Systematic Evaluation of Chemically Distinct Tissue Optical Clearing Techniques in Murine Lymph Nodes

Semi-automated protocol to quantify and characterize fluorescent three-dimensional vascular images

The microvasculature facilitates gas exchange, provides nutrients to cells, and regulates blood flow in response to stimuli. Vascular abnormalities are an indicator of pathology for various conditions, such as compromised vessel integrity in small vessel disease and angiogenesis in tumors. Traditional immunohistochemistry enables the visualization of tissue cross-sections containing exogenously labeled vasculature. Although this approach can be utilized to quantify vascular changes within small fields of view, it is not a practical way to study the vasculature on the scale of whole organs. Three-dimensional (3D) imaging presents a more appropriate method to visualize the vascular architecture in tissue. Here we describe the complete protocol that we use to characterize the vasculature of different organs in mice encompassing the methods to fluorescently label vessels, optically clear tissue, collect 3D vascular images, and quantify these vascular images with a semi-automated approach. To validate the automated segmentation of vascular images, one user manually segmented one hundred random regions of interest across different vascular images. The automated segmentation results had an average sensitivity of 83±11% and an average specificity of 91±6% when compared to manual segmentation. Applying this procedure of image analysis presents a method to reliably quantify and characterize vascular networks in a timely fashion. This procedure is also applicable to other methods of tissue clearing and vascular labels that generate 3D images of microvasculature.

A simple and effective vascular network labeling method for transparent tissues of mice

Vascular network labeling in transparent tissues provides more complete information on blood vessels. To achieve a fast and efficient method for vascular network labeling in transparent tissues, we compared various vascular labeling methods under different tissue clearing protocols. FITC-Dextran labeling and CUBIC cleaning treatment were found to be the best options for vascular network labeling in cleared mouse tissues. Satisfactory labeling of vascular networks in various organs can be achieved by selecting FITC-Dextran with different molecular weights and different administration methods.

A 3D Analysis of Cleared Human Melanoma

Cutaneous melanoma is one of the most aggressive and deadliest cancers in human beings due to its invasiveness and other factors. Histopathological analysis is crucial for a proper diagnosis. Optical tissue clearing is a novel field that allows 3D image acquisition of large-scale biological tissues. Optical clearing and immunolabeling for 3D fluorescence imaging has yet to be extensively applied to melanoma. In the present manuscript, we establish, for the first time, an optical clearing and immunostaining procedure for human melanoma and human cell line-derived melanoma xenograft models using the CUBIC (clear, unobstructed brain imaging cocktails) technique. We have successfully cleared the samples and achieved 3D volumetric visualization of the tumor microenvironment, vasculature, and cell populations.

Imaging of fluorescent polymer dots in relation to channels and immune cells in the lymphatic system

Polymer dots (Pdots) have been applied to imaging lymph nodes (LNs) and lymphatic vessels (LVs) in living mice and rats. However, the mechanism of absorption, distribution, metabolism, and excretion of Pdots in LNs and LVs is still unclear. Therefore, the relationship between Pdots and immune cells, LVs and collagen fibers in lymphatics was studied by multiple in vivo and ex vivo microscopic imaging methods and detection techniques. Flow cytometry showed that Pdots could be phagocytosed by macrophages and monocytes, and had no relationship with B cells, T cells and dendric cells in LNs. Silver staining, immunofluorescence and two-photon microscope showed that Pdots gathered in collagen fibers and LVs of LNs. Furthermore, immunofluorescence imaging results verified that Pdots were distributed in the extracellular space of collecting LVs endothelial cells. In addition, Pdots in the collecting LVs were basically cleared by leaking into the surrounding tissue or draining LNs after 21 days of injection. During the long-time observation, Pdots also helped monitor the contraction frequency and variation range of LV. Our study lays a foundation on the research of Pdots as the carrier to study lymphatic structure and function in the future.

Inhibition of arginase modulates T-cell response in the tumor microenvironment of lung carcinoma

Immunotherapy has demonstrated significant activity in a broad range of cancer types, but still the majority of patients receiving it do not maintain durable therapeutic responses. Amino acid metabolism has been proposed to be involved in the regulation of immune response. Here, we investigated in detail the role of arginase 1 (Arg1) in the modulation of antitumor immune response against poorly immunogenic Lewis lung carcinoma. We observed that tumor progression is associated with an incremental increase in the number of Arg1⁺ myeloid cells that accumulate in the tumor microenvironment and cause systemic depletion of ʟ-arginine. In advanced tumors, the systemic concentrations of ʟ-arginine are decreased to levels that impair the proliferation of antigen-specific T-cells. Systemic or myeloid-specific Arg1 deletion improves antigen-induced proliferation of adoptively transferred T-cells and leads to inhibition of tumor growth. Arginase inhibitor was demonstrated to modestly inhibit tumor growth when used alone, and to potentiate antitumor effects of anti-PD-1 monoclonal antibodies and STING agonist. The effectiveness of the combination immunotherapy was insufficient to induce complete antitumor responses, but was significantly better than treatment with the checkpoint inhibitor alone. Together, these results indicate that arginase inhibition alone is of modest therapeutic benefit in poorly immunogenic tumors; however, in combination with other treatment strategies it may significantly improve survival outcomes.

Can Developments in Tissue Optical Clearing Aid Super-Resolution Microscopy Imaging?

The rapid development of super-resolution microscopy (SRM) techniques opens new avenues to examine cell and tissue details at a nanometer scale. Due to compatibility with specific labelling approaches, in vivo imaging and the relative ease of sample preparation, SRM appears to be a valuable alternative to laborious electron microscopy techniques. SRM, however, is not free from drawbacks, with the rapid quenching of the fluorescence signal, sensitivity to spherical aberrations and light scattering that typically limits imaging depth up to few micrometers being the most pronounced ones. Recently presented and robustly optimized sets of tissue optical clearing (TOC) techniques turn biological specimens transparent, which greatly increases the tissue thickness that is available for imaging without loss of resolution. Hence, SRM and TOC are naturally synergistic techniques, and a proper combination of these might promptly reveal the three-dimensional structure of entire organs with nanometer resolution. As such, an effort to introduce large-scale volumetric SRM has already started; in this review, we discuss TOC approaches that might be favorable during the preparation of SRM samples. Thus, special emphasis is put on TOC methods that enhance the preservation of fluorescence intensity, offer the homogenous distribution of molecular probes, and vastly decrease spherical aberrations. Finally, we review examples of studies in which both SRM and TOC were successfully applied to study biological systems.

Perspective: Extending the Utility of Three-Dimensional Organoids by Tissue Clearing Technologies

An organoid, a self-organizing organ-like tissue developed from stem cells, can exhibit a miniaturized three-dimensional (3D) structure and part of the physiological functions of the original organ. Due to the reproducibility of tissue complexity and ease of handling, organoids have replaced real organs and animals for a variety of uses, such as investigations of the mechanisms of organogenesis and disease onset, and screening of drug effects and/or toxicity. The recent advent of tissue clearing and 3D imaging techniques have great potential contributions to organoid studies by allowing the collection and analysis of 3D images of whole organoids with a reasonable throughput and thus can expand the means of examining the 3D architecture, cellular components, and variability among organoids. Genetic and histological cell-labeling methods, together with organoid clearing, also allow visualization of critical structures and cellular components within organoids. The collected 3D data may enable image analysis to quantitatively assess structures within organoids and sensitively/effectively detect abnormalities caused by perturbations. These capabilities of tissue/organoid clearing and 3D imaging techniques not only extend the utility of organoids in basic biology but can also be applied for quality control of clinical organoid production and large-scale drug screening.

Tutorial: practical considerations for tissue clearing and imaging

Tissue clearing has become a powerful technique for studying anatomy and morphology at scales ranging from entire organisms to subcellular features. With the recent proliferation of tissue-clearing methods and imaging options, it can be challenging to determine the best clearing protocol for a particular tissue and experimental question. The fact that so many clearing protocols exist suggests there is no one-size-fits-all approach to tissue clearing and imaging. Even in cases where a basic level of clearing has been achieved, there are many factors to consider, including signal retention, staining (labeling), uniformity of transparency, image acquisition and analysis. Despite reviews citing features of clearing protocols, it is often unknown a priori whether a protocol will work for a given experiment, and thus some optimization is required by the end user. In addition, the capabilities of available imaging setups often dictate how the sample needs to be prepared. After imaging, careful evaluation of volumetric image data is required for each combination of clearing protocol, tissue type, biological marker, imaging modality and biological question. Rather than providing a direct comparison of the many clearing methods and applications available, in this tutorial we address common pitfalls and provide guidelines for designing, optimizing and imaging in a successful tissue-clearing experiment with a focus on light-sheet fluorescence microscopy (LSFM).

Tissue clearing-based method for unobstructed three-dimensional imaging of mouse penis with subcellular resolution

Although mice are widely used to elucidate factors contributing to penile disorders and develop treatment options, quantification of tissue changes upon intervention is either limited to minuscule tissue volume (histology) or acquired with limited spatial resolution (MRI/CT). Thus, imaging method suitable for expeditious acquisition of the entire mouse penis with subcellular resolution is described that relies on both aqueous- (clear, unobstructed brain imaging cocktails and computational analysis) and solvent-based (fluorescence-preserving capability imaging of solvent-cleared organs) tissue optical clearing (TOC). The combined TOC approach allows to image mouse penis innervation and vasculature with unprecedented detail and, for the first time, reveals the three-dimensional structure of murine penis fibrocartilage.