolic deuterium incorporation demonstrates no apparent adverse effects on EV secretion, marker expression, morphology, or global composition, indicating its capacity for minimally obstructive EV labelling. As such, our metabolic labelling strategy could provide integral insights into EV biocomposition and trafficking. This approach has the potential to enable a deeper understanding of many of the biological mechanisms underpinning EVs, with profound implications for the design of EVs as therapeutic delivery vectors and applications as disease biomarkers.

Raman spectroscopy and neuroscience: from fundamental understanding to disease diagnostics and imaging

Neuroscience would directly benefit from more effective detection techniques, leading to earlier diagnosis of disease. The specificity of Raman spectroscopy is unparalleled, given that a molecular fingerprint is attained for each species. It also allows for label-free detection with relatively inexpensive instrumentation, minimal sample preparation, and rapid sample analysis. This review summarizes Raman spectroscopy-based techniques that have been used to advance the field of neuroscience in recent years.

Kinetic analysis of bioorthogonal reaction mechanisms using Raman microscopy

Raman spectroscopy is well-suited to the study of bioorthogonal reaction processes because it is a non-destructive technique, which employs relatively low energy laser irradiation, and water is only very weakly scattered in the Raman spectrum enabling live cell imaging. In addition, Raman spectroscopy allows species-specific label-free visualisation; chemical contrast may be achieved when imaging a cell in its native environment without fixatives or stains. Combined with the rapid advances in the field of Raman imaging over the last decade, particularly in stimulated Raman spectroscopy (SRS), this technique has the potential to revolutionise our mechanistic understanding of the biochemical and medicinal chemistry applications of bioorthogonal reactions. Current approaches to the kinetic analysis of bioorthogonal reactions (including heat flow calorimetry, UV-vis spectroscopy, fluorescence, IR, NMR and MS) have a number of practical shortcomings for intracellular applications. We highlight the advantages offered by Raman microscopy for reaction analysis in the context of both established and emerging bioorthogonal reactions, including the copper(i) catalysed azide-alkyne cycloaddition (CuAAC) click reaction and Glaser-Hay coupling.

Biological imaging of chemical bonds by stimulated Raman scattering microscopy

All molecules consist of chemical bonds, and much can be learned from mapping the spatiotemporal dynamics of these bonds. Since its invention a decade ago, stimulated Raman scattering (SRS) microscopy has become a powerful modality for imaging chemical bonds with high sensitivity, resolution, speed and specificity. We introduce the fundamentals of SRS microscopy and review innovations in SRS microscopes and imaging probes. We highlight examples of exciting biological applications, and share our vision for potential future breakthroughs for this technology.

Cellular Imaging Using Stimulated Raman Scattering Microscopy

Cellular imaging is an active area of research that enables researchers to monitor cellular dynamics, as well as responses to various external stimuli (physiological stress, exogenous compounds, etc.). Stimulated Raman scattering (SRS) microscopy is one popular experimental tool used to image cells, largely because of its chemical specificity, high spatial resolution, and high image acquisition speed. In this Perspective, the theoretical background and experimental implementation of SRS microscopy are discussed and recent developments in the field of cellular imaging with SRS are highlighted and summarized.

Probe design for super-multiplexed vibrational imaging

Optical microscopy has served biomedical research for decades due to its high temporal and spatial resolutions. Among various optical imaging techniques, fluorescence imaging offers superb sensitivity down to single molecule level but its multiplexing capacity is limited by intrinsically broad bandwidth. To simultaneously capture a vast number of targets, the newly emerging vibrational microscopy technique draws increasing attention as vibration spectroscopy features narrow transition linewidth. Nonetheless, unlike fluorophores that have been studied for centuries, a systematic investigation on vibrational probes is underemphasized. Herein, we reviewed some of the recent developments of vibrational probes for multiplex imaging applications, particularly those serving stimulated Raman scattering (SRS) microscopy, which is one of the most promising vibrational imaging techniques. We wish to summarize the general guidelines for developing bioorthogonal vibrational probes with high sensitivity, chemical specificity and most importantly, tunability to fulfill super-multiplexed optical imaging. Future directions to significantly improve the performance are also discussed.

Raman Imaging of Small Biomolecules

Imaging techniques greatly facilitate the comprehensive knowledge of biological systems. Although imaging methodology for biomacromolecules such as protein and nucleic acids has been long established, microscopic techniques and contrast mechanisms are relatively limited for small biomolecules, which are equally important participants in biological processes. Recent developments in Raman imaging, including both microscopy and tailored vibrational tags, have created exciting opportunities for noninvasive imaging of small biomolecules in living cells, tissues, and organisms. Here, we summarize the principle and workflow of small-biomolecule imaging by Raman microscopy. Then, we review recent efforts in imaging, for example, lipids, metabolites, and drugs. The unique advantage of Raman imaging has been manifested in a variety of applications that have provided novel biological insights.

Raman Imaging of Nanocarriers for Drug Delivery

The efficacy of pharmaceutical agents can be greatly improved through nanocarrier delivery. Encapsulation of pharmaceutical agents into a nanocarrier can enhance their bioavailability and biocompatibility, whilst also facilitating targeted drug delivery to specific locations within the body. However, detailed understanding of the in vivo activity of the nanocarrier-drug conjugate is required prior to regulatory approval as a safe and effective treatment strategy. A comprehensive understanding of how nanocarriers travel to, and interact with, the intended target is required in order to optimize the dosing strategy, reduce potential off-target effects, and unwanted toxic effects. Raman spectroscopy has received much interest as a mechanism for label-free, non-invasive imaging of nanocarrier modes of action in vivo. Advanced Raman imaging techniques, including coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS), are paving the way for rigorous evaluation of nanocarrier activity at the single-cell level. This review focuses on the development of Raman imaging techniques to study organic nanocarrier delivery in cells and tissues.

Greasing the Wheels of Lipid Biology with Chemical Tools

Biological lipids are a structurally diverse and historically vexing group of hydrophobic metabolites. Here, we review recent advances in chemical imaging techniques that reveal changes in lipid biosynthesis, metabolism, dynamics, and interactions. We highlight tools for tagging many lipid classes via metabolic incorporation of bioorthogonally functionalized precursors, detectable via click chemistry, and photocaged, photoswitchable, and photocrosslinkable variants of different lipids. Certain lipid probes can supplant traditional protein-based markers of organelle membranes in super-resolution microscopy, and emerging vibrational imaging methods, such as stimulated Raman spectroscopy (SRS), enable simultaneous imaging of more than a dozen different types of target molecule, including lipids. Collectively, these chemical imaging techniques will illuminate, in living color, previously hidden aspects of lipid biology.

Integration of stimulated Raman gain and stimulated Raman losses detection modes in a single nonlinear microscope

This work addresses some key challenges in the fields of bio and nanophotonics by stimulated Raman microscopy. We present the design and the implementation of a femtosecond stimulated Raman scattering microscope, equipped with three femtosecond laser sources, which allows the coexistence of stimulated Raman gain (SRG) and stimulate Raman losses (SRL) detection modes in a single microscopy setup and to generate images of the same region in succession, without adding or removing components. In order to demonstrate the switching between the two detection modes, SRL and SRG images of polystyrene beads are acquired and the images quality are evaluated and compared.

Live Intracellular Biorthogonal Imaging by Surface Enhanced Raman Spectroscopy using Alkyne-Silver Nanoparticles Clusters

Live intracellular imaging is a valuable tool in modern diagnostics and pharmacology. Surface Enhanced Raman Spectroscopy (SERS) stands out as a non-destructive and multiplexed technique, but intracellular SERS imaging still suffers from interfering background from endogenous components. Here we show the assembly of small colloidal SERS probes with Raman signal in the cell-silent window of 1800–2900 cm⁻¹ for biorthogonal intracellular SERS imaging of dopamine that was undistinguishable from the endogenous cell background. By linking colloidal silver nanoparticles with alkyne-dopamine adducts, clusters are formed by 2–6 nanoparticles spaced by tight interparticle gaps that exhibited high electric field enhancement and strong SERS signals of alkyne and dopamines. Due to the cell-silent signals of the alkyne, intracellular in-vitro Raman imaging shows that the dopamines on the internalized clusters remain distinguishable across the cytoplasm with good spatial resolution. Our method can be a general-purpose method for real-time imaging of biomolecules, such as proteins, peptides, DNA and drugs.

Optical imaging of metabolic dynamics in animals

Direct visualization of metabolic dynamics in living animals with high spatial and temporal resolution is essential to understanding many biological processes. Here we introduce a platform that combines deuterium oxide (D2O) probing with stimulated Raman scattering (DO-SRS) microscopy to image in situ metabolic activities. Enzymatic incorporation of D2O-derived deuterium into macromolecules generates carbon-deuterium (C-D) bonds, which track biosynthesis in tissues and can be imaged by SRS in situ. Within the broad vibrational spectra of C-D bonds, we discover lipid-, protein-, and DNA-specific Raman shifts and develop spectral unmixing methods to obtain C-D signals with macromolecular selectivity. DO-SRS microscopy enables us to probe de novo lipogenesis in animals, image protein biosynthesis without tissue bias, and simultaneously visualize lipid and protein metabolism and reveal their different dynamics. DO-SRS microscopy, being noninvasive, universally applicable, and cost-effective, can be adapted to a broad range of biological systems to study development, tissue homeostasis, aging, and tumor heterogeneity.

Electronic Preresonance Stimulated Raman Scattering Microscopy

Optical microscopy has generated great impact for modern research. While fluorescence microscopy provides the ultimate sensitivity, it generally lacks chemical information. Complementarily, vibrational imaging methods provide rich chemical-bond-specific contrasts. Nonetheless, they usually suffer from unsatisfying sensitivity or compromised biocompatibility. Recently, electronic preresonance stimulated Raman scattering (EPR-SRS) microscopy was reported, achieving simultaneous high detection sensitivity and superb vibrational specificity of chromophores. With newly synthesized Raman-active dyes, this method readily breaks the optical color barrier of fluorescence microscopy and is well-suited for supermultiplex imaging in biological samples. In this Perspective, we first review previous utilizations of electronic resonance in various Raman spectroscopy and microscopy. We then discuss the physical origin and uniqueness of the electronic preresonance region, followed by quantitative analysis of the enhancement factors involved in EPR-SRS microscopy. On this basis, we provide an outlook for future development as well as the broad applications in biophotonics.

Stimulated Raman scattering of polymer nanoparticles for multiplexed live-cell imaging

A novel nanoparticle-based imaging strategy is introduced that couples biocompatible organic nanoparticles and stimulated Raman scattering (SRS) microscopy. Polymer nanoparticles with vibrational labels incorporated were readily prepared for multi-color SRS imaging with excellent photo-stability. The Raman-active polymer dots are nontoxic, rapidly enter various cell types, and are applied in multiplexed cell-type sorting.

Copper-catalyzed aminoalkynylation of alkenes with hypervalent iodine reagents

A copper-catalyzed aminoalkynylation of alkenes is achieved with ethynylbenziodoxolone (EBX) reagents under mild conditions with only 1 mol% copper catalyst. This transformation allows for rapid construction of diverse important azahetereocycles and installation of valuable alkyne groups in one step. The developed method features remarkable substrate scope for both terminal and internal alkenes as well as different alkynyl groups, presenting great potential for broad applications in synthesis, bioconjugation, and molecular imaging.

Mitochondrial Imaging with Combined Fluorescence and Stimulated Raman Scattering Microscopy Using a Probe of the Aggregation-Induced Emission Characteristic

In vivo quantitative measurement of biodistribution plays a critical role in the drug/probe development and diagnosis/treatment process monitoring. In this work, we report a probe, named AIE-SRS-Mito, for imaging mitochondria in live cells via fluorescence (FL) and stimulated Raman scattering (SRS) imaging. The probe features an aggregation-induced emission (AIE) characteristic and possesses an enhanced alkyne Raman peak at 2223 cm^-1. The dual-mode imaging of AIE-SRS-Mito for selective mitochondrion-targeting was examined on a homemade FL-SRS microscope system. The detection limit of the probe in the SRS imaging was estimated to be 8.5 μM. Due to the linear concentration dependence of SRS and inertness of the alkyne Raman signal to environmental changes, the intracellular distribution of the probe was studied, showing a local concentration of >2.0 mM in the mitochondria matrix, which was >100-fold higher than the incubation concentration. To the best of our knowledge, this is the first time that the local concentration of AIE molecules inside cells has been measured noninvasively and directly. Also, the nonquenching effect of such AIE molecules in cell imaging has been verified by the positive correlation of FL and SRS signals. Our work will encourage the utilization of SRS microscopy for quantitative characterization of FL probes or other nonfluorescent compounds in living biological systems and the development of FL-SRS dual-mode probes for specific biotargets.

Applications of vibrational tags in biological imaging by Raman microscopy

As a superb tool to visualize and study the spatial-temporal distribution of chemicals, Raman microscopy has made a big impact in many disciplines of science. While label-free imaging has been the prevailing strategy in Raman microscopy, recent development and applications of vibrational/Raman tags, particularly when coupled with stimulated Raman scattering (SRS) microscopy, have generated intense excitement in biomedical imaging. SRS imaging of vibrational tags has enabled researchers to study a wide range of small biomolecules with high specificity, sensitivity and multiplex capability, at a single live cell level, tissue level or even in vivo. As reviewed in this article, this platform has facilitated imaging distribution and dynamics of small molecules such as glucose, lipids, amino acids, nucleic acids, and drugs that are otherwise difficult to monitor with other means. As both the vibrational tags and Raman instrumental development progress rapidly and synergistically, we anticipate that this technique will shed light onto an even broader spectrum of biomedical problems.

Bioorthogonal chemical imaging of metabolic changes during epithelial-mesenchymal transition of cancer cells by stimulated Raman scattering microscopy

Study of metabolic changes during epithelial-mesenchymal transition (EMT) of cancer cells is important for basic understanding and therapeutic management of cancer progression. We here used metabolic labeling and stimulated Raman scattering (SRS) microscopy, a strategy of bioorthogonal chemical imaging, to directly visualize changes in anabolic metabolism during cancer EMT at a single-cell level. MCF-7 breast cancer cell is employed as a model system. Four types of metabolites (amino acids, glucose, fatty acids, and choline) are labeled with either deuterium or alkyne (C≡C) tag. Their intracellular incorporations into MCF-7 cells before or after EMT are visualized by SRS imaging targeted at the signature vibration frequency of C-D or C≡C bonds. Overall, after EMT, anabolism of amino acids, glucose, and choline is less active, reflecting slower protein and membrane synthesis in mesenchymal cells. Interestingly, we also observed less incorporation of glucose and palmitate acids into membrane lipids, but more of them into lipid droplets in mesenchymal cells. This result indicates that, although mesenchymal cells synthesize fewer membrane lipids, they are actively storing energy into lipid droplets, either through de novo lipogenesis from glucose or direct scavenging of exogenous free fatty acids. Hence, metabolic labeling coupled with SRS can be a straightforward method in imaging cancer metabolism.

Noncanonical Function of a Small-Molecular Virulence Factor Coronatine against Plant Immunity: An In Vivo Raman Imaging Approach

Coronatine (1), a small-molecular virulence factor produced by plant-pathogenic bacteria, promotes bacterial infection by inducing the opening of stomatal pores, the major route of bacterial entry into the plant, via the jasmonate-mediated COI1-JAZ signaling pathway. However, this pathway is also important for multiple plant functions, including defense against wounding by herbivorous insects. Thus, suppression of the COI1-JAZ signaling pathway to block bacterial infection would concomitantly impair plant defense against herbivorous wounding. Here, we report additional, COI1-JAZ-independent, action of 1 in Arabidopsis thaliana guard cells. First, we found that a stereoisomer of 1 regulates the movement of Arabidopsis guard cells without affecting COI1-JAZ signaling. Second, we found using alkyne-tagged Raman imaging (ATRI) that 1 is localized to the endoplasmic reticulum (ER) of living guard cells of Arabidopsis. The use of arc6 mutant lacking chloroplast formation was pivotal to circumvent the issue of autofluorescence during ATRI. These findings indicate that 1 has an ER-related action on Arabidopsis stomata that bypasses the COI1-JAZ signaling module. It may be possible to suppress the action of 1 on stomata without impairing plant defense responses against herbivores.