Q&A: How can advances in tissue clearing and optogenetics contribute to our understanding of normal and diseased biology?

Novel fluorescent staining protocol for thick sections of human osteochondral tissues to facilitate correlation with MRI and CT

OBJECTIVE

To describe a novel fluorescent histochemical protocol to visualize osteoclasts, vasculature, and nerves in thick sections of human osteochondral tissues and to demonstrate its feasibility for use in radiologic-pathologic research correlation studies.

MATERIALS AND METHODS

Consecutive patients scheduled for total knee arthroplasty surgeries underwent pre-operative MRI. CT imaging was performed after tissue collection, and abnormal osteochondral regions were sectioned to 1-2 mm in thickness and decalcified. Fluorescent labeling of osteoclasts was performed by staining for tartrate-resistant alkaline phosphatase activity with a fluorescent substrate. Vascular structure was visualized with fluorescently labeled lectin Ulex europaeus Agglutinin I (UEA-I). Immunostaining was performed for proteins including smooth muscle actin expressed in smooth muscle cells surrounding arterioles and fibrotic myofibroblasts, as well as for neuropeptide Y expressed in sympathetic nerves. Sections were then recut at 5 μm and stained with hematoxylin and eosin (H&E).

RESULTS

Edema-like and cyst-like regions identified with MRI and CT were easily located in fluorescent images and appeared to have increased osteoclast activity. Fibrotic regions were identified with thickened arterioles and increased myofibroblasts. Sympathetic nerve fibers traveled alongside arborizing blood vessels. Stained sections became transparent in a water-based refractive index-matched medium, permitting deep 3D visualization of the elaborate neurovascular network in bone. Sequential staining procedures were successfully performed with the same sections, demonstrating the potential to compare multiple cellular markers from the same locations. Routine H&E staining could be performed after the fluorescent staining protocol.

CONCLUSION

We have developed a multimodal framework to facilitate comparisons between histology and clinical MRI and CT.

A simple optical tissue clearing pipeline for 3D vasculature imaging of the mediastinal organs in mice

Optical tissue clearing (OTC) methods render tissue transparent by matching the refractive index within a sample to enable three-dimensional (3D) imaging with advanced microscopes. The application of OTC method in mediastinal organs in mice remains poorly understand. Our aim was to establish a simple protocol pipeline for 3D imaging of the mediastinal organs in mice. Trachea, oesophagus, thymus and heart were harvested from mice after retrograde perfusion via the abdominal aorta. We combined and optimized antibody labelling of thick tissue samples, OTC with cheap and non-toxic solvent ethyl cinnamate (ECi), and light-sheet fluorescence microscopy (LSFM) or laser confocal fluorescence microscopy (LCFM) to visualize the vasculature of those tissues. A high degree of optical transparency of trachea, oesophagus, thymus and heart was achieved after ECi-based OTC. With anti-CD31 antibody immunofluorescence labelling before ECi-based OTC, the vasculature of these tissues with their natural morphology, location and organizational network was imaged using LSFM or LCFM. This simple protocol pipeline provides an easy-to-setup and comprehensive way to study the vasculature of mediastinal organs in 3D without any special equipment. We anticipate that it will facilitate diverse applications in biomedical research of thoracic diseases and even other organs.

Whole-Brain Profiling of Cells and Circuits in Mammals by Tissue Clearing and Light-Sheet Microscopy

Tissue clearing and light-sheet microscopy have a 100-year-plus history, yet these fields have been combined only recently to facilitate novel experiments and measurements in neuroscience. Since tissue-clearing methods were first combined with modernized light-sheet microscopy a decade ago, the performance of both technologies has rapidly improved, broadening their applications. Here, we review the state of the art of tissue-clearing methods and light-sheet microscopy and discuss applications of these techniques in profiling cells and circuits in mice. We examine outstanding challenges and future opportunities for expanding these techniques to achieve brain-wide profiling of cells and circuits in primates and humans. Such integration will help provide a systems-level understanding of the physiology and pathology of our central nervous system.

Tissue clearing and its applications in neuroscience

State-of-the-art tissue-clearing methods provide subcellular-level optical access to intact tissues from individual organs and even to some entire mammals. When combined with light-sheet microscopy and automated approaches to image analysis, existing tissue-clearing methods can speed up and may reduce the cost of conventional histology by several orders of magnitude. In addition, tissue-clearing chemistry allows whole-organ antibody labelling, which can be applied even to thick human tissues. By combining the most powerful labelling, clearing, imaging and data-analysis tools, scientists are extracting structural and functional cellular and subcellular information on complex mammalian bodies and large human specimens at an accelerated pace. The rapid generation of terabyte-scale imaging data furthermore creates a high demand for efficient computational approaches that tackle challenges in large-scale data analysis and management. In this Review, we discuss how tissue-clearing methods could provide an unbiased, system-level view of mammalian bodies and human specimens and discuss future opportunities for the use of these methods in human neuroscience.

Establishment and Analysis of a 3D Co-Culture Spheroid Model of Pancreatic Adenocarcinoma for Application in Drug Discovery

The high attrition rate of oncology drug candidates can be in part explained by the disconnect between the standard preclinical models (e.g., 2D culture, xenograft tumors) commonly employed for drug discovery and the complex multicellular microenvironment of human cancers. As such, significant focus has recently shifted to the establishment of preclinical models that more closely recapitulate human tumors, such as patient-derived xenografts, 3D spheroids, humanized mice, and mixed-culture models. For these models to be suited to drug discovery, they should optimally exhibit reproducibility, high-throughput, and robust and simple assay readouts. In this article, we describe a protocol for the generation of an in vitro 3D co-culture spheroid model that recapitulates the interaction of tumor cells with stromal fibroblasts in pancreatic adenocarcinoma. We additionally describe protocols relevant to the analysis of these spheroids in high-throughput drug discovery campaigns such as the assessment of spheroid proliferation, immunofluorescence and immunohistochemistry staining of spheroids, live-cell and confocal imaging and analysis of cell surface markers.

Systemic AAV vectors for widespread and targeted gene delivery in rodents

We recently developed adeno-associated virus (AAV) capsids to facilitate efficient and noninvasive gene transfer to the central and peripheral nervous systems. However, a detailed protocol for generating and systemically delivering novel AAV variants was not previously available. In this protocol, we describe how to produce and intravenously administer AAVs to adult mice to specifically label and/or genetically manipulate cells in the nervous system and organs, including the heart. The procedure comprises three separate stages: AAV production, intravenous delivery, and evaluation of transgene expression. The protocol spans 8 d, excluding the time required to assess gene expression, and can be readily adopted by researchers with basic molecular biology, cell culture, and animal work experience. We provide guidelines for experimental design and choice of the capsid, cargo, and viral dose appropriate for the experimental aims. The procedures outlined here are adaptable to diverse biomedical applications, from anatomical and functional mapping to gene expression, silencing, and editing.

Whole-Brain Analysis of Cells and Circuits by Tissue Clearing and Light-Sheet Microscopy

In this photo essay, we present a sampling of technologies from laboratories at the forefront of whole-brain clearing and imaging for high-resolution analysis of cell populations and neuronal circuits. The data presented here were provided for the eponymous Mini-Symposium presented at the Society for Neuroscience's 2018 annual meeting.