Stem cells from development to the clinic

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.

An engineered patch of retinal pigment epithelium generated from human embryonic stem cells is transplanted into the eyes of two patients.

Autologous transgenic epidermal stem cell cultures are used to reconstitute almost the entire epidermis of a patient with severe junctional epidermolysis bullosa.

Long-term cultures of human brain organoids display a high degree of cellular diversity, mature spontaneous neuronal networks and are sensitive to light.

Human pluripotent stem cells were used to develop dorsal and ventral forebrain 3D spheroids, which can be assembled to study interneuron migration and to derive a functionally integrated forebrain system with cortical interneurons and glutamatergic neurons.

In a preclinical study, dopaminergic neurons derived from human induced pluripotent stem cells were implanted into a primate model of Parkinson’s disease, where they were found to exhibit long-term survival, function as mid-brain dopaminergic neurons, and increase spontaneous movements.

This Review discusses how stem cell bioengineering can advance regenerative medicine by giving insight into the design principles that underlie different levels of stem cell systems — from the inner circuitry in single cells and the stem cell niche to systemic interactions between organs and tissues.

The fusion of patterned cerebral organoids into more complex structures enables modeling of inter-regional processes such as neuronal migration.

The Huntington's disease (HD) induced pluripotent stem cell (iPSC) consortium describe the combined use of differentiated patient-derived iPSCs and systems biology to discover underlying mechanisms in HD. They identify neurodevelopmental deficits in HD cells that can be corrected in cells and in vivo with a small molecule.

Direct neuronal conversion of skin fibroblasts from individuals with Huntington’s disease (HD) generates a population of medium spiny neurons that recapitulate hallmarks of HD, including aggregation of mutant huntingtin protein, DNA damage and spontaneous cell death.

Wound healing is essential to repair the skin after injury and distinct stem cells in the epidermis are known to contribute to the process. Here the authors perform molecular, functional and clonal analysis and reveal the individual contribution of stem cells coming from different epidermal compartments to the wound-healing process in mice.

This protocol describes procedures for building the SpinΩ bioreactor for 3D tissue culture and differentiating human iPSCs into different brain region–specific organoids resembling developing human dorsal forebrain, midbrain and hypothalamus.

This protocol describes how to grow a functional and transplantable corneal epithelium and how to generate ocular-like cell lineages resembling neuroectoderm, neural crest, ocular-surface ectoderm, or surface ectoderm derived from human iPS cells.

Cruz-Acuña et al. develop synthetic hydrogels that support the generation and expansion of viable human intestinal organoids from pluripotent stem cells and can be used as injectable vehicles for organoid engraftment and wound healing.

2017 has witnessed major advances in gut stem cell and cancer stem cell research, delivering key insights into their regulation, more defined culture methods and novel stem cell markers that collectively drive us ever closer to breakthroughs for regenerative medicine and cancer treatment in the clinic.

Endocrine (such as diabetes) and exocrine (such as pancreatitis) disorders of the pancreas have a substantial burden worldwide. This Review explores the potential of regenerative medicine and cell-based approaches to restore both endocrine and exocrine pancreatic function, describing insights into cell replacement, implantation and reprogramming.

The stomach responds to injury via two main patterns, the superficial response and the glandular response. In this Review, Sáenz and Mills discuss cellular plasticity and reprogramming in the stomach in the context of disease (such as gastric cancer) and during repair and homeostasis.

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.

This protocol describes how to recapitulate biliary development by differentiation of hPSCs into endoderm, foregut progenitor cells, hepatoblasts, cholangiocyte progenitors and mature 3D cholangiocyte-like cell organoids.

Cardiomyocytes derived from human stem cells act as a biological pacemaker in the rat heart.

The conflicting results of cell therapy clinical trials for heart regeneration have led to some confusion over the efficacy of this approach. This Review summarizes the main outcomes of these studies and gives perspectives for future cell-based regenerative trials largely based on the primary therapeutic target: regeneration of lost myocardium by exogenous cells or promotion of intrinsic repair though paracrine signalling.

Human induced pluripotent stem cells (hiPSCs) can be differentiated into many cardiovascular cell types, including cardiomyocytes and endothelial cells. hiPSC-derived cardiovascular cells can recapitulate patient-specific and disease-specific phenotypes. In this Review, Chen et al. discuss how hiPSCs can be used as a platform for cardiovascular drug development and disease modelling, and can facilitate individualized therapy in the era of precision medicine.

This protocol differentiates hPSCs into self-renewing epicardial cells by appropriate differentiation-stage-specific application of Gsk3 inhibitor, Wnt inhibitor, and then Gsk3 inhibitor again in a completely defined, xeno-free system.

This protocol describes the generation of early-developing cardiac organoids from human pluripotent stem cells. Geometric confinement of the hiPSCs drives spatial organization of the cells from a 2D layer into 3D cardiac microchambers.

Mouse tumor organoids are characterized as a model to study tumor biology and drug resistance.

This Review discusses the roles of deregulated RNA processing, including RNA methylation, RNA editing, RNA splicing and RNA binding protein activity, in cancer stem cells and highlights the potential of these events as biomarkers and therapeutic targets.

In this Review, Drost and Clevers discuss the recent advances in organoid models of cancer and how they can be exploited to drive the translation of basic cancer research into novel patient-specific treatment regimens in the clinic.

Chen et al. generate lung bud organoids from human pluripotent stem cells that recapitulate early lung development, such as branching airway formation and early alveolar structures, which could potentially be used to model lung disease.

Turco et al. derive long-term genetically stable organoids from normal endometrium and the decidua that recapitulate characteristics of in vivo uterine glands, respond to hormones and differentiate into secretory and ciliated endometrial cells.

An efficient and chemically defined protocol for the differentiation of human induced pluripotent stem cells into podocytes enables the recapitulation of the differential clearance of the human kidney glomerulus in an organ-on-a-chip.

Tissue mimics are of great interest in understanding diseases. Here, organoids were developed that resemble polycystic kidney disease cysts and it was demonstrated how material environment and adhesion can affect cystogenesis and disease progression.

Volumetric muscle loss leads to functional muscle impairment, and current stem cell-based treatments show limited efficacy. Here, the authors generate a stem cell scaffold, implant it in mice, and show that an exercise regimen enhances innervation and restoration of muscle function in mice.

Adult muscles contain quiescent stem cells, known as satellite cells, which are activated upon injury, enabling muscle repair and replenishment of the stem cell pool. Recent studies have shed light on the molecular circuitry regulating satellite cell fate decision and the impairment of this circuitry during degenerative muscle diseases and ageing.

Advances in the derivation of pluripotent stem cells (PSCs) and their differentiation to specific cell types could have diverse clinical applications. Trounson and DeWitt provide an overview of the progress in using embryonic stem cell and induced PSC derivatives for disease treatment and discuss the potential and limitations of such approaches.

The use of cultured human pluripotent stem cells (PSCs) to model human diseases has revolutionized the ways in which we study monogenic, multigenic and epigenetic disorders, by overcoming some of the limitations of animal models. PSC-based disease models are generated using various strategies and can be used for the discovery of new drugs and therapies.

Replacement of pathogenic mitochondrial DNA in human embryos is poised for clinical application.

This protocol describes the generation of mice entirely derived from genome-edited embryonic stem cells, enabling the production of transgenic mice in a single generation.

An artificial recombination locus, Polylox, that can generate hundreds of thousands of individual barcodes is used to trace the fates of haematopoietic stem cells in mice.

On the basis of transplantation experiments it is generally believed that a very small number of haematopoietic stem cells maintain multi-lineage haematopoiesis by stably producing a hierarchy of short-lived progenitor cells; here a new transposon-based labelling technique shows that this might not be the case during non-transplant haematopoiesis, but rather that a large number of long-lived progenitors are the main drivers of steady-state haematopoiesis during most of adulthood.

Analysis of transplantation of single haematopoietic stem cells in mice defines stable lineage-restricted fates in long-term self-renewing multipotent stem cells, including a class of multipotent stem cells that exclusively replenishes the megakaryocyte/platelet lineage.

Single-cell transcriptomics, fate assays and a computational theory enable prediction of cell fates during haematopoiesis, discovery of regulators of erythropoiesis and reveal coupling between the erythroid, basophil and mast cell fates.

Ascorbate depletion in mice increased haematopoietic stem-cell frequency and promoted leukaemogenesis, partly by reducing the function of the Tet2 tumour suppressor enzyme.

This paper describes a fully defined, nonxenogeneic in vitro niche for the differentiation of haematopoietic stem and progenitor cells to progenitor T cells in mouse and human.

This paper describes an in vitro method to generate human T cells from hematopoietic stem and progenitor cells (HSPCs). It should be useful for both basic and applied studies using T cells.

Gutierrez-Martinez et al. show that an impaired DNA damage response and reduced apoptotic priming in old haematopoietic stem cells (HSCs) contribute to the survival and expansion of damaged HSCs in the bone marrow of aged mice.

Velten et al. use single-cell transcriptomics and functional data to map the early lineage commitment of human haematopoietic stem cells as a continuous process of cells passing through transitory states rather than demarcating discrete progenitors.

Lineage-tracing experiments in the mouse show that Lgr6, but not Lgr5, functions as a cancer stem marker in skin squamous cell carcinomas (SCCs). The authors also show that Lgr6-knockout mice are predisposed to SCC development, through a mechanism that includes compensatory upregulation of Lgr5.

Michael Kharas and colleagues characterize the MSI2 protein interactome in leukemia cells and subsequently perform a functional screen identifying 24 genes required for leukemia in vivo. They focus on the RNA-binding protein SYNCRIP, showing that it regulates Hoxa9 and other transcripts involved in a myeloid leukemia stem cell program.

Applying a new, more sensitive single-cell transcriptomics method to diagnosis, remission and progression samples from patients with chronic myeloid leukemia reveals insight into the heterogeneity of cells that resist treatment with targeted therapy, as well as into the dynamics of disease progression and its effects on nontransformed hematopoietic stem cells.

Microenvironmental pressures in glioblastoma select for glioma stem cells (GSCs) subpopulations that are maintained through preferential activation of BMI1 and EZH2 in different niches. Given the high degree of intratumor heterogeneity, combined pharmacological inhibition of Polycomb repressive complexes targets proneural and mesenchynmal GSCs and expands lifespan in mice, warranting the therapeutic evaluation of this approach in patients with glioblastoma.

Adult stem cells are essential for the maintenance of tissue homeostasis and wound repair, but cancer can hijack their tissue regenerative functions to promote malignancy. Ge and Fuchs review recent insights into the determinants and general principles underlying stem cell plasticity under homeostasis, stress and cancer.

Stem cells are long-lived and possess unique mechanisms related to quiescence, DNA damage response and apoptosis that protect them throughout their lifespan and during tissue repair. These mechanisms may also have a role in cancer stem cells and tumorigenesis.

Notch signalling is a fundamental negative regulator of epidermal stemness. Here, the authors show that cell mechanics through YAP/TAZ activity prevent primary human keratinocytes from differentiating by inhibiting cell-autonomous Notch signals.

Individual human epidermal cells differ in their self-renewal ability. Here the authors perform genome-wide pooled RNAi screens to uncover the molecular basis for this heterogeneity, and identify genes conferring a clonal growth advantage on normal and neoplastic human epidermal cells.

This paper reports the efficient generation of human alveolar cells from induced pluripotent stem cells and their expansion in 3D culture.

This paper describes methods for the 3D culture of mouse lung progenitor cells that can differentiate in vitro and in vivo along all epithelial lineages.

Decline in stem cell function causes loss of tissue homeostasis and increased incidence of age-related diseases. During ageing, adult stem cells accumulate damage and the niche in which they reside malfunctions. These defects are associated with changes in the epigenome that contribute to organ dysfunction and disease.

The role of epigenetic regulation in adult stem cell function depends on the specific tissue and factor, but it commonly affects stem cell maintenance, self-renewal and differentiation without disrupting germ-layer fate.

Some terminally differentiated cells have the capacity to de-differentiate or transdifferentiate under physiological conditions as part of a normal response to injury. Recent insights have been gained into the role of this cell plasticity in maintaining tissue and organ homeostasis, and this has important implications for cell-based therapies.

The mechanism by which cell geometry regulates cell signalling is reported to be modulated by lipid rafts within the plasma membrane, which are now shown to be responsible for geometry-dependent mesenchymal stem cell differentiation.

The authors surveyed whole-exome and RNA-sequencing data from 252 unique pluripotent stem cell lines, some of which are in the pipeline for clinical use, and found that approximately 5% of cell lines had acquired mutations in the TP53 gene that allow mutant cells to rapidly outcompete non-mutant cells, but do not prevent differentiation.

Genetic and phenotypic analysis reveals expression quantitative trait loci in human induced pluripotent stem cell lines associated with cancer and disease.

A screen in which combinatorial pairs of transcription factors are exogenously expressed in fibroblasts identifies different combinations that reprogram these cells into induced neuronal cells with diverse functional properties.

Mouse fibroblasts are reprogrammed to induced pluripotent stem cells using single-chain antibodies in place of transcription-factor genes.

Expression of the minimally polymorphic HLA-E molecule prevents NK-cell-mediated rejection of cells lacking expression of HLA-A, B and C.

Human iPSC-derived neurons are generated from individuals with or without Alzheimer's disease carrying different APOE alleles and reveal a toxic, neuron-intrinsic gain of function of the ApoE4 variant that is a strong genetic risk factor for AD.

Human ALS/FTD patient iPSC-derived neurons are used to uncover mechanisms by which C9ORF72 mutations cause neurodegeneration.

The authors analyze time-resolved changes in genome topology, gene expression, transcription-factor binding, and chromatin state during iPSC generation. They conclude that 3D genome reorganization generally precedes gene expression changes and that removal of locus-specific topological barriers explains why pluripotency genes are activated sequentially during reprogramming.

TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit bivalent promoter hypermethylation without a corresponding decrease in gene expression in the undifferentiated state. However, PAX6 promoter hypermethylation in TKO hESCs impairs neural differentiation.

Ernesto Guccione and colleagues report that the transcription factor PRDM15 regulates naive pluripotency in mouse embryos and embryonic stem cells and in derivation of mouse and human iPSCs. They further show that PRDM15 promotes WNT signaling and inhibits MAPK–ERK signaling by directly regulating the expression of R-spondin1 and Sprouty1, respectively.

This study identifies regulatory variants in sensory neurons derived from induced pluripotent stem cells. Despite differentiation-induced variability, an allele-specific method allowed detection of loci influencing gene expression, chromatin accessibility and RNA splicing.

Transient transcription factor expression rapidly induces a homogenous population of mature GABAergic neurons from human pluripotent stem cells, aiding the study of inhibitory neuron function and disease.

Combining each sgRNA with a unique molecular identifier in a genome-wide screen increases sensitivity and robustness in both positive and negative selection.

This study compares naive human pluripotent stem cells, either reprogrammed directly from somatic cells or converted from primed cells, under a variety of culture conditions.

Pastor et al. demonstrate a role for TFAP2C in the promotion and maintenance of human naive pluripotency by facilitating the opening of enhancers close to pluripotency factors.

Yilmaz et al. generate a genome-wide loss-of-function library using human haploid embryonic stem cells and define genes that are essential for cell survival, growth and pluripotency maintenance, as well as growth-restricting genes.

Pandya et al. describe a protocol to differentiate human and mouse iPSCs into cells with the phenotype, transcriptional profile and functional properties of microglia. The treatment of murine intracranial malignant gliomas with these cells demonstrates their potential clinical use. These microglia-like cells will enable further studies into the role of microglia in health and disease.

A new chemically defined culture medium for the long-term culture of human pluripotent stem cells uses only three chemical compounds and a lower number of recombinant proteins than used in commercially available media.

Epigenetic and transcriptomic differences in human induced pluripotent stem cells generated from the same fibroblast population reveals that the reprogramming method affects the cells’ gene-expression levels but not their differentiation potential.

Cell state transitions during embryonic development are associated with epigenetic changes that alter chromatin structure and gene expression. Interplay between epigenetic regulatory layers can be studied using genomic technologies and embryonic stem cell cultures that reflectin vivocell states.

In this article, the authors review the mechanisms by which the pluripotency gene regulatory network governs the acquisition, maintenance and dissolution of the pluripotent state, including the interaction of these networks with chromatin-mediated and RNA-mediated regulatory mechanisms. They discuss recent evidence for alternative pluripotency states and the factors that affect transitions between these states.

The ectopic expression of a defined set of transcription factors can experimentally reprogramme somatic cells into other cell types, including pluripotent cells. This method enables exploration of the molecular characteristics of pluripotency, cell specification, differentiation and cell fate stability, as well as their transcriptional and epigenetic regulation.

Recent advances in our understating of the molecular underpinnings of alternative primed- and naive-like pluripotent states in rodents and humans highlight potential functional benefits of naive pluripotency and identify key unanswered questions in this rapidly evolving field.

This year marks the tenth anniversary of the generation of induced pluripotent stem cells (iPSCs) by transcription factor-mediated somatic cell reprogramming. Takahashi and Yamanaka portray the path towards this ground-breaking discovery and discuss how, since then, research has focused on understanding the mechanisms underlying iPSC generation and on translating such advances to the clinic.

Regulation of pluripotency: Li and Belmonte review the pluripotency gene regulatory network, the molecular principles of pluripotency gene function, regulation by RNA-binding proteins and alternative splicing, heterogeneity and alternative pluripotency states.

Genome editing in human zygotes shows that OCT4 is required for normal development at an earlier stage in humans than in mice.

Trophoblast and embryonic stem cells interact in vitro to form structures that resemble early blastocysts, and the embryo provides signals that drive early trophectoderm development and implantation.

Exit of epiblasts from an unrestricted naive pluripotent state is required for epithelialization and generation of the pro-amniotic cavity in mouse embryos and for amniotic cavity formation in human embryos and human embryonic stem cells.

Kian Peng Koh and colleagues report that TET1 regulates lineage-specific genes in the mouse postimplantation embryo, many of them independently of DNA methylation changes, through regulation of JMJD8 expression. They show that Tet1 deletion causes embryonic defects, which are partially penetrant in an inbred strain but fully lethal in non-inbred mice.

Maria-Elena Torres-Padilla and colleagues use a targeted epigenomic approach to investigate the role of LINE-1 retroelements during early mouse development. Their data suggest that timely activation of LINE-1 regulates global chromatin accessibility and is integral to the mouse developmental program.

Didier Trono and colleagues show that both human DUX4 and mouse Dux are expressed before zygotic genome activation (ZGA) and lead to activation of ZGA-associated genes. Dux knockout in mouse embryonic stem cells prevents cycling through a 2-cell-like state, and zygotic depletion of Dux impairs embryonic development.

Bradley Cairns, Douglas Carrell, Stephen Tapscott and colleagues transcriptionally profile human oocytes and preimplantation embryos and highlight DUX4-family proteins as activators of cleavage-stage genes and repetitive elements. They show that Dux expression converts mouse embryonic stem cells into two-cell (2C) embryo-like cells, thus suggesting mouse DUX and human DUX4 as drivers of the mammalian cleavage/2C state.

Fang et al. identify a PAX5–OCT4–PRDM1 transcriptional network that acts as a developmental switch in the transition from human pluripotent stem cells to the primordial germ cell lineage.

Is it time to reassess the 14-day rule for human embryo research?

Single-cell technologies are transforming our understanding of pre-implantation and early post-implantation development and of in vitro pluripotency. Specifically, single-cell transcriptomics and imaging and the accompanying bioinformatics methods have enabled precision interrogation of cell fate choices and cell lineage diversification, which occur at the level of the individual cell.

This protocol extension describes how to obtain functionally mature oocytes from embryonic or induced pluripotent stem cells. These oocytes can be used to produce live mouse offspring.

A deep learning approach enables fast and robust prediction of hematopoietic stem cell lineage choice in time-lapse imaging three generations before conventional marker onset.

Ibarra-Soria et al. study cellular diversity, transcriptional signatures, lineage specification and somitogenesis on a single-cell level in E8.25 mouse embryos, and reveal the regulation of blood progenitor formation by the leukotriene pathway.

Human pluripotent stem cells constitute a unique system to study the earliest stages of human embryonic haematopoiesis and the origins of human blood cell diseases, and they are an invaluable tool for the generation of haematopoietic stem and progenitor cell populations for cell-based regenerative therapies.

Recruitment of young neurons to the hippocampus decreases rapidly during the first years of life, and neurogenesis does not continue, or is extremely rare, in the adult human brain.

Human cerebral organoids undergo vascularization and maturation in the mouse brain.

Engineering human brain organoids with floating scaffolds enhances the maturity and reproducibility of cortical tissue structure.

Using single-cell RNA-seq, the authors show that early developmental neurogenesis in the dentate gyrus of the hippocampus is largely conserved in the adult, but with a perinatal transformation of stem cells to an adult type.

Mechanical cues play critical roles in embryonic development. A micropatterned neuroectoderm developmental model based on human pluripotent stem cells now reveals how morophogenetic signals such as cell shape and contractility regulate neural tissue development.

The dynamics of progenitor cells in human neocortex development has not been studied directly. Here, the authors timelapse image human neuroepithelial (NE) and radial glial (RG) cells in embryonic brain slices and find properties of NE cells and RG that are mimicked in cerebral organoids.

Single-cell RNA sequencing analysis of two- and three-dimensional hepatic differentiation reveals that both systems recapitulate certain transcriptomic features of human hepatogenesis.

Human pluripotent stem cells are differentiated into inner ear organoids containing cells similar to hair cells and sensory neurons.

FateID identifies fate biases in early multipotent progenitor populations from single-cell RNA-seq data.

Jiang et al. trace two embryonic fibroblast lineages in the mouse, one that does not express engrailed and mediates early dermal development and one that expresses engrailed and mediates scar tissue formation.

The role of stem/progenitor cell populations in mammary gland morphogenesis is not well understood. Here, the authors show that a transcriptional repressor, Blimp1, is expressed in a rare luminal stem cell population, which contribute to duct formation, and survive multiple rounds of pregnancy and involution.

HoangDinh Huynh and Yihong Wan investigate the role of the mTORC1 pathway during osteoclastogenesis and find that the cytokine RANKL inactivates mTORC1 via calcineurin-mediated dephosphorylation, leading to activation of NFATc1 by reducing its phosphorylation. These findings have implications for bone diseases and mTORC1/NFATc1 signaling.

This protocol uses a three-layer system to organize rat primary testicular cells into organoids that can both establish and maintain germ cells in an environment containing a functional blood–testis barrier.