Three-dimensional intact-tissue sequencing of single-cell transcriptional states

Using single cell analysis for translational studies in immune mediated diseases: Opportunities and challenges

The difficulty of studying small tissue samples and rare cell populations have been some of the main limitations in performing efficient translational studies of immune mediated diseases. Many of these conditions are grouped under the name of a single disease whilst there are strong suggestions that disease heterogeneity leads to variable disease progression as well as therapeutic responses. The recent development of single cell techniques, such as single cell RNA sequencing, gene expression profiling, or multiparametric cytometry, is likely to be a turning point. Single cell approaches provide researchers the opportunity to finally dissect disease pathology at a level that will allow mechanistic classifications and precision therapeutic strategies. In this review, we will give an overview of the current and developing repertoire of single cell techniques, the benefits and limitations of each, and provide an example of how single cell techniques can be utilized to understand complex immune mediated diseases and their translation from mouse to human.

The Impact of Pancreatic Beta Cell Heterogeneity on Type 1 Diabetes Pathogenesis

PURPOSE OF REVIEW

To discuss advances in our understanding of beta-cell heterogeneity and the ramifications of this for type 1 diabetes (T1D) and its therapy.

RECENT FINDINGS

A number of studies have challenged the long-standing dogma that the majority of beta cells are eliminated in T1D. As many as 80% are present in some T1D subjects. Why don't these cells function properly to release insulin in response to high glucose? Other findings deploying single-cell "omics" to study both healthy and diseased cells-from patients with both T1D and type 2 diabetes (T2D)-have revealed cell subpopulations and heterogeneity at the transcriptomic/protein level between individual cells. Finally, our own and others' findings have demonstrated the importance of functional beta-cell subpopulations for insulin secretion. Heterogeneity may endow beta cells with molecular features that predispose them to failure/death during T1D.

Single-cell genomics to guide human stem cell and tissue engineering

To understand human development and disease, as well as to regenerate damaged tissues, scientists are working to engineer certain cell types in vitro and to create 3D microenvironments in which cells behave physiologically. Single-cell genomics (SCG) technologies are being applied to primary human organs and to engineered cells and tissues to generate atlases of cell diversity in these systems at unparalleled resolution. Moving beyond atlases, SCG methods are powerful tools for gaining insight into the engineering and disease process. Here we discuss how scientists can use single-cell sequencing to optimize human cell and tissue engineering by measuring precision, detecting inefficiencies, and assessing accuracy. We also provide a perspective on how emerging SCG methods can be used to reverse-engineer human cells and tissues and unravel disease mechanisms.

Visualizing and discovering cellular structures with super-resolution microscopy

Super-resolution microscopy has overcome a long-held resolution barrier-the diffraction limit-in light microscopy and enabled visualization of previously invisible molecular details in biological systems. Since their conception, super-resolution imaging methods have continually evolved and can now be used to image cellular structures in three dimensions, multiple colors, and living systems with nanometer-scale resolution. These methods have been applied to answer questions involving the organization, interaction, stoichiometry, and dynamics of individual molecular building blocks and their integration into functional machineries in cells and tissues. In this Review, we provide an overview of super-resolution methods, their state-of-the-art capabilities, and their constantly expanding applications to biology, with a focus on the latter. We will also describe the current technical challenges and future advances anticipated in super-resolution imaging.

Sequencing Diversity One Cell at a Time

Single-cell RNA sequencing provides a new approach to an old problem: how to study cellular diversity in complex biological systems. Three studies-Saunders et al., Zeisel et al., and Davie et al.-deploy this technique on an unprecedented scale to reveal transcriptional patterns that distinguish cells in the nervous systems of mice and flies.