Stem cells constitute a source of self-renewing cells with a potential for differentiation into multiple cell lineages. In the embryo, these cells supply the cell lineages that specify different tissues. Adult tissues retain stem cell types with tissue-specific capabilities for tissue turnover and repair. Embryonic and haematopoietic stem cell research has shown that stem cell fates are controlled by their surrounding microenvironment, referred to as the stem cell niche. The niche is formed by the ensemble of stromal cells and the components they produce, including adhesive signals, soluble factors, and matrix proteins. While we have some understanding of the interactions between adult stem cells and their environment, the requisite components of the stem cell niche are still unclear. Furthermore, tissue specific stem cells are likely to reside in specialized niches that require further characterisation. Progress towards understanding and building a stem cell niche will be necessary to advance in situ applications of in vitro reprogrammed cells, differentiated embryonic stem cells, and targeted adult stem cell expansion in tissue regeneration. Stem cell niche mechanisms could additionally reveal how abnormal cell microenvironments, for example, the leukaemic stem cell niche, can contribute to cancer initiation and progression.

This special issue is intended to present novel research and concepts that link stem cell function to the in vivo stem cell microenvironment, including research in stem cell niche in vitro models. We welcome submission of high-quality research studies as well as review articles.

Potential topics include but are not limited to the following:

• The early embryo as a stem cell niche: comparisons of embryonic stem cells to naïve embryonic stem cell states
• Haematopoietic stem cells in the yolk sac, AGM, liver, and bone marrow niches
• Mesenchymal stem cells and microenvironment-directed fate changes
• Tissue-specific adult stem cell niches: similarities and differences
• Maintaining the stem cell niche: contributions from ECM and cellular interactions
• Engineering the stem cell niche: mechanical and topological requirements for the niche