FDISCO: Advanced solvent-based clearing method for imaging whole organs

The Role of Herb-Partitioned Moxibustion in the Angiogenesis of Colitis-Associated Cancer in Rats

Purpose

Angiogenesis in tumors is imperative to tumor growth. Our previous studies revealed that herb-partitioned moxibustion (HPM) could delay colitis-associated cancer (CAC), but the mechanism of the effects on the angiogenesis remains largely undiscovered. We aimed to investigate whether HPM delays CAC by inhibiting the angiogenesis with emergent three-dimensional (3D) imaging technologies.

Materials and Methods

The CAC model was induced by azoxymethane (AOM)/dextran sodium sulphate (DSS). The rats were randomly divided into normal, model and HPM groups. The tumorigenesis, number of tumors, and tumor diameter were observed. Immunohistochemistry or enzyme-linked immunosorbent assay (ELISA) was performed to assess the microvessel density (MVD), reactive oxygen species (ROS), hypoxia-inducible factor-1 alpha (HIF-1α), vascular endothelial growth factor A (VEGFA), vascular endothelial growth factor receptor 1 (VEGFR1), interleukin-6 (IL-6), interleukin-1 beta (IL-1β) and tumor necrosis factor-alpha (TNF-α). The three-dimensional imaging of solvent-cleared organs with superior fluorescence-preserving capability (FDISCO) tissue clearing technique was used to clear colon tissues, and the platelet endothelial cells were stained and labelled with platelet endothelial cell adhesion molecule 1 (PECAM-1). Imaris software was used to perform 3D measurement and analysis of the colonic vascular architecture.

Results

The HPM group were found decreased in the colon tumor diameter, MVD, ROS, HIF-1α, VEGFA, VEGFR1, IL-6, IL-1β, and TNF-α in colon tissues compared with those in the model group. 3D imaging revealed that the number of vessels, number of branch points, and vessel branch level in the HPM group were lower than those in the model group. The number of branch points and vessel branch level were negatively correlated with the average vessel length.

Conclusion

HPM plays a role in inhibiting CAC angiogenesis. This study may provide new evidence at the macroscopic level of vascular architecture for HPM to inhibit the progression of CAC by FDISCO tissue clearing technique for 3D imaging.

Hypoxia-Driven Neurovascular Impairment Underlies Structural-Functional Dissociation in Diabetic Sudomotor Dysfunction

Sudomotor dysfunction in diabetic patients increases the risk of fissures, infections, and diabetic foot ulcers (DFUs), thereby reducing the quality of life. Despite its clinical importance, the mechanisms underlying this dysfunction remain inadequately elucidated. This study addresses this gap by demonstrating that despite structural integrity, sweat glands (SGs) in diabetic individuals with DFUs, and a murine model of diabetic neuropathy (DN), exhibit functional impairments, as confirmed by histological and functional assays. Integrated transcriptome and proteome analysis revealed significant upregulation of the SG microenvironment in response to hypoxia, highlighting potential underlying pathways involved. In addition, histological staining and tissue clearing techniques provided evidence of impaired neurovascular networks adjacent to SGs. Single-cell RNA sequencing unveiled intricate intercellular communication networks among endothelial cells (ECs), neural cells (NCs), and sweat gland cells (SGCs), emphasizing intricate cellular interactions within the SG microenvironment. Furthermore, an in vitro SGC-NC interaction model (SNIM) was employed to validate the supportive role of NCs in regulating SGC functions, highlighting the neurovascular-SG axis in diabetic pathophysiology. These findings confirm the hypoxia-driven upregulation of the SG microenvironment and underscore the critical role of the neurovascular-SG axis in diabetic pathophysiology, providing insights into potential therapeutic targets for managing diabetic complications and improving patient outcomes.

SST neurons in the periaqueductal gray regulate urination and bladder function

Urination, a fundamental physiological process, is intricately regulated by central neural circuits. The periaqueductal gray (PAG) is a critical hub for urination control, yet the specific neuronal subtypes involved remain undefined. Here, we identified somatostatin (SST)-expressing neurons in the lateral and ventrolateral PAG (l/vlPAG) as key regulators of urination. SST+ neurons in the l/vlPAG exhibited activity closely aligned with urination onset in freely moving animals. Optogenetic activation of these neurons reliably triggered urination and bladder contraction, whereas their acute inhibition at urination onset halted ongoing urination. Moreover, activation of l/vlPAG SST+ neurons projecting to the pontine micturition center (PMC) elicited urination and bladder contraction, effects that were absent following pelvic nerve transection. These findings reveal that l/vlPAG SST+ neurons regulate urination through the PAG-PMC pathway, providing new insights into bladder control and potential therapeutic targets for bladder dysfunction.

Cartilage targeting cationic peptide carriers display deep cartilage penetration and retention in a rabbit model of post-traumatic osteoarthritis

OBJECTIVE

Drug delivery to cartilage is limited by its complex architecture and avascularity. Cationic peptide carriers (CPCs) have previously been optimized for improved cartilage transport and retention of drugs in vitro. In this study, we evaluated the kinetics, stability, and immunogenicity of CPCs after a single intra-articular injection using a rabbit knee injury model.

DESIGN

New Zealand White rabbits were administered a single dose of Cy5-labeled CPCs in knees receiving anterior cruciate ligament transection (ACLT) or Sham surgery. CPC biodistribution and retention within joint tissues and synovial fluid were evaluated 1 and 7 days after administration, and extra-articular kinetics were assessed in serum. Histology, immunohistochemistry, and reverse transcription quantitative polymerase chain reaction were performed to assess synovitis and protease activity. Proteolytic analysis of CPCs in the presence of arthritic enzymes was evaluated using synovial fluid size-exclusion filtration, Fluorescence Resonance Energy Transfer analysis, and computational molecular docking.

RESULTS

CPCs penetrated the full depth of sulfated glycosaminoglycan (sGAG)-rich tissues, notably cartilage, and were retained through the latest timepoint measured (one week) in both Sham and ACLT knees. Compared to ACLT, Sham knees had greater joint retention at Day 1 (1.6-fold) and Day 7 (1.8-fold). CPC intra-tissue concentration strongly correlated with tissue sGAG density, which did not considerably differ between surgical conditions at these timepoints. However, CPCs exhibited elevated vascular clearance and proteolytic fragmentation in inflammatory conditions. CPCs did not increase macrophage abundance, cytokine expression, or alter tissue morphology.

CONCLUSION

CPCs target the deep layers of cartilage, even in inflamed joints, and can be utilized to substantially improve intra-joint bioavailability of therapeutics.

High-Throughput Volumetric Mapping Facilitated by Active Tissue SHRINK

Comprehensive visualization of tissue architecture in large organs such as the brain is crucial for understanding functional relationships across key tissue regions. However, the large size of whole organs makes it challenging to image their entirety with subcellular resolution, often requiring prolonged imaging sessions, volume reconstruction, and compromises in spatial coverage. Here, Scalable Hydrogel-embedded Rapid Imaging of tissue NetworK (SHRINK) is reported to address this challenge through active tissue shrinkage and clearing. Utilizing the identified hydrogel network to preserve the spatial pattern of proteins in situ and remove the uncrosslinked biomolecules to create space, it is shown that SHRINK isotropically drives the reduction of sample sizes down to 16% of their original volume while maintaining high cellular and tissue-level integrity in a reversible manner. The size reduction and the corresponding 3D concentrating of the biomolecules render a more than sixfold enhancement for throughput and signal respectively, which addresses a key bottleneck for the stimulated Raman scattering (SRS) microscopy, ideal for 3D, label-free and super-multiplex tissue mapping. It is further demonstrated that SHRINK-SRS achieves organ-scale mapping of brain, intestine, heart, and kidney tissues. SHRINK offers a powerful approach to overcome traditional imaging barriers, enabling rapid and detailed visualization of large organs.

A multiwell plate approach to increase the sample throughput during tissue clearing

Tissue clearing, coupled with immunostaining, enables the transition from two-dimensional to three-dimensional pathology and has the potential to substantially improve data quality for biomedical diagnostics. Nevertheless, the workflows are limited by the complex sample processing protocols. Approaches for the parallel processing of samples, to include tissue clearing, immunostaining, imaging and analysis can increase three-dimensional pathology throughput. Here we detail a step-by-step approach that combines a tissue clearing device with a six-well multiwell plate to increase the throughput compared with methods using conventional clearing protocols. The six-well multiplate allows for parallel tissue clearing of multiple samples and is compatible with passive tissue clearing methods including Clear, Unobstructed Brain/Body Imaging Cocktails and Computational (CUBIC) analysis. In addition, gel embedding is performed without moving the samples from the wells, and a series of steps such as imaging with a high-speed light-sheet microscope and analysis in the cloud can be performed. Although this procedure slightly extends the overall time required for preparing and analyzing a single sample, it reduces the effort required at each step, such as reagent exchange and gel embedding, which results in an overall reduction in hands-on time due to the parallel sample processing. We describe a series of whole-organ analyses, including high-throughput tissue clearing, staining, gel embedding, imaging and data analysis in the cloud, as a useful platform for cellular biology and pathology. The total process varies depending on the presence or absence of immunostaining, but for some six-well plates, the tissue clearing process, imaging and data analysis can be completed within 10 d.

Lymphatic Endothelial Branched-Chain Amino Acid Catabolic Defects Undermine Cardiac Lymphatic Integrity and Drive HFpEF

BACKGROUND

Heart failure with preserved ejection fraction (HFpEF) has become the most prevalent type of heart failure, but effective treatments are lacking. Cardiac lymphatics play a crucial role in maintaining heart health by draining fluids and immune cells. However, their involvement in HFpEF remains largely unexplored.

METHODS

We examined cardiac lymphatic alterations in mice with HFpEF with comorbid obesity and hypertension, and in heart tissues from patients with HFpEF. Using genetically engineered mouse models and various cellular and molecular techniques, we investigated the role of cardiac lymphatics in HFpEF and the underlying mechanisms.

RESULTS

In mice with HFpEF, cardiac lymphatics displayed substantial structural and functional anomalies, including decreased lymphatic endothelial cell (LEC) density, vessel fragmentation, reduced branch connections, and impaired capacity to drain fluids and immune cells. LEC numbers and marker expression levels were also decreased in heart tissues from patients with HFpEF. Stimulating lymphangiogenesis with an adeno-associated virus expressing an engineered variant of vascular endothelial growth factor C (VEGFCC156S) that selectively activates vascular endothelial growth factor receptor 3 (VEGFR3) in LECs restored cardiac lymphatic integrity and substantially alleviated HFpEF. Through discovery-driven approaches, defective branched-chain amino acid (BCAA) catabolism was identified as a predominant metabolic signature in HFpEF cardiac LECs. Overexpression of branched-chain ketoacid dehydrogenase kinase (encoded by the Bckdk gene), which inactivates branched-chain ketoacid dehydrogenase (the rate-limiting enzyme in BCAA catabolism), resulted in spontaneous lymphangiogenic defects in LECs. In mice, inducible Bckdk gene deletion in LECs to enhance their BCAA catabolism preserved cardiac lymphatic integrity and protected against HFpEF. BCAA catabolic defects caused ligand-independent phosphorylation of VEGFR3 in the cytoplasm by Src kinase, leading to lysosomal degradation of VEGFR3 instead of its trafficking to the cell membrane. Reduced VEGFR3 availability on the cell surface impeded downstream Akt (protein kinase B) activation, hindered glucose uptake and utilization, and inhibited lymphangiogenesis in LECs with BCAA catabolic defects.

CONCLUSIONS

Our study provides evidence that cardiac lymphatic disruption, driven by impaired BCAA catabolism in LECs, is a key factor contributing to HFpEF. These findings unravel the crucial role of BCAA catabolism in modulating lymphatic biology, and suggest that preserving cardiac lymphatic integrity may present a novel therapeutic strategy for HFpEF.

3D visualization of neurovascular networks in pulp-exposed rat molars using tissue clearing techniques

To explore the spatial distribution of the neurovascular network following pulp exposure using tissue clearing technology and three-dimensional imaging. An animal model with dental pulp exposure was established in maxillary molars of Sprague-Dawley rats using a round bur under water cooling. Histological evaluation was performed at various time points, and samples at 24 h postoperatively was selected for tissue clearing and whole-mount immunofluorescence staining using markers for blood vessels, nerves, lymphatics, and mesenchymal stem cells. Three-dimensional images were captured with a light-sheet microscope. Three-dimensional imaging revealed the spatial arrangement of nerves, blood vessels, and lymphatic vessels, as well as the relative positions of sympathetic and sensory nerves in the maxilla. The neurovascular network structure in pulp-exposed molars showed significant alterations compared to healthy molars. Additionally, nerves passing through lateral canals were visualized in three-dimensional space. Numerous STRO-1-positive cells were identified in the maxilla, although their distribution lacked a defined spatial pattern. This study sheds light on the three-dimensional architecture of vascular, neural, and lymphatic networks in dental pulp and surrounding tissues under healthy and pathological conditions. Tissue clearing proves to be a valuable technique for visualizing the spatial organization of dental pulp tissue in physiological and pathological states.

ADAPT-3D: Accelerated Deep Adaptable Processing of Tissue for 3-Dimensional Fluorescence Tissue Imaging for Research and Clinical Settings

Light sheet microscopy and preparative clearing methods that improve light penetration in 3D tissues have revolutionized imaging in biomedical research. While most clearing methods focus on removing molecules that scatter light, the methods generally involve immersing tissues in solutions that minimize refraction of light to enhance detection of fluorescent signal deeper into tissues. Here, we developed a new tissue preparative method called ADAPT-3D with broad applicability across species and tissue types. This method enables efficient antibody staining and detection of endogenous fluorophores and offers advantages in terms of speed at which tissue staining and clearing is achieved. In about 4 days from tissue harvest to imaging, human intestinal tissue could be Axed, decolored and delipidated to remove light-interfering substances and stained with antibodies for imaging. In the intact mouse skull and brain, involving an 8-day protocol from tissue harvest to completion of imaging, the aqueous and non-shrinking ADAPT-3D method allowed the specialized channels between skull and underlying tissue to be detected without meningeal tearing. Overall, ADAPT-3D provides a highly versatile preparative method for 3D fixed tissue imaging with superior time savings, sensitivity and preservation of tissue morphology compared with previously described methods.

From morphology to single-cell molecules: high-resolution 3D histology in biomedicine

High-resolution three-dimensional (3D) tissue analysis has emerged as a transformative innovation in the life sciences, providing detailed insights into the spatial organization and molecular composition of biological tissues. This review begins by tracing the historical milestones that have shaped the development of high-resolution 3D histology, highlighting key breakthroughs that have facilitated the advancement of current technologies. We then systematically categorize the various families of high-resolution 3D histology techniques, discussing their core principles, capabilities, and inherent limitations. These 3D histology techniques include microscopy imaging, tomographic approaches, single-cell and spatial omics, computational methods and 3D tissue reconstruction (e.g. 3D cultures and spheroids). Additionally, we explore a wide range of applications for single-cell 3D histology, demonstrating how single-cell and spatial technologies are being utilized in the fields such as oncology, cardiology, neuroscience, immunology, developmental biology and regenerative medicine. Despite the remarkable progress made in recent years, the field still faces significant challenges, including high barriers to entry, issues with data robustness, ambiguous best practices for experimental design, and a lack of standardization across methodologies. This review offers a thorough analysis of these challenges and presents recommendations to surmount them, with the overarching goal of nurturing ongoing innovation and broader integration of cellular 3D tissue analysis in both biology research and clinical practice.

Brain-wide immunolabeling and tissue clearing applications for engram research

In recent years, there has been significant progress in memory research, driven by genetic and imaging technological advances that have given unprecedented access to individual memory traces or engrams. Although Karl Lashley argued since the 1930s that an engram is not confined to a particular area but rather distributed across the entire brain, most current studies have focused exclusively on a single or few brain regions. However, this compartmentalized approach overlooks the interactions between multiple brain regions, limiting our understanding of engram mechanisms. More recently, several studies have begun to investigate engrams across the brain, but research is still limited by a lack of standardized techniques capable of reconstructing multiple ensembles at single-cell resolution across the entire brain. In this review, we guide researchers through the latest technological advancements and discoveries in immediate early gene (IEG) techniques, tissue clearing methods, microscope modalities, and automated large-scale analysis. These innovations could propel the field forward in building brain-wide engram maps of normal and disease states, thus, providing unprecedented new insights. Ultimately, this review aims to bridge the gap between research focused on single brain regions and the need for a comprehensive understanding of whole-brain engrams, revealing new approaches for exploring the neuronal mechanisms underlying engrams.

Tissue Clearing and Its Application in Nanoparticle Development

Nanoparticles are widely used in biomedical applications due to their small size, large surface area, and unique physicochemical properties. These characteristics make them ideal for drug delivery, diagnostic imaging, and therapeutic interventions. Their ability to interact with biological systems at the cellular and molecular levels enables targeted treatments. Understanding the biodistribution of nanoparticles at the cellular level within whole organisms is crucial for assessing their safety and effectiveness; however, proper technologies have been lacking to achieve this. For example, traditional imaging techniques like magnetic resonance imaging (MRI) and computed tomography (CT) often lack the resolution needed, while tissue-section-based methods miss the whole-body systemic view. Recent tissue clearing methods have emerged as a promising solution for 3D visualization of nanoparticles in entire organs, as they enable cellular-level imaging of whole organisms without the need for sectioning. This review explores advancements in diverse tissue clearing techniques and their application in studying nanoparticle biodistribution, providing insights crucial for the development of nanoparticle-based therapies.

Intracalvariosseous injection: an approach for central nervous system drug delivery through skull bone marrow with a preclinical research in stroke

BACKGROUND

Central nervous system (CNS) accessibility constitutes a major hurdle for drug development to treat neurological diseases. Existing drug delivery methods rely on breaking the blood-brain barrier (BBB) for drugs to penetrate the CNS. Researchers have discovered natural microchannels between the skull bone marrow and the dura mater, providing a pathway for drug delivery through the skull bone marrow. However, there has been no research on the feasibility, safety, and efficacy of this delivery method for drug treatment of stroke.

METHODS

We used a microporous method for intracalvariosseous (ICO) injection to deliver drugs directly into brain parenchyma through skull bone marrow. Safety of ICO was assessed by monitoring changes in skull and peripheral blood neutrophil counts, and FITC-dextran extravasation across the BBB. Drug delivery pathways were observed through transparent skull-dura mater-brain tissue. In a rodent stroke model, NA-1 or Y-3 neuroprotective agents were administered via ICO to evaluate safety and efficacy by assessing neurological deficits, infarct size, neuroinflammatory factors, neuronal apoptosis, and liver/kidney function. Drug concentration in tissues was measured using fluorescence tracing and high-performance liquid chromatography to gauge ICO delivery efficiency.

FINDINGS

ICO injection delivers drugs to the brain parenchyma through microchannels between the skull bone marrow and the dura mater, offering higher delivery efficiency than intravenous injection. After ICO injection, there were no changes in neutrophil counts in the skull bone marrow and peripheral blood, and the amount of FITC-dextran passing through the BBB remained unchanged. This confirmed that ICO injection does not cause skull infection or break BBB, which suggested ICO injection is safe and feasible. In the treatment of stroke with neuroprotective agents, although the drug dosage of ICO injection was lower than intravenous injection, drug accumulation in the brain increased after ICO injection, which helped repair nerve damage, reduce neuronal apoptosis, and decrease the expression of inflammatory factors.

INTERPRETATION

ICO injection is a central nervous system drug delivery method that utilizes natural microchannels between the skull and dura mater for efficient drug delivery. Our results assessed the feasibility and safety of ICO injection at the preclinical level and evaluated its efficacy in animal models of stroke. The findings provided a foundation for the clinical translation of ICO injection.

FUNDING

This study was supported by The National Natural Science Foundation of China (No. 82425101); Beijing Municipal Science & Technology Commission (No. Z231100004823036); Capital's Funds for Health Improvement and Research (2022-2-2045); National Key Research & Development Program of China (2022YFF1501500, 2022YFF1501501, 2022YFF1501502, 2022YFF1501503, 2022YFF1501504, 2022YFF1501505).

Rescue-like behavior in a bystander mouse toward anesthetized conspecifics promotes arousal via a tongue-brain connection

Prosocial behaviors are advantageous to social species, but the neural mechanism(s) through which others receive benefit remain unknown. Here, we found that bystander mice display rescue-like behavior (tongue dragging) toward anesthetized cagemates and found that this tongue dragging promotes arousal from anesthesia through a direct tongue-brain circuit. We found that a direct circuit from the tongue → glutamatergic neurons in the mesencephalic trigeminal nucleus (MTNGlu) → noradrenergic neurons in the locus coeruleus (LCNE) drives rapid arousal in the anesthetized mice that receive the rescue-like behavior from bystanders. Artificial inhibition of this circuit abolishes the rapid arousal effect induced by the rescue-like behavior. Further, we revealed that glutamatergic neurons in the paraventricular nucleus of the thalamus (PVTGlu) that project to the nucleus accumbens shell (NAcSh) mediate the rescue-like behavior. These findings reveal a tongue-brain connection underlying the rapid arousal effects induced by rescue-like behavior and the circuit basis governing this specific form of prosocial behavior.

Intramuscular Injection of rAAV2-retro for Low Motor Neuron Transduction: Evaluating Five Promoters

Recombinant adeno-associated viral vectors (rAAVs) can effectively deliver transgene to the nervous system. The selection of AAV serotype and promoter significantly influences the dynamics of the transgene expression, including its strength and cell-specificity. Previous studies demonstrated that in neonatal mice, the intramuscular (IM) injection of the rAAV2-retro vector could efficiently deliver transgene to lower motor neurons (LMNs) of the brainstem and spinal cord. However, the best promoter for the expression of transgene in the central neural system (CNS) using rAAV2-retro remains undetermined. This study compared five commonly used promoters, including mouse phosphoglycerate kinase (mPGK), CMV early enhancer/chicken β-actin/short β-globulin intron (CAG), human cytomegalovirus (hCMV), chicken β-actin (CBA), and human synapsin (hSyn) promoters. The IM (unilateral gastrocnemius muscle) injection of rAAV2-retro vectors packaged with the reporter constructs containing each promoter was performed in the newborn C57BL/6J mice. The levels of gene expression and the types of cells were examined using the light-sheet illumination imaging technique and confocal microscopy. Our findings revealed that rAAV2-retro primarily targeted the brainstem and spinal cord within the CNS. Among the five promoters tested, CAG and hCMV showed the highest gene expression. Almost all the transduced cells were identified as LMNs. Additionally, gene expression driven by hCMV was found to be dependent of the inclusion of WPRE and β-globin intron elements. Importantly, none of the promoters induced hepatotoxicity, ensuring the safety of rAAV2-retro-mediated expression. This study provided valuable insights for optimizing the rAAV2-retro-mediated gene delivery system to LMNs in the brainstem and spinal cord, which might have potential implications for research on motor neuron-related diseases.

Strongly absorbing molecules make tissue transparent: a new insight for understanding tissue optical clearing

Optical imaging plays a central role in the field of biomedicine, but it suffers from the light scattering of tissues. The research group from Stanford University has reported a counterintuitive observation that strongly absorbing molecules could achieve optical transparency in live animals, providing a new insight for understanding tissue optical clearing. It empowers scientists to leverage optical imaging techniques for in vivo observation of a wide range of deep-seated structures and activities.

A functional tacrolimus-releasing nerve wrap for enhancing nerve regeneration following surgical nerve repair

JOURNAL/nrgr/04.03/01300535-202501000-00036/figure1/v/2024-05-14T021156Z/r/image-tiff Axonal regeneration following surgical nerve repair is slow and often incomplete, resulting in poor functional recovery which sometimes contributes to lifelong disability. Currently, there are no FDA-approved therapies available to promote nerve regeneration. Tacrolimus accelerates axonal regeneration, but systemic side effects presently outweigh its potential benefits for peripheral nerve surgery. The authors describe herein a biodegradable polyurethane-based drug delivery system for the sustained local release of tacrolimus at the nerve repair site, with suitable properties for scalable production and clinical application, aiming to promote nerve regeneration and functional recovery with minimal systemic drug exposure. Tacrolimus is encapsulated into co-axially electrospun polycarbonate-urethane nanofibers to generate an implantable nerve wrap that releases therapeutic doses of bioactive tacrolimus over 31 days. Size and drug loading are adjustable for applications in small and large caliber nerves, and the wrap degrades within 120 days into biocompatible byproducts. Tacrolimus released from the nerve wrap promotes axon elongation in vitro and accelerates nerve regeneration and functional recovery in preclinical nerve repair models while off-target systemic drug exposure is reduced by 80% compared with systemic delivery. Given its surgical suitability and preclinical efficacy and safety, this system may provide a readily translatable approach to support axonal regeneration and recovery in patients undergoing nerve surgery.

Three-dimensional characteristics of T cells and vasculature in the development of mouse esophageal cancer

Esophageal squamous cell carcinoma (ESCC) is a common malignancy, characterized by a multistep pathogenic process regulated spatiotemporally within the esophageal epithelial microenvironment, including vessel normalization and immune infiltration. However, empirical evidence elucidating esophageal vascular remodeling and immune infiltration during ESCC tumorigenesis in situ is lacking. In this study, utilizing a mouse model recapitulating progressive human ESCC stages, we established a tissue clearing workflow for three-dimensional visualization and analysis of esophageal vessels and T cell distribution. Through this workflow, we delineated the spatial dynamics of vascular remodeling, CD3+ T cells, and characteristic T cell aggregates employing high-resolution light-sheet fluorescence microscopy across five ESCC pathogenic stages. Vessel remodeling might be coupled with T cell infiltration, and their interactions predominantly occurred at the inflammatory stage. These findings provided insights into research methodologies of esophageal cancer and spatiotemporal landscapes of vascular and T cell during ESCC initiation and progression.

Delivery and kinetics of immersion optical clearing agents in tissues: Optical imaging from ex vivo to in vivo

Advanced optical imaging provides a powerful tool for the structural and functional analysis of tissues with high resolution and contrast, but the imaging performance decreases as light propagates deeper into the tissue. Tissue optical clearing technique demonstrates an innovative way to realize deep-tissue imaging and have emerged substantially in the last two decades. Here, we briefly reviewed the basic principles of tissue optical clearing techniques in the view of delivery strategies via either free diffusion or external forces-driven advection, and the commonly-used optical techniques for monitoring kinetics of clearing agents in tissue, as well as their ex vivo to in vivo applications in multiple biomedical research fields. With future efforts on the even distribution of both clearing agents and probes, excavation of more effective clearing agents, and automation of tissue clearing processes, tissue optical clearing should provide more insights into the fundamental questions in biological events clinical diagnostics.

3D light-sheet fluorescence microscopy in preclinical and clinical drug discovery

Light-sheet fluorescence microscopy (LSFM) combined with tissue clearing has emerged as a powerful technology in drug discovery. LSFM is applicable to a variety of samples, from rodent organs to clinical tissue biopsies, and has been used for characterizing drug targets in tissues, demonstrating the biodistribution of pharmaceuticals and determining their efficacy and mode of action. LSFM is scalable to high-throughput analysis and provides resolution down to the single cell level. In this review, we describe the advantages of implementing LSFM into the drug discovery pipeline and highlight recent advances in this field.

WISH-BONE: Whole-mount in situ histology, to label osteocyte mRNA and protein in 3D adult mouse bones

Bone is a three-dimensional (3D) highly dynamic tissue under constant remodeling. Commonly used tools to investigate bone biology require sample digestion for biomolecule extraction or provide only two-dimensional (2D) spatial information. There is a need for 3D tools to investigate spatially preserved biomarker expression in osteocytes. In this work, we present a new method, WISH-BONE, to label osteocyte messenger RNA (mRNA) and protein in whole-mount mouse bone. For mRNA labeling, we used hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) to label genes of interest in osteocytes. For protein labeling, samples were preserved using an epoxy-based solution that protects tissue structure and biomolecular components. Then an enzymatic matrix permeabilization step was performed to enable antibody penetration. Immunostaining was used to label various proteins involved in bone homeostasis. We also demonstrate the use of customized fluorescent nanobodies to target and label proteins in the cortical bone (CB). However, the relatively dim signal observed from nanobodies' staining limited detection. mRNA and protein labeling were performed in separate samples. In this study, we share protocols, highlight opportunities, and identify the challenges of this novel 3D labeling method. They are the first protocols for whole-mount osteocyte 3D labeling of mRNA and protein in mature mouse bones. WISH-BONE will allow the investigation of molecular signaling in bone cells in their 3D environment and could be applied to various bone-related fields of research.

FLUID: a fluorescence-friendly lipid-compatible ultrafast clearing method

Many clearing methods achieve high transparency by removing lipid components from tissues, which damages microstructure and limits their application in lipid research. As for methods which preserve lipid, it is difficult to balance transparency, fluorescence preservation and clearing speed. In this study, we propose a rapid water-based clearing method that is fluorescence-friendly and preserves lipid components. FLUID allows for preservation of endogenous fluorescence over 60 days. It shows negligible tissue distortion and is compatible with various types of fluorescent labeling and tissue staining methods. High quality imaging of human brain tissue and compatibility with pathological staining demonstrated the potential of our method for three-dimensional (3D) biopsy and clinical pathological diagnosis.

SOLID: minimizing tissue distortion for brain-wide profiling of diverse architectures

Brain-wide profiling of diverse biological components is fundamental for understanding complex brain pathology. Despite the availability in whole-brain imaging, it is still challenging to conduct multiplexed, brain-wide analysis with current tissue clearing techniques. Here, we propose SOLID, a hydrophobic tissue clearing method that can minimize tissue distortion while offering impressive clearing performance. SOLID achieves high-quality imaging of multi-color labeled mouse brain, and the acquired datasets can be effectively registered to the Allen Brain Atlas via commonly-used algorithms. SOLID enables generation of neural and vascular maps within one mouse brain, as well as tracing of specific neural projections labeled with viruses. SOLID also allows cross-channel investigations of β-amyloid plaques and neurovascular lesions in the reconstructed all-in-one panorama, providing quantitative insights into structural interactions at different stages of Alzheimer's disease. Altogether, SOLID provides a robust pipeline for whole-brain mapping, which may widen the utility of tissue clearing techniques in diverse neuroscience research.

T-CLEARE: a pilot community-driven tissue clearing protocol repository

Selecting and implementing a tissue clearing protocol is challenging. Established more than 100 years ago, tissue clearing is still a rapidly evolving field of research. There are currently many published protocols to choose from, and each performs better or worse across a range of key evaluation factors (e.g., speed, cost, tissue stability, fluorescence quenching). Additionally, tissue clearing protocols are often optimized for specific experimental contexts, and applying an existing protocol to a new problem can require a lengthy period of adaptation by trial and error. Although the primary literature and review articles provide a useful starting point for optimization, there is growing recognition that results can vary dramatically with changes to tissue type or antibody used. To help address this issue, we have developed a novel, freely available repository of tissue clearing protocols named T-CLEARE (Tissue CLEAring protocol REpository; https://doryworkspace.org/doryviz). T-CLEARE incorporates community responses to an open survey designed to capture details not commonly found in the scientific literature, including modifications to published protocols required for specific use cases and instances when tissue clearing protocols did not perform well (negative results). The goal of T-CLEARE is to help the community share evaluations and modifications of tissue clearing protocols for various tissue types and potentially identify best-in-class methods for a given application.

Low-cost and scalable projected light-sheet microscopy for the high-resolution imaging of cleared tissue and living samples

Light-sheet fluorescence microscopy (LSFM) is a widely used technique for imaging cleared tissue and living samples. However, high-performance LSFM systems are typically expensive and not easily scalable. Here we introduce a low-cost, scalable and versatile LSFM framework, which we named 'projected light-sheet microscopy' (pLSM), with high imaging performance and small device and computational footprints. We characterized the capabilities of pLSM, which repurposes readily available consumer-grade components, optimized optics, over-network control architecture and software-driven light-sheet modulation, by performing high-resolution mapping of cleared mouse brains and of post-mortem pathological human brain samples, and via the molecular phenotyping of brain and blood-vessel organoids derived from human induced pluripotent stem cells. We also report a method that leverages pLSM for the live imaging of the dynamics of sparsely labelled multi-layered bacterial pellicle biofilms at an air-liquid interface. pLSM can make high-resolution LSFM for biomedical applications more accessible, affordable and scalable.

Lung megakaryocytes engulf inhaled airborne particles to promote intrapulmonary inflammation and extrapulmonary distribution

Many lung immune cells are known to respond to inhaled particulate matter. However, current known responses cannot explain how particles induce thrombosis in the lung and how they translocate to distant organs. Here, we demonstrate that lung megakaryocytes (MKs) in the alveolar and interstitial regions display location-determined characteristics and act as crucial responders to inhaled particles. They move rapidly to engulf particles and become activated with upregulation in inflammatory responses and thrombopoiesis. Comprehensive in vivo, in vitro and ex vivo results unraveled that MKs were involved in particle-induced lung damages and shed particle-containing platelets into blood circulation. Moreover, MK-derived platelets exhibited faster clotting, stronger adhesion than normal resting platelets, and inherited the engulfed particles from parent MKs to assist in extrapulmonary particle transportation. Our findings collectively highlight that the specific responses of MKs towards inhaled particles and their roles in facilitating the translocation of particles from the lungs to extrapulmonary organs for clearance.

Intravital two-photon microscopy of the native mouse thymus

The thymus, a key organ in the adaptive immune system, is sensitive to a variety of insults including cytotoxic preconditioning, which leads to atrophy, compression of the blood vascular system, and alterations in hemodynamics. Although the thymus has innate regenerative capabilities, the production of T cells relies on the trafficking of lymphoid progenitors from the bone marrow through the altered thymic blood vascular system. Our understanding of thymic blood vascular hemodynamics is limited due to technical challenges associated with accessing the native thymus in live mice. To overcome this challenge, we developed an intravital two-photon imaging method to visualize the native thymus in vivo and investigated functional changes to the vascular system following sublethal irradiation. We quantified blood flow velocity and shear rate in cortical blood vessels and identified a subtle but significant increase in vessel leakage and diameter ~24 hrs post-sublethal irradiation. Ex vivo whole organ imaging of optically cleared thymus lobes confirmed a disruption of the thymus vascular structure, resulting in an increase in blood vessel diameter and vessel area, and concurrent thymic atrophy. This novel two-photon intravital imaging method enables a new paradigm for directly investigating the thymic microenvironment in vivo.

Flexible solid immersion meniscus lens (SIMlens) approach for enhancing biological imaging of cleared samples

Tissue-clearing techniques have revolutionized the field of biological imaging by rendering biological specimens transparent and enabling inside optical detection. Light-sheet fluorescence microscopy (LSFM) is a powerful tool for three-dimensional imaging of large biological samples. Combining tissue-clearing techniques with LSFM has advanced the efficient 3D visualization of these samples. A crucial challenge with LSFM is the requirement for the objective to operate within the clearing reagent, which can cause aberrations. To address this issue, we introduce a novel, to our knowledge, approach for the flexible design of the solid immersion refractive meniscus lens (SIMlens), facilitating the use of air objectives with cleared samples. Compared to the previous SIMlens, this method not only eliminates aberrations but also offers customized options for enhancing the numerical aperture and working distance of the objective lens, achieving at least a 10% improvement. We have demonstrated the feasibility of this new method using mouse brain samples.

Clay Sculpture-Inspired 3D Printed Microcage Module Using Bioadhesion Assembly for Specific-Shaped Tissue Vascularization and Regeneration

3D bioprinting techniques have enabled the fabrication of irregular large-sized tissue engineering scaffolds. However, complicated customized designs increase the medical burden. Meanwhile, the integrated printing process hinders the cellular uniform distribution and local angiogenesis. A novel approach is introduced to the construction of sizable tissue engineering grafts by employing hydrogel 3D printing for modular bioadhesion assembly, and a poly (ethylene glycol) diacrylate (PEGDA)-gelatin-dopamine (PGD) hydrogel, photosensitive and adhesive, enabling fine microcage module fabrication via DLP 3D printing is developed. The PGD hydrogel printed micocages are flexible, allowing various shapes and cell/tissue fillings for repairing diverse irregular tissue defects. In vivo experiments demonstrate robust vascularization and superior graft survival in nude mice. This assembly strategy based on scalable 3D printed hydrogel microcage module could simplify the construction of tissue with large volume and complex components, offering promise for diverse large tissue defect repairs.

A robust vessel-labeling pipeline with high tissue clearing compatibility for 3D mapping of vascular networks

The combination of vessel-labeling, tissue-clearing, and light-sheet imaging techniques provides a potent tool for accurately mapping vascular networks, enabling the assessment of vascular remodeling in vascular-related disorders. However, most vascular labeling methods face challenges such as inadequate labeling efficiency or poor compatibility with current tissue clearing technology, which significantly undermines the image quality. To address this limitation, we introduce a vessel-labeling pipeline, termed Ultralabel, which relies on a specially designed dye hydrogel containing lysine-fixable dextran and gelatins for double enhancement. Ultralabel demonstrates not only excellent vessel-labeling capability but also strong compatibility with all tissue clearing methods tested, which outperforms other vessel-labeling methods. Consequently, Ultralabel enables fine mapping of vascular networks in diverse organs, as well as multi-color labeling alongside other labeling techniques. Ultralabel should provide a robust and user-friendly method for obtaining 3D vascular networks in different biomedical applications.

Applications of Tissue Clearing in Central and Peripheral Nerves

The techniques of tissue clearing have been proposed and applied in anatomical and biomedical research since the 19th century. As we all know, the original study of the nervous system relied on serial ultrathin sections and stereoscopic techniques. The 3D visualization of the nervous system was established by software splicing and reconstruction. With the development of science and technology, microscope equipment had constantly been upgraded. Despite the great progress that has been made in this field, the workload is too complex, and it needs high technical requirements. Abundant mistakes due to manual sections were inescapable and structural integrity remained questionable. According to the classification of tissue transparency methods, we introduced the latest application of transparency methods in central and peripheral nerve research from optical imaging, molecular markers and data analysis. This review summarizes the application of transparent technology in neural pathways. We hope to provide some inspiration for the continuous optimization of tissue clearing methods.

Spatial analysis of tissue immunity and vascularity by light sheet fluorescence microscopy

The pathogenesis of cancer and cardiovascular diseases is subjected to spatiotemporal regulation by the tissue microenvironment. Multiplex visualization of the microenvironmental components, including immune cells, vasculature and tissue hypoxia, provides critical information underlying the disease progression and therapy resistance, which is often limited by imaging depth and resolution in large-volume tissues. To this end, light sheet fluorescence microscopy, following tissue clarification and immunostaining, may generate three-dimensional high-resolution images at a whole-organ level. Here we provide a detailed description of light sheet fluorescence microscopy imaging analysis of immune cell composition, vascularization, tissue perfusion and hypoxia in mouse normal brains and hearts, as well as brain tumors. We describe a procedure for visualizing tissue vascularization, perfusion and hypoxia with a transgenic vascular labeling system. We provide the procedures for tissue collection, tissue semi-clearing and immunostaining. We further describe standard methods for analyzing tissue immunity and vascularity. We anticipate that this method will facilitate the spatial illustration of structure and function of the tissue microenvironmental components in cancer and cardiovascular diseases. The procedure requires 1-2 weeks and can be performed by users with expertise in general molecular biology.

An MR-based brain template and atlas for optical projection tomography and light sheet fluorescence microscopy in neuroscience

Introduction

Optical Projection Tomography (OPT) and light sheet fluorescence microscopy (LSFM) are high resolution optical imaging techniques, ideally suited for ex vivo 3D whole mouse brain imaging. Although they exhibit high specificity for their targets, the anatomical detail provided by tissue autofluorescence remains limited.

Methods

T1-weighted images were acquired from 19 BABB or DBE cleared brains to create an MR template using serial longitudinal registration. Afterwards, fluorescent OPT and LSFM images were coregistered/normalized to the MR template to create fusion images.

Results

Volumetric calculations revealed a significant difference between BABB and DBE cleared brains, leading to develop two optimized templates, with associated tissue priors and brain atlas, for BABB (OCUM) and DBE (iOCUM). By creating fusion images, we identified virus infected brain regions, mapped dopamine transporter and translocator protein expression, and traced innervation from the eye along the optic tract to the thalamus and superior colliculus using cholera toxin B. Fusion images allowed for precise anatomical identification of fluorescent signal in the detailed anatomical context provided by MR.

Discussion

The possibility to anatomically map fluorescent signals on magnetic resonance (MR) images, widely used in clinical and preclinical neuroscience, would greatly benefit applications of optical imaging of mouse brain. These specific MR templates for cleared brains enable a broad range of neuroscientific applications integrating 3D optical brain imaging.

MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution

Analyzing immune cell interactions in the bone marrow is vital for understanding hematopoiesis and bone homeostasis. Three-dimensional analysis of the complete, intact bone marrow within the cortex of whole long bones remains a challenge, especially at subcellular resolution. We present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur, enabling identification and spatial characterization of hematopoietic and stromal cell subsets. By combining a pre-processing algorithm for stripe artifact removal with a machine-learning approach, we demonstrate reliable cell segmentation down to the deepest bone marrow regions. This reveals age-related changes in the marrow. It highlights the interaction between CX3CR1+ cells and the vascular system in homeostasis, in contrast to other myeloid cell types, and reveals their spatial characteristics after injury. The broad applicability of this method will contribute to a better understanding of bone marrow biology.

Understanding glioblastoma stromal barriers against NK cell attack using tri-culture 3D spheroid model

Glioblastoma multiforme (GBM), a highly aggressive tumor type with a dismal survival rate, has a poor outcome which is at least partly attributed to the crosstalk between cancer cells and cells from the tumor microenvironment such as astrocytes and microglia. We aimed to decipher the effect of these cells on GBM progression and on cell-based therapies using 3D co-cultures. Co-culturing of glioblastoma cells with patient-derived astrocytes or microglia or both formed dense and heterogeneous spheroids. Both, astrocytes and microglia, enhanced the spheroid growth rate and formed a physical barrier for macromolecules penetration, while only astrocytes enhanced the migration. Interestingly bi-/tri-cultured spheroids showed significant resistance against NK-92 cells, likely attributed to dense stroma and induced expression of immunosuppressive genes such as IDO1 or PTGES2. Altogether, our novel 3D GBM spheroid model recapitulates the cell-to-cell interactions of human glioblastoma and can serve as a suitable platform for evaluating cancer therapeutics.

Whole-Body and Whole-Organ 3D Imaging of Hypoxia Using an Activatable Covalent Fluorescent Probe Compatible with Tissue Clearing

Elucidation of biological phenomena requires imaging of microenvironments in vivo. Although the seamless visualization of in vivo hypoxia from the level of whole-body to single-cell has great potential to discover unknown phenomena in biological and medical fields, no methodology for achieving it has been established thus far. Here, we report the whole-body and whole-organ imaging of hypoxia, an important microenvironment, at single-cell resolution using activatable covalent fluorescent probes compatible with tissue clearing. We initially focused on overcoming the incompatibility of fluorescent dyes and refractive index matching solutions (RIMSs), which has greatly hindered the development of fluorescent molecular probes in the field of tissue clearing. The fluorescent dyes compatible with RIMS were then incorporated into the development of activatable covalent fluorescent probes for hypoxia. We combined the probes with tissue clearing, achieving comprehensive single-cell-resolution imaging of hypoxia in a whole mouse body and whole organs.

Combining near infrared fluorescence and laser speckle imaging with optical tissue clearing for in vivo transcranial monitoring of cerebral blood vessels damaged by photodynamic nanoformulation

In vivo near infrared (NIR) fluorescence imaging and laser speckle contrast imaging (LSCI) are emerging optical bioimaging modalities, which can provide information on blood vessels morphology, volume and the blood flow velocity. Optical tissue clearing (OTC) technique addresses a light scattering problem in optical bioimaging, which is imperative for the transcranial brain imaging. Herein, we report an approach combining NIR fluorescence and LSC microscopy imaging with OTC. A liposomal nanoformulation comprising NIR fluorescent dye ICG and photosensitizer BPD was synthesized and injected intravenously into mouse with OTC treated skull. Transcranial excitation of BPD in nanoliposomes resulted in the localized, irradiation dose dependent photodynamic damage of the brain blood vessels, which was manifested both in NIR fluorescence and LSC transcranial imaging, revealing changes in the vessels morphology, volume and the blood flow rate. The developed approach allows for bimodal imaging guided, localized vascular PDT of cancer and other diseases.

Deepened Photodynamic Therapy through Skin Optical Clearing Technology in the Visible Light Window

The trade-off that shorter wavelength light facilitates the efficient generation of reactive oxygen species (ROS) from photosensitizer (PS) while facing the drawback of limited penetration depth through skin tissue restricts the further development of photodynamic therapy (PDT). Here, we address this contradiction and achieve visible-light-tailored deep PDT combined with the skin optical clearing technology. With the help of the prepared skin optical clearing gel, the refractive index inhomogeneity between skin tissue components is greatly attenuated, and the light scattering effect within the skin tissue is remarkably reduced. As a consequence, the transmittance of visible light at 600 nm through in vitro porcine skin and in vivo mouse skin after treatment increases from approximately 10 and 40 to 70 and 70%, respectively. Furthermore, in the tumor cell eradication experiment, the local ROS generation efficiency in the experimental group is several times higher than that in the control group owing to improved visible transmittance, which is thus responsible for the complete eradication of tumor cells, even when shaded by skin tissue. The results suggest that this strategy may serve as a valuable supplement to the current deep PDT strategies.

Spatiotemporal Mapping and Molecular Basis of Whole-brain Circuit Maturation

Brain development is highly dynamic and asynchronous, marked by the sequential maturation of functional circuits across the brain. The timing and mechanisms driving circuit maturation remain elusive due to an inability to identify and map maturing neuronal populations. Here we create DevATLAS (Developmental Activation Timing-based Longitudinal Acquisition System) to overcome this obstacle. We develop whole-brain mapping methods to construct the first longitudinal, spatiotemporal map of circuit maturation in early postnatal mouse brains. Moreover, we uncover dramatic impairments within the deep cortical layers in a neurodevelopmental disorders (NDDs) model, demonstrating the utility of this resource to pinpoint when and where circuit maturation is disrupted. Using DevATLAS, we reveal that early experiences accelerate the development of hippocampus-dependent learning by increasing the synaptically mature granule cell population in the dentate gyrus. Finally, DevATLAS enables the discovery of molecular mechanisms driving activity-dependent circuit maturation.

Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level

The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.

Rapid 3D isotropic imaging of whole organ with double-ring light-sheet microscopy and self-learning side-lobe elimination

Bessel-like plane illumination forms a new type of light-sheet microscopy with ultra-long optical sectioning distance that enables rapid 3D imaging of fine cellular structures across an entire large tissue. However, the side-lobe excitation of conventional Bessel light sheets severely impairs the quality of the reconstructed 3D image. Here, we propose a self-supervised deep learning (DL) approach that can completely eliminate the residual side lobes for a double-ring-modulated non-diffraction light-sheet microscope, thereby substantially improving the axial resolution of the 3D image. This lightweight DL model utilizes the own point spread function (PSF) of the microscope as prior information without the need for external high-resolution microscopy data. After a quick training process based on a small number of datasets, the grown-up model can restore sidelobe-free 3D images with near isotropic resolution for diverse samples. Using an advanced double-ring light-sheet microscope in conjunction with this efficient restoration approach, we demonstrate 5-minute rapid imaging of an entire mouse brain with a size of ∼12 mm × 8 mm  ×  6 mm and achieve uniform isotropic resolution of ∼4 µm (1.6-µm voxel) capable of discerning the single neurons and vessels across the whole brain.

Successful 3D imaging of cleared biological samples with light sheet fluorescence microscopy

In parallel with the development of tissue-clearing methods, over the last decade, light sheet fluorescence microscopy has contributed to major advances in various fields, such as cell and developmental biology and neuroscience. While biologists are increasingly integrating three-dimensional imaging into their research projects, their experience with the technique is not always up to their expectations. In response to a survey of specific challenges associated with sample clearing and labeling, image acquisition, and data analysis, we have critically assessed the recent literature to characterize the difficulties inherent to light sheet fluorescence microscopy applied to cleared biological samples and to propose solutions to overcome them. This review aims to provide biologists interested in light sheet fluorescence microscopy with a primer for the development of their imaging pipeline, from sample preparation to image analysis. Importantly, we believe that issues could be avoided with better anticipation of image analysis requirements, which should be kept in mind while optimizing sample preparation and acquisition parameters.

An optimized visualization and quantitative protocol for in-depth evaluation of lymphatic vessel architecture in the liver

The liver lymphatic system is essential for maintaining tissue fluid balance and immune function. The detailed structure of lymphatic vessels (LVs) in the liver remains to be fully demonstrated. The aim of this study is to reveal LV structures in normal and diseased livers by developing a tissue-clearing and coimmunolabeling protocol optimized for the tissue size and the processing time for three-dimensional (3-D) visualization and quantification of LVs in the liver. We showed that our optimized protocol enables in-depth exploration of lymphatic networks in the liver, consisting of LVs along the portal tract (deep lymphatic system) and within the collagenous Glisson's capsule (superficial lymphatic system) in different species. With this protocol, we have shown 3-D LVs configurations in relation to blood vessels and bile ducts in cholestatic mouse livers, in which LVs were highly dilated and predominantly found around highly proliferating bile ducts and peribiliary vascular plexuses in the portal tract. We also established a quantification method using a 3-D volume-rendering approach. We observed a 1.6-fold (P < 0.05) increase in the average diameter of LVs and a 2.4-fold increase (P < 0.05) in the average branch number of LVs in cholestatic/fibrotic livers compared with control livers. Furthermore, cholestatic/fibrotic livers showed a 4.3-fold increase (P < 0.05) in total volume of LVs compared with control livers. Our optimized protocol and quantification method demonstrate an efficient and simple liver tissue-clearing procedure that allows the comprehensive analysis of liver lymphatic system.NEW & NOTEWORTHY This article showed a comprehensive 3-D-structural analysis of liver lymphatic vessel (LV) in normal and diseased livers in relation to blood vessels and bile ducts. In addition to the LVs highly localized at the portal tract, we revealed capsular LVs in mouse, rat, and human livers. In cholestatic livers, LVs are significantly increased and dilated compared with normal livers. Our optimized protocol provides detailed spatial information for LVs remodeling in normal and pathological conditions.

Perineurial Window is Critical for Experimental Reverse End-to-Side Nerve Transfer

BACKGROUND

The depth of connective tissue window in the side of a recipient nerve in reverse end-to-side transfers (RETS) remains controversial.

OBJECTIVE

To test whether the depth of connective tissue disruption influences the efficiency of donor axonal regeneration in the context of RETS.

METHODS

Sprague-Dawley rats (n = 24) were assigned to 1 of the 3 groups for obturator nerve to motor femoral nerve RETS: group 1, without epineurium opening; group 2, with epineurium only opening; and group 3, with epineurium and perineurium opening. Triple retrograde labeling was used to assess the number of motor neurons that had regenerated into the recipient motor femoral branch. Thy1-GFP rats (n = 8) were also used to visualize the regeneration pathways in the nerve transfer networks at 2- and 8-week time point using light sheet fluorescence microscopy.

RESULTS

The number of retrogradely labeled motor neurons that had regenerated distally toward the target muscle was significantly higher in group 3 than that in groups 1 and 2. Immunohistochemistry validated the degree of connective tissue disruption among the 3 groups, and optical tissue clearing methods demonstrated donor axons traveling outside the fascicles in groups 1 and 2 but mostly within the fascicles in group 3.

CONCLUSION

Creating a perineurial window in the side of recipient nerves provides the best chances of robust donor axonal regeneration across the RETS repair site. This finding aids nerve surgeons by confirming that a deep window should be undertaken when doing a RETS procedure.

Optimization of the optical transparency of bones by PACT-based passive tissue clearing

Recent developments in tissue clearing methods such as the passive clearing technique (PACT) have allowed three-dimensional analysis of biological structures in whole, intact tissues, thereby providing a greater understanding of spatial relationships and biological circuits. Nonetheless, the issues that remain in maintaining structural integrity and preventing tissue expansion/shrinkage with rapid clearing still inhibit the wide application of these techniques in hard bone tissues, such as femurs and tibias. Here, we present an optimized PACT-based bone-clearing method, Bone-mPACT+, that protects biological structures. Bone-mPACT+ and four different decalcifying procedures were tested for their ability to improve bone tissue clearing efficiency without sacrificing optical transparency; they rendered nearly all types of bone tissues transparent. Both mouse and rat bones were nearly transparent after the clearing process. We also present a further modification, the Bone-mPACT+ Advance protocol, which is specifically optimized for processing the largest and hardest rat bones for easy clearing and imaging using established tissue clearing methods.

Affordable optical clearing and immunolabelling in mouse brain slices

Traditional histological analysis is conducted on thin tissue sections, limiting the data capture from large tissue volumes to 2D profiles, and requiring stereological methods for 3D assessment. Recent advances in microscopical and tissue clearing methods have facilitated 3D reconstructions of tissue structure. However, staining of large tissue blocks remains a challenge, often requiring specialised and expensive equipment to clear and immunolabel tissue. Here, we present the Affordable Brain Slice Optical Clearing (ABSOC) method: a modified iDISCO protocol which enables clearing and immunolabeling of mouse brain slices up to 1 mm thick using inexpensive reagents and equipment, with no intensive expert training required. We illustrate the use of ABSOC in 1 mm C57BL/6J mouse coronal brain slices sectioned through the dorsal hippocampus and immunolabelled with an anti-calretinin antibody. The ABSOC method can be readily used for histological studies of mouse brain in order to move from the use of very thin tissue sections to large volumes of tissue - giving more representative analysis of biological samples, without the need for sampling of small regions only.

Protocol for fine casting, imaging, and analysis of murine vascular networks with VALID

The majority of fluorescent vessel labeling techniques currently available are limited by their expense, incomplete labeling, or complexity. Here, we present VALID (vessel labeling via gelatin-based lipophilic dye solution)-a protocol for complete labeling of different vascular networks. We describe steps for preparing different dye hydrogels, murine vascular casting and tissue harvesting, immunolabeling, tissue clearing, and imaging, as well as detailed analysis of the vascular networks. This protocol is helpful for evaluating vascular lesions in studying different vessel-associated diseases. For complete details on the use and execution of this protocol, please refer to Zhu et al.1.

Application of fluorescence micro-optical sectioning tomography in the cerebrovasculature and applicable vascular labeling methods

Fluorescence micro-optical sectioning tomography (fMOST) is a three-dimensional (3d) imaging method at the mesoscopic level. The whole-brain of mice can be imaged at a high resolution of 0.32 × 0.32 × 1.00 μm3. It is useful for revealing the fine morphology of intact organ tissue, even for positioning the single vessel connected with a complicated vascular network across different brain regions in the whole mouse brain. Featuring its 3d visualization of whole-brain cross-scale connections, fMOST has a vast potential to decipher brain function and diseases. This article begins with the background of fMOST technology including a widespread 3D imaging methods comparison and the basic technical principal illustration, followed by the application of fMOST in cerebrovascular research and relevant vascular labeling techniques applicable to different scenarios.

Tissue optical clearing and 3D imaging of virus infections

Imaging pathogens within 3D environment of biological tissues provides spatial information about their localization and interactions with the host. Technological advances in fluorescence microscopy and 3D image analysis now permit visualization and quantification of pathogens directly in large tissue volumes and in great detail. In recent years large volume imaging became an important tool in virology research helping to understand the properties of viruses and the host response to infection. In this chapter we give a review of fluorescence microscopy modalities and tissue optical clearing methods used for large volume tissue imaging. A summary of recent applications for virus research is provided with particular emphasis on studies using light sheet fluorescence microscopy. We describe the challenges and approaches for volumetric image analysis. Practical examples of volumetric imaging implemented in virology laboratories and addressing specialized research questions, such as virus tropism and immune host response are described. We conclude with an overview of the emerging technologies and their potential for virus research.