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The mechanisms regulating multipotency in glandular epithelia remain unclear. Here, the authors identify the key role of collagen signaling and ECM stiffness in regulating stem cell multipotency in glandular epithelia.

In this Tools of the Trade article, Francisco Lorenzo-Martín and Matthias Lutolf present mini-colons as a new ex vivo cancer model that incorporates microfabrication, tissue engineering and optogenetics.

The authors have designed modular synthetic hydrogel networks for mouse and human intestinal stem cell cultures that support intestinal organoid formation.

The microbiota influences the cytotoxicity of chemotherapy in patients with colorectal cancer but the impact on metastatic relapse is less clear. Here, the authors report that chemotherapy-induced intestinal mucositis induces systemic immune changes via production the microbial metabolite, indole-3-propionic acid (IPA), preventing metastases.

Previous approaches to derive embryoids either lack physiological morphology and signaling interactions, or are unconducive to model post-gastrulation development. Here the authors use a high-throughput approach to induce mouse embryonic stem cells into epiblast-like aggregates, which are then co-cultured with mouse trophoblast stem cell aggregates, to yield embryoids with axial morphogenesis and anterior development.

Current knowledge of the mechanisms that underly Helicobacter pylori (H. pylori) infections remains limited. Here, the authors present an in vitro gastric model that combines structural complexity with experimental accessibility, enabling improved research into H. pylori-induced pathogenesis.

The enhanced observability of bilaterally accessible gastrointestinal organoid-derived monolayers facilitates the study of parasite infection of the gut.

This protocol integrates state-of-the-art microfabrication, tissue engineering and optogenetic approaches to generate topobiologically complex miniature colons capable of undergoing tumorigenesis in vitro.

Topobiologically complex mini-colons—which enable the faithful in vitro recapitulation of colorectal cancer tumorigenesis and its environmental determinants—offer the possibility to reduce animal use in a wide range of experimental applications.

Organoid avatars of colorectal cancer and its microenvironment model immune interactions and drug efficacy.

3D liver organoids hold great promise for regenerative medicine but the use of ill-defined matrices limits their potential. Here, the authors generate human and mouse liver organoids using a chemically defined matrix, and reveal a link between matrix stiffness and organoid growth that does not require acto-myosin contraction.

The influence of stress relaxation of the extracellular matrix on the formation of intestinal organoids was investigated. It was shown that a stress-relaxing synthetic matrix promotes crypt budding through increased symmetry breaking and niche cell formation.

Haematopoietic stem cells rely on glycolysis for their energy demands but whether this affects their fate is unknown. Here, the authors show that forcing the cells to rely on glycolysis is important for self-renewal and that this involves a reduction in mitochondrial mass.

A combination of two light-induced reactions has been used to attach peptides to a polymeric gel, and then to detach them from it. This feat opens up opportunities for studying the effects of signalling molecules on cell behaviour in vitro.

By using light to control the degradation of hydrogel components in space and time, researchers have generated a tool to help them reconstruct functional biological tissues in a culture dish.

Human brain morphodynamics are explored using organoids.

Miniature gut tubes grown in vitro from mouse intestinal stem cells are perfusable, can be colonized with microorganisms and exhibit a similar arrangement and diversity of specialized cell types to intestines in vivo.

Thousands of individual gastrointestinal organoids cultured on microcavity arrays without a solid extracellular matrix allow for high-throughput drug screening and for high-content image-based phenotypic analyses.

The human endoderm-derived organoid cell atlas (HEOCA) presents an integrative analysis of single-cell transcriptomes across different conditions, sources and protocols. It compares cell types and states between models, and harmonizes cell annotations through mapping to primary tissues.

A microfluidic approach allows spatiotemporal control of morphogen distribution in human pluripotent stem cell cultures. This approach recapitulates early developmental processes such as localized signaling and symmetry-breaking events.

Soft hydrogel microwell arrays with controllably variable stiffness are spotted with proteins of interest, individually or in combination. The system permits in vitro study of the biophysical and biochemical aspects of the stem-cell niche.

Patterning physiologically relevant proteins in three-dimensional hydrogels without affecting the activity and stability of the proteins has been difficult. Now, by using enzymatic crosslinking reactions, in situ control over the phototriggered immobilization of virtually any desired protein in a synthetic hydrogel is demonstrated. The approach can be used to manipulate cells, as demonstrated by the three-dimensional control of the invasion of mesenchymal stem cells within poly(ethylene glycol) hydrogels.

The confinement imposed by the three-dimensional microenvironment promotes the induction of pluripotency in somatic cells through an accelerated mesenchymal-to-epithelial transition and increased epigenetic remodelling.

Haematopoietic stem cell (HSC) self-renewal is not sufficiently understood to recapitulate in vitro. Here, the authors generate gene signature and cell cycle hallmarks of single murine HSCs, and use identified endothelial receptors Esam and JamC as substrates to enhance HSC growth in engineered niches.

The human genome harbors more than 4.5 million transposable element (TE)-derived insertions, the result of recurrent waves of invasion and internal propagation. Here they show that TEs belonging to evolutionarily recent subfamilies go on to regulate later stages of human embryonic development, notably conditioning the expression of genes involved in gastrulation and early organogenesis.

Adult neural stem and progenitor cells (NSPCs) show high levels of fatty acid synthase (Fasn)-dependent de novo lipogenesis, a process that is controlled by Spot14 to regulate the rate of proliferation; this indicates a functional coupling between the regulation of lipid metabolism and adult NSPC proliferation.

Researchers developed an open-hardware structured illumination microscopy add-on. This affordable upgrade provides super-resolution capabilities for normal optical microscopes. Detailed instructions enable easy reproduction to help democratize advanced microscopy.

Contact spotting with standard microarray printing tools can be used to generate high-density arrays of living mammalian cells, permitting the arraying of cell libraries without complex fluid manipulation.

3D cell culture matrices more closely resemble the natural microenvironments of stem cells than 2D systems. Here, the authors present a 3D cell culture approach to screen for the influence of environmental parameters on self-renewal and differentiation of single mouse embryonic stem cells.

DisCo is a deterministic droplet microfluidics tool for single-cell analysis on low cell input samples, which is demonstrated to profile individual intestinal organoids and in vivo-derived small tissues.

A 3D bioprinting approach has been developed to facilitate tissue morphogenesis by directly depositing organoid-forming stem cells in an extracellular matrix, with the ability to generate intestinal epithelia and branched vascular tissue constructs.

Cultures grown from small aggregates of mouse embryonic stem cells can be induced to organize spatial and temporal patterns of gene expression that parallel those of the early embryo, offering a potentially useful system for studying early development.

Nowell et al. report that chronic inflammation of the corneal epithelium activates β-catenin signalling through YAP/TAZ-dependent mechanotransduction, leading to epidermal differentiation on the ocular surface and corneal squamous cell metaplasia.

This Review highlights the recent emergence of stem-cell-derived embryo models for the purpose of advancing our understanding of mammalian embryology as well as their potential uses in regenerative and reproductive medicine.

This Review summarizes limitations in the current techniques used for patient-derived cancer organoid culture and highlights recent advancements and future opportunities for their standardization.

Organoids are cellular 3D models of organs, which provide powerful in vitro platforms for the investigation of tissue and disease biology. In this Review, the authors investigate engineering approaches, including cellular engineering, designer matrices and microfluidics, to improve the reproducibility and physiological relevance of organoids.

Organoids are 3D structures derived from stem cells that recapitulate some key characteristics of real organs. The authors review recent progress in organoid derivation and applications and outline how advances in other disciplines might lead to more physiologically relevant organoids.

This protocol describes the synthesis and application of hydrogel matrices comprising a poly(ethylene glycol) backbone, functionalized with cell adhesion cues and laminin-111. Uses include expanding stem cells and differentiating them into organoids.