Tissue clearing and imaging methods for cardiovascular development

An anatomically informed computational fluid dynamics modeling approach for quantifying hemodynamics in the developing heart

Congenital heart defects occur in approximately 1% of newborns in the US annually. Currently, less than a third of congenital heart defects can be traced to a known genetic or environmental cause, suggesting that a large proportion of disease-causing mechanisms have yet to be fully characterized. Hemodynamic forces such as wall shear stress are critical for heart development and are known to induce changes in embryonic cardiac patterning leading to malformations. However, measuring these hemodynamic factors in vivo is infeasible due to physical limitations, such as the small size and constant motion of the embryonic heart. This serves as a significant barrier towards developing a mechanics-based understanding of the origins of congenital heart defects. An alternative approach is to recapitulate the hemodynamic environment by simulating blood flow and calculating the resulting hemodynamic forces through computational fluid dynamics modeling. Thus, we have developed a robust computational fluid dynamics modeling pipeline to quantify hemodynamics within cell-accurate anatomies of embryonic chick hearts. Here we describe the implementation of single plane illumination light sheet fluorescent microscopy to generate full three-dimensional reconstructions of the embryonic heart in silico, quantitative geometric morphometric methods for identifying anatomic variability across samples, and computational fluid dynamic approaches for calculating flow, pressure, and wall shear stress within complex tissue architectures. Together, these methods produce a fast, robust, and accessible system of analysis for generating high-resolution, quantitative descriptions of anatomical variability and hemodynamic forces in the embryonic heart.

Molecular signature-based labeling techniques for vascular endothelial cells

Vascular endothelial cells (VECs) play a crucial role in the development and maintenance of vascular biology specific to the tissue types. Molecular signature-based labeling and imaging of VECs help researchers understand potential mechanisms linking VECs to disease pathology, serving as valuable biomarkers in clinical settings and trials. Labeling techniques involve selectively tagging or marking VECs for visualization. Immunolabeled employs antibodies that specifically bind to VECs markers, while fluorescent tracers or dyes can directly label VECs for imaging. Some techniques use specific carbohydrate residues on cell surface, while others employ endothelial-specific promoters to express fluorescent proteins. Additionally, VEC can be labeled with contrast agents, radiolabeled tracers, and nanoparticles. The choice of labeling technique depends on study context, including whether it involves animal models, in vitro cell cultures, or clinical applications. Herein, we discussed the various labeling methods utilized to label VECs and the techniques to visualize them.

Unveiling the native architecture of adult cardiac tissue using the 3D-NaissI method

Accurately imaging adult cardiac tissue in its native state is essential for regenerative medicine and understanding heart disease. Current fluorescence methods encounter challenges with tissue fixation. Here, we introduce the 3D-NaissI (3D-Native Tissue Imaging) method, which enables rapid, cost-effective imaging of fresh cardiac tissue samples in their closest native state, and has been extended to other tissues. We validated the efficacy of 3D-NaissI in preserving cardiac tissue integrity using small biopsies under hypothermic conditions in phosphate-buffered saline, offering unparalleled resolution in confocal microscopy for imaging fluorescent small molecules and antibodies. Compared to conventional histology, 3D-NaissI preserves cardiac tissue architecture and native protein epitopes, facilitating the use of a wide range of commercial antibodies without unmasking strategies. We successfully identified specific cardiac protein expression patterns in cardiomyocytes (CMs) from rodents and humans, including for the first time ACE2 localization in the lateral membrane/T-Tubules and SGTL2 in the sarcoplasmic reticulum. These findings shed light on COVID-19-related cardiac complications and suggest novel explanations for therapeutic benefits of iSGLT2 in HFpEF patients. Additionally, we challenge the notion of "connexin-43 lateralization" in heart pathology, suggesting it may be an artifact of cardiac fixation, as 3D-NaissI clearly revealed native connexin-43 expression at the lateral membrane of healthy CMs. We also discovered previously undocumented periodic ring-like 3D structures formed by pericytes that cover the lateral surfaces of CMs. These structures, positive for laminin-2, delineate a specific spatial architecture of laminin-2 receptors on the CM surface, underscoring the pivotal role of pericytes in CM function. Lastly, 3D-NaissI facilitates the mapping of native human protein expression in fresh cardiac autopsies, offering insights into both pathological and non-pathological contexts. Therefore, 3D-NaissI provides unparalleled insights into native cardiac tissue biology and holds the promise of advancing our understanding of physiology and pathophysiology, surpassing standard histology in both resolution and accuracy.

The Interaction Between Vasculogenic Mimicry and the Immune System: Mechanistic Insights and Dual Exploration in Cancer Therapy

Vasculogenic mimicry (VM) represents a novel form of angiogenesis discovered in numerous malignant tumours in recent years. Unlike traditional angiogenesis, VM facilitates tumour blood supply independently of endothelial cells by enabling tumour cells to form functional vascular networks. This phenomenon, where tumour cells replace endothelial cells to form tubular structures, plays a pivotal role in tumour growth and metastasis. Tumour progression is influenced by a variety of factors, including immune components. The immune system serves as a critical defence mechanism by identifying and eliminating abnormal entities, such as tumour cells. This inevitably reminds us of the intricate connection between the immune system and VM. Indeed, in recent years, some studies have shown that immune responses and related immune cells play different regulatory roles in the formation of VM. Therefore, this review provides a comprehensive discussion on the mechanisms underlying VM formation, its interplay with the immune system, and the potential of leveraging immunotherapy to target VM.

Multiscale Three-Dimensional Evaluation and Analysis of Murine Lung Vasculature From Macro- to Micro-Structural Level

The pulmonary vasculature plays a pivotal role in the development and progress of chronic lung diseases. Due to limitations of conventional two-dimensional histological methods, the complexity and the detailed anatomy of the lung blood circulation might be overlooked. In this study, we demonstrate the practical use of optical serial block face imaging (SBFI), ex vivo microcomputed tomography (micro-CT), and nondestructive optical tomography for visualization and quantification of the pulmonary circulation's 3D architecture from macro- to micro-structural levels in murine lung samples. We demonstrate that SBFI can provide rapid, cost-effective, and label-free visualization of mouse lung macrostructures and large pulmonary vessels. Micro-CT offers high-resolution imaging and captures microvascular and (pre)capillary structures, with microstructural quantification. Optical microscopy techniques such as optical projection tomography (OPT) and light sheet fluorescence microscopy, allows noninvasive, mesoscopic imaging of optically cleared mouse lungs, still enabling 3D microscopic reconstruction down to the precapillary level. By integrating SBFI, micro-CT, and nondestructive optical microscopy, we provide a framework for detailed and 3D understanding of the pulmonary circulation, with emphasis on vascular pruning and rarefaction. Our study showcases the applicability and complementarity of these techniques for organ-level vascular imaging, offering researchers flexibility in selecting the optimal approach based on their specific requirements. In conclusion, we propose 3D-directed approaches for a detailed whole-organ view on the pulmonary vasculature in health and disease, to advance our current knowledge of diseases affecting the pulmonary vasculature.

Diagnostic and therapeutic optical imaging in cardiovascular diseases

Cardiovascular disease (CVD) is one of the most prevalent health threats globally. Traditional diagnostic methods for CVDs, including electrocardiography, ultrasound, and cardiac magnetic resonance imaging, have inherent limitations in real-time monitoring and high-resolution visualization of cardiovascular pathophysiology. In recent years, optical imaging technology has gained considerable attention as a non-invasive, high-resolution, real-time monitoring solution in the study and diagnosis of CVD. This review discusses the latest advancements, and applications of optical techniques in cardiac imaging. We compare the advantages of optical imaging over traditional modalities and especially scrutinize techniques such as optical coherence tomography, photoacoustic imaging, and fluorescence imaging. We summarize their investigations in atherosclerosis, myocardial infarction, and heart valve disease, etc. Additionally, we discuss challenges like deep-tissue imaging and high spatiotemporal resolution adjustment, and review existing solutions such as multimodal integration, artificial intelligence, and enhanced optical probes. This article aims to drive further development in optical imaging technologies to provide more precise and efficient tools for early diagnosis, pathological mechanism exploration, and treatment of CVD.

In situ reprogramming of cardiac fibroblasts into cardiomyocytes in mouse heart with chemicals

Cardiomyocytes are terminal differentiated cells and have limited ability to proliferate or regenerate. Condition like myocardial infarction causes massive death of cardiomyocytes and is the leading cause of death. Previous studies have demonstrated that cardiac fibroblasts can be induced to transdifferentiate into cardiomyocytes in vitro and in vivo by forced expression of cardiac transcription factors and microRNAs. Our previous study have demonstrated that full chemical cocktails could also induce fibroblast to cardiomyocyte transdifferentiation both in vitro and in vivo. With the development of tissue clearing techniques, it is possible to visualize the reprogramming at the whole-organ level. In this study, we investigated the effect of the chemical cocktail CRFVPTM in inducing in situ fibroblast to cardiomyocyte transdifferentiation with two strains of genetic tracing mice, and the reprogramming was observed at whole-heart level with CUBIC tissue clearing technique and 3D imaging. In addition, single-cell RNA sequencing (scRNA-seq) confirmed the generation of cardiomyocytes from cardiac fibroblasts which carries the tracing marker. Our study confirms the use of small molecule cocktails in inducing in situ fibroblast to cardiomyocyte reprogramming at the whole-heart level and proof-of-conceptly providing a new source of naturally incorporated cardiomyocytes to help heart regeneration.

A comparison of fixation and immunofluorescence protocols for successful reproducibility and improved signal in human left ventricle cardiac tissue

Immunohistochemistry (IHC) and immunofluorescence (IF) are crucial techniques for studying cardiac physiology and disease. The accuracy of these techniques is dependent on various aspects of sample preparation and processing. However, standardised protocols for sample preparation of tissues, particularly for fresh-frozen human left ventricle (LV) tissue, have yet to be established and could potentially lead to differences in staining and interpretation. Thus, this study aimed to optimise the reproducibility and quality of IF staining in fresh-frozen human LV tissue by systematically investigating crucial aspects of the sample preparation process. To achieve this, we subjected fresh-frozen human LV tissue to different fixation protocols, primary antibody incubation temperatures, antibody penetration reagents, and fluorescent probes. We found that neutral buffered formalin fixation reduced image artefacts and improved antibody specificity compared to both methanol and acetone fixation. Additionally, incubating primary antibodies at 37°C for 3 h improved fluorescence intensity compared to the commonly practised 4°C overnight incubation. Furthermore, we found that DeepLabel, an antibody penetration reagent, and smaller probes, such as fragmented antibodies and Affimers, improved the visualisation depth of cardiac structures. DeepLabel also improved antibody penetration in CUBIC cleared thick LV tissue fragments. Thus, our data underscores the importance of standardised protocols in IF staining and provides various means of improving staining quality. In addition to contributing to cardiac research by providing methodologies for IF, the findings and processes presented herein also establish a framework by which staining of other tissues may be optimised.

Breaking Biomphalaria black box by in situ revelation of fluorescent Schistosoma mansoni parasites

Tissue clearing is an old-fashioned method developed in the 1900's and used to turn an opaque biological object into a 3D visualizable transparent structure. Developed and diversified over the last decade, this method is most of the time applied to mammals' tissues, and especially mouse and human tissues for cytological, histological and pathophysiological studies. Through autofluorescence, immunofluorescence, in situ hybridization, intercalating agents, fluorescent transfection markers or fluorescent particle uptake, optically cleared samples can be monitored to discover new biological structures and cellular interactions through 3D-visualization, which can be more challenging in some extend through classical histological methods. Most of the tissue clearing procedures have been developed for specific applications like endogenous fluorescence visualization, immunolabeling or for revealing specific organs. Thus, choosing the adapted protocol may be empirical for non-model species, especially for mollusks for which very little related literature is available. Herein, we suggest an effective optical tissue clearing procedure for the freshwater snail Biomphalaria glabrata, known as the intermediate host of the human parasite Schistosoma mansoni. This clearing procedure involves solvents with a minimal toxicity, preserves the endogenous fluorescence of labeled parasites inside snail tissues and is compatible with an immunolabeling procedure.

Three-dimensional visualization of Hertwig's epithelial root sheath during tooth root development with the miniTESOS tissue clearing method

OBJECTIVE

Hertwig's epithelial root sheath (HERS) acts as a signaling center that regulates the size, shape, and number of tooth roots. Therefore, understanding the anatomical changes in HERS during development is crucial for investigating its effect on root formation. However, the three-dimensional morphology of HERS and its changes during tooth root development remain largely unknown due to the limitations of traditional histological techniques.

METHODS

We developed an improved tissue clearing method for mouse embryonic and early postnatal mandibles, designated as a mini Transparent Embedding Solvent System (miniTESOS), based on the Transparent Embedding Solvent System (TESOS). We applied this method to the K14-Cre;Ai14 mouse line to systematically investigate the spatiotemporal dynamics of HERS at the cellular level during the development of the roots of mandibular first molars (MM1) and mandibular second molars (MM2). Additionally, using MM1 as a model, we quantitatively investigated the spatiotemporal changes in HERS in the root bifurcation region during the development of two-rooted teeth.

RESULTS

In the early stages of root development, differences in growth rates and developmental patterns between MM1 and MM2 were observed in the mesiodistal and buccolingual directions, from the initiation to the fusion of buccal and lingual HERS. In the elongation stage of two-rooted teeth, continuous HERS was found exclusively at the leading edge of the root, gradually decreasing in length as the root extended. In the root bifurcation area, HERS undergoes four developmental stages: initiation, elongation, contact, and complete fragmentation, each characterized by specific morphological features.

CONCLUSION

This study improves the understanding of the alterations in HERS during root development and summarizes its developmental pattern in the root bifurcation region. The miniTESOS tissue clearing method provides a new strategy to investigate tooth development.

Participation of ventricular trabeculae in neonatal cardiac regeneration leads to ectopic recruitment of Purkinje-like cells

Unlike adult mammals, newborn mice can regenerate a functional heart after myocardial infarction; however, the precise origin of the newly formed cardiomyocytes and whether the distal part of the conduction system (the Purkinje fiber (PF) network) is properly formed in regenerated hearts remains unclear. PFs, as well as subendocardial contractile cardiomyocytes, are derived from trabeculae, transient myocardial ridges on the inner ventricular surface. Here, using connexin 40-driven genetic tracing, we uncover a substantial participation of the trabecular lineage in myocardial regeneration through dedifferentiation and proliferation. Concomitantly, regeneration disrupted PF network maturation, resulting in permanent PF hyperplasia and impaired ventricular conduction. Proliferation assays, genetic impairment of PF recruitment, lineage tracing and clonal analysis revealed that PF network hyperplasia results from excessive recruitment of PFs due to increased trabecular fate plasticity. These data indicate that PF network hyperplasia is a consequence of trabeculae participation in myocardial regeneration.

Rigor and reproducibility in human brain organoid research: Where we are and where we need to go

Human brain organoid models have emerged as a promising tool for studying human brain development and function. These models preserve human genetics and recapitulate some aspects of human brain development, while facilitating manipulation in an in vitro setting. Despite their potential to transform biology and medicine, concerns persist about their fidelity. To fully harness their potential, it is imperative to establish reliable analytic methods, ensuring rigor and reproducibility. Here, we review current analytical platforms used to characterize human forebrain cortical organoids, highlight challenges, and propose recommendations for future studies to achieve greater precision and uniformity across laboratories.

Revisiting Cardiac Biology in the Era of Single Cell and Spatial Omics

Throughout our lifetime, each beat of the heart requires the coordinated action of multiple cardiac cell types. Understanding cardiac cell biology, its intricate microenvironments, and the mechanisms that govern their function in health and disease are crucial to designing novel therapeutical and behavioral interventions. Recent advances in single-cell and spatial omics technologies have significantly propelled this understanding, offering novel insights into the cellular diversity and function and the complex interactions of cardiac tissue. This review provides a comprehensive overview of the cellular landscape of the heart, bridging the gap between suspension-based and emerging in situ approaches, focusing on the experimental and computational challenges, comparative analyses of mouse and human cardiac systems, and the rising contextualization of cardiac cells within their niches. As we explore the heart at this unprecedented resolution, integrating insights from both mouse and human studies will pave the way for novel diagnostic tools and therapeutic interventions, ultimately improving outcomes for patients with cardiovascular diseases.

3D exploration of gene expression in chicken embryos through combined RNA fluorescence in situ hybridization, immunofluorescence, and clearing

BACKGROUND

Fine characterization of gene expression patterns is crucial to understand many aspects of embryonic development. The chicken embryo is a well-established and valuable animal model for developmental biology. The period spanning from the third to sixth embryonic days (E3 to E6) is critical for many organ developments. Hybridization chain reaction RNA fluorescent in situ hybridization (HCR RNA-FISH) enables multiplex RNA detection in thick samples including embryos of various animal models. However, its use is limited by tissue opacity.

RESULTS

We optimized HCR RNA-FISH protocol to efficiently label RNAs in whole mount chicken embryos from E3.5 to E5.5 and adapted it to ethyl cinnamate (ECi) tissue clearing. We show that light sheet imaging of HCR RNA-FISH after ECi clearing allows RNA expression analysis within embryonic tissues with good sensitivity and spatial resolution. Finally, whole mount immunofluorescence can be performed after HCR RNA-FISH enabling as exemplified to assay complex spatial relationships between axons and their environment or to monitor GFP electroporated neurons.

CONCLUSIONS

We could extend the use of HCR RNA-FISH to older chick embryos by optimizing HCR RNA-FISH and combining it with tissue clearing and 3D imaging. The integration of immunostaining makes possible to combine gene expression with classical cell markers, to correlate expressions with morphological differentiation and to depict gene expressions in gain or loss of function contexts. Altogether, this combined procedure further extends the potential of HCR RNA-FISH technique for chicken embryology.

Exploring copper (II) porphyrin complexes and their derivatives for electrochemical analysis and biological assessment in the study of breast cancer (MCF-7) cell lines

In this study, several derivatives of tetraphenylporphyrin were synthesized, each with unique meso-substituent groups including phenyl, methoxyphenyl, butyloxyphenyl, octyloxyphenyl, and dectyloxyphenyl. Additionally, their corresponding copper complexes were prepared and thoroughly characterized. The structural confirmation of all compounds was established through CHN elemental analysis, mass spectrometry, and FT-IR spectroscopy. As the number of carbon atoms in the alkyl long-chain increased, a slight red shift in the electronic absorption band was observed, which was attributed to the electronic influence of the alkyl group. DFT analysis indicated that electron density predominantly localized on the porphyrin ring of both the metal free porphyrins and copper (II) porphyrin complexes, with relatively low electron density in the p orbital of the meso-aryl long-chain substituent group. EPR spectroscopy of the Copper (II) ion complexes revealed signals, indicating their paramagnetic properties. Additionally, the Copper (II) tetraphenylporphyrin (CuTPP) complexes displayed two reversible oxidation peaks at +0.97 V and +1.35 V, whereas other derivatives exhibited lower oxidation potentials. The cytotoxicity of these compounds against MCF-7 cell lines was assessed using MTT assay, revealing cytotoxic effects in all cases. Among them, Copper (II) tetrakis (4-methyloxyphenyl)porphyrin (CuTOMPP) demonstrated the highest potential, with an IC50 value of 32.07 μg/mL.

Acto3D: an open-source user-friendly volume rendering software for high-resolution 3D fluorescence imaging in biology

Advances in fluorescence microscopy and tissue-clearing have revolutionised 3D imaging of fluorescently labelled tissues, organs and embryos. However, the complexity and high cost of existing software and computing solutions limit their widespread adoption, especially by researchers with limited resources. Here, we present Acto3D, an open-source software, designed to streamline the generation and analysis of high-resolution 3D images of targets labelled with multiple fluorescent probes. Acto3D provides an intuitive interface for easy 3D data import and visualisation. Although Acto3D offers straightforward 3D viewing, it performs all computations explicitly, giving users detailed control over the displayed images. Leveraging an integrated graphics processing unit, Acto3D deploys all pixel data to system memory, reducing visualisation latency. This approach facilitates accurate image reconstruction and efficient data processing in 3D, eliminating the need for expensive high-performance computers and dedicated graphics processing units. We have also introduced a method for efficiently extracting lumen structures in 3D. We have validated Acto3D by imaging mouse embryonic structures and by performing 3D reconstruction of pharyngeal arch arteries while preserving fluorescence information. Acto3D is a cost-effective and efficient platform for biological research.

Light-Sheet Imaging to Reveal Cardiac Structure in Rodent Hearts

Light-sheet microscopy (LSM) plays a pivotal role in comprehending the intricate three-dimensional (3D) structure of the heart, providing crucial insights into fundamental cardiac physiology and pathologic responses. We hereby delve into the development and implementation of the LSM technique to elucidate the micro-architecture of the heart in mouse models. The methodology integrates a customized LSM system with tissue clearing techniques, mitigating light scattering within cardiac tissues for volumetric imaging. The combination of conventional LSM with image stitching and multiview deconvolution approaches allows for the capture of the entire heart. To address the inherent trade-off between axial resolution and field of view (FOV), we further introduce an axially swept light-sheet microscopy (ASLM) method to minimize out-of-focus light and uniformly illuminate the heart across the propagation direction. In the meanwhile, tissue clearing methods such as iDISCO enhance light penetration, facilitating the visualization of deep structures and ensuring a comprehensive examination of the myocardium throughout the entire heart. The combination of the proposed LSM and tissue clearing methods presents a promising platform for researchers in resolving cardiac structures in rodent hearts, holding great potential for the understanding of cardiac morphogenesis and remodeling.

Guidelines on antibody use in physiology research

Antibodies are one of the most used reagents in scientific laboratories and are critical components for a multitude of experiments in physiology research. Over the past decade, concerns about many biological methods, including those that use antibodies, have arisen as several laboratories were unable to reproduce the scientific data obtained in other laboratories. The lack of reproducibility could be largely attributed to inadequate reporting of detailed methods, no or limited verification by authors, and the production and use of unvalidated antibodies. The goal of this guideline article is to review best practices concerning commonly used techniques involving antibodies, including immunoblotting, immunohistochemistry, and flow cytometry. Awareness and integration of best practices will increase the rigor and reproducibility of these techniques and elevate the quality of physiology research.

Efficient 3D imaging and pathological analysis of the human lymphoma tumor microenvironment using light-sheet immunofluorescence microscopy

Rationale: The composition and spatial structure of the lymphoma tumor microenvironment (TME) provide key pathological insights for tumor survival and growth, invasion and metastasis, and resistance to immunotherapy. However, the 3D lymphoma TME has not been well studied owing to the limitations of current imaging techniques. In this work, we take full advantage of a series of new techniques to enable the first 3D TME study in intact lymphoma tissue. Methods: Diverse cell subtypes in lymphoma tissues were tagged using a multiplex immunofluorescence labeling technique. To optically clarify the entire tissue, immunolabeling-enabled three-dimensional imaging of solvent-cleared organs (iDISCO+), clear, unobstructed brain imaging cocktails and computational analysis (CUBIC) and stabilization to harsh conditions via intramolecular epoxide linkages to prevent degradation (SHIELD) were comprehensively compared with the ultimate dimensional imaging of solvent-cleared organs (uDISCO) approach selected for clearing lymphoma tissues. A Bessel-beam light-sheet fluorescence microscope (B-LSFM) was developed to three-dimensionally image the clarified tissues at high speed and high resolution. A customized MATLAB program was used to quantify the number and colocalization of the cell subtypes based on the acquired multichannel 3D images. By combining these cutting-edge methods, we successfully carried out high-efficiency 3D visualization and high-content cellular analyses of the lymphoma TME. Results: Several antibodies, including CD3, CD8, CD20, CD68, CD163, CD14, CD15, FOXP3 and Ki67, were screened for labeling the TME in lymphoma tumors. The 3D imaging results of the TME from three types of lymphoma, reactive lymphocytic hyperplasia (RLN), diffuse large B-cell lymphoma (DLBCL), and angioimmunoblastic T-cell lymphoma (AITL), were quantitatively analyzed, and their cell number, localization, and spatial correlation were comprehensively revealed. Conclusion: We present an advanced imaging-based method for efficient 3D visualization and high-content cellular analysis of the lymphoma TME, rendering it a valuable tool for tumor pathological diagnosis and other clinical research.

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.

Vacuum-assisted tissue embedding for whole-heart imaging

The use of combined optical imaging and tissue sectioning has potential for use in visualizing heart-wide fine structures at single-cell resolution. However, existing tissue preparation methods fail to generate ultrathin cavity-containing cardiac tissue slices with minimal deformation. This study developed an efficient vacuum-assisted tissue embedding method to prepare high-filled, agarose-embedded whole-heart tissue. Utilizing optimized vacuum parameters, we achieved 94% filled whole-heart tissue with the thinnest cut slice of 5 µm. We subsequently imaged a whole mouse heart sample using vibratome-integrated fluorescence micro-optical sectioning tomography (fMOST) with a voxel size of 0.32 µm × 0.32 µm × 1 µm. The imaging results indicated that the vacuum-assisted embedding method enabled whole-heart tissue to withstand long-term thin cutting while ensuring that slices were consistent and of high quality.

Catecholaminergic axon innervation and morphology in flat-mounts of atria and ventricles of mice

Sympathetic efferent axons regulate cardiac functions. However, the topographical distribution and morphology of cardiac sympathetic efferent axons remain insufficiently characterized due to the technical challenges involved in immunohistochemical labeling of the thick walls of the whole heart. In this study, flat-mounts of the left and right atria and ventricles of FVB mice were immunolabeled for tyrosine hydroxylase (TH), a marker of sympathetic nerves. Atrial and ventricular flat-mounts were scanned using a confocal microscope to construct montages. We found (1) In the atria: A few large TH-immunoreactive (IR) axon bundles entered both atria, branched into small bundles and then single axons that eventually formed very dense terminal networks in the epicardium, myocardium and inlet regions of great vessels to the atria. Varicose TH-IR axons formed close contact with cardiomyocytes, vessels, and adipocytes. Multiple intrinsic cardiac ganglia (ICG) were identified in the epicardium of both atria, and a subpopulation of the neurons in the ICG were TH-IR. Most TH-IR axons in bundles traveled through ICG before forming dense varicose terminal networks in cardiomyocytes. We did not observe varicose TH-IR terminals encircling ICG neurons. (2) In the left and right ventricles and interventricular septum: TH-IR axons formed dense terminal networks in the epicardium, myocardium, and vasculature. Collectively, TH labeling is achievable in flat-mounts of thick cardiac walls, enabling detailed mapping of catecholaminergic axons and terminal structures in the whole heart at single-cell/axon/varicosity scale. This approach provides a foundation for future quantification of the topographical organization of the cardiac sympathetic innervation in different pathological conditions.

Optical Tissue Clearing to Study the Intra-Pulmonary Biodistribution of Intravenously Delivered Mesenchymal Stromal Cells and Their Interactions with Host Lung Cells

Mesenchymal stromal cells (MSCs) injected intravenously are trapped in the capillaries of the lungs and die within the first 24 h. Studying the biodistribution and fate of labelled therapeutic cells in the 3D pulmonary context is important to understand their function in this organ and gain insights into their mechanisms of action. Optical tissue clearing enables volumetric cell tracking at single-cell resolution. Thus, we compared three optical tissue-clearing protocols (Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis (CUBIC), modified stabilised 3D imaging of solvent-cleared organs (s-DISCO) and ethyl cinnamate (ECi)) to evaluate their potential to track the biodistribution of human umbilical cord MSCs expressing the tdTomato fluorescence reporter and investigate how they interact with host cells in the mouse lung. The results showed that although CUBIC clearing is the only method that enables direct imaging of fluorescently labelled MSCs, combining s-DISCO or ECi with immunofluorescence or dye labelling allows the interaction of MSCs with endothelial and immune cells to be studied. Overall, this comparative study offers guidance on selecting an optical tissue-clearing method for cell tracking applications.

Optimal combinations of fluorescent vessel labeling and tissue clearing methods for three-dimensional visualization of vasculature

SIGNIFICANCE

Visualization of intact vasculatures is crucial to understanding the pathogeneses of different neurological and vascular diseases. Although various fluorescent vessel labeling methods have been used in combination with tissue clearing for three-dimensional (3D) visualization of different vascular networks, little has been done to quantify the labeling effect of each vessel labeling routine, as well as their applicability alongside various clearing protocols, making it difficult to select an optimal combination for finely constructing different vasculatures. Therefore, it is necessary to systematically assess the overall performance of these common vessel labeling methods combined with different tissue-clearing protocols.

AIM

A comprehensive evaluation of the labeling quality of various vessel labeling routines in different organs, as well as their applicability alongside various clearing protocols, were performed to find the optimal combinations for 3D reconstruction of vascular networks with high quality.

APPROACH

Four commonly-used vessel labeling techniques and six typical tissue optical clearing approaches were selected as candidates for the systematic evaluation.

RESULTS

The vessel labeling efficiency, vessel labeling patterns, and compatibility of each vessel labeling method with different tissue-clearing protocols were quantitatively evaluated and compared. Based on the comprehensive evaluation results, the optimal combinations were selected for 3D reconstructions of vascular networks in several organs, including mouse brain, liver, and kidney.

CONCLUSIONS

This study provides valuable insight on selecting the proper pipelines for 3D visualization of vascular networks, which may facilitate understanding of the underlying mechanisms of various neurovascular diseases.

High-Resolution 3D Heart Models of Cardiomyocyte Subpopulations in Cleared Murine Heart

Biological tissues are naturally three-dimensional (3D) opaque structures, which poses a major challenge for the deep imaging of spatial distribution and localization of specific cell types in organs in biomedical research. Here we present a 3D heart imaging reconstruction approach by combining an improved heart tissue-clearing technique with high-resolution light-sheet fluorescence microscopy (LSFM). We have conducted a three-dimensional and multi-scale volumetric imaging of the ultra-thin planes of murine hearts for up to 2,000 images per heart in x-, y-, and z three directions. High-resolution 3D volume heart models were constructed in real-time by the Zeiss Zen program. By using such an approach, we investigated detailed three-dimensional spatial distributions of two specific cardiomyocyte populations including HCN4 expressing pacemaker cells and Pnmt+ cell-derived cardiomyocytes by using reporter mouse lines Hcn4DreER/tdTomato and PnmtCre/ChR2-tdTomato. HCN4 is distributed throughout right atrial nodal regions (i.e., sinoatrial and atrioventricular nodes) and the superior-inferior vena cava axis, while Pnmt+ cell-derived cardiomyocytes show distinct ventral, left heart, and dorsal side distribution pattern. Our further electrophysiological analysis indicates that Pnmt + cell-derived cardiomyocytes rich left ventricular (LV) base is more susceptible to ventricular arrhythmia under adrenergic stress than left ventricular apex or right ventricle regions. Thus, our 3D heart imaging reconstruction approach provides a new solution for studying the geometrical, topological, and physiological characteristics of specific cell types in organs.

Optical tissue clearing associated with 3D imaging: application in preclinical and clinical studies

Understanding the inner morphology of intact tissues is one of the most competitive challenges in modern biology. Since the beginning of the twentieth century, optical tissue clearing (OTC) has provided solutions for volumetric imaging, allowing the microscopic visualization of thick sections of tissue, organoids, up to whole organs and organisms (for example, mouse or rat). Recently, tissue clearing has also been introduced in clinical settings to achieve a more accurate diagnosis with the support of 3D imaging. This review aims to give an overview of the most recent developments in OTC and 3D imaging and to illustrate their role in the field of medical diagnosis, with a specific focus on clinical applications.

Microphysiological stem cell models of the human heart

Models of heart disease and drug responses are increasingly based on human pluripotent stem cells (hPSCs) since their ability to capture human heart (dys-)function is often better than animal models. Simple monolayer cultures of hPSC-derived cardiomyocytes, however, have shortcomings. Some of these can be overcome using more complex, multi cell-type models in 3D. Here we review modalities that address this, describe efforts to tailor readouts and sensors for monitoring tissue- and cell physiology (exogenously and in situ) and discuss perspectives for implementation in industry and academia.

Ventricular Arrhythmias in Ischemic Cardiomyopathy-New Avenues for Mechanism-Guided Treatment

Ischemic heart disease is the most common cause of lethal ventricular arrhythmias and sudden cardiac death (SCD). In patients who are at high risk after myocardial infarction, implantable cardioverter defibrillators are the most effective treatment to reduce incidence of SCD and ablation therapy can be effective for ventricular arrhythmias with identifiable culprit lesions. Yet, these approaches are not always successful and come with a considerable cost, while pharmacological management is often poor and ineffective, and occasionally proarrhythmic. Advances in mechanistic insights of arrhythmias and technological innovation have led to improved interventional approaches that are being evaluated clinically, yet pharmacological advancement has remained behind. We review the mechanistic basis for current management and provide a perspective for gaining new insights that centre on the complex tissue architecture of the arrhythmogenic infarct and border zone with surviving cardiac myocytes as the source of triggers and central players in re-entry circuits. Identification of the arrhythmia critical sites and characterisation of the molecular signature unique to these sites can open avenues for targeted therapy and reduce off-target effects that have hampered systemic pharmacotherapy. Such advances are in line with precision medicine and a patient-tailored therapy.

Tissue clearing and 3D imaging in developmental biology

Tissue clearing increases the transparency of late developmental stages and enables deep imaging in fixed organisms. Successful implementation of these methodologies requires a good grasp of sample processing, imaging and the possibilities offered by image analysis. In this Primer, we highlight how tissue clearing can revolutionize the histological analysis of developmental processes and we advise on how to implement effective clearing protocols, imaging strategies and analysis methods for developmental biology.