Collection |

Stem cells from development to the clinic

Recent advances in our understanding of stem cell differentiation and fate determination have enabled us to use stem cells in vitro and in vivo in a variety of applications, such as disease modelling, drug screening and for transplantations. This Collection of primary research articles, reviews and protocols from across the Nature journals involves both basic and translational research.

Research articles presented here highlight important work on stem cell differentiation, pluripotency states, lineage specification, development, genetic & epigenetic changes and metabolic regulation. They further explore how this knowledge can be applied to develop stem cell technologies that allow more detailed study of the onset of neural, intestinal, liver, lung, cardiac, muscle and blood diseases, as well as cancer. We showcase papers on the use of stem cells in the clinic to treat a genetic skin disorder and macular degeneration. In addition, the collection includes a number of peer-reviewed protocols from Nature Protocols that focus on iPSC reprogramming and the generation of organoids. Opinion and Review articles discuss the advances in this field, ethical implications of the work, as well as challenges faced by the scientific community as researchers attempt to apply the knowledge gained from basic studies in the clinic. 

Disease modelling & Regeneration

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.

Review Article | | Nature Reviews Genetics

Patients with junctional epidermolysis bullosa (JEB) carry mutations in genes that encode components of the basement membrane, which ensures the integrity between the epidermis and the dermis, such as laminin-332. These mutations cause blistering of the skin and chronic wounds. Following initial treatment of an adult patient with a limited affected region, Michele De Luca and colleagues reconstruct the full epidermis of a 7-year-old patient with autologous transgenic cells transduced with a virus vector carrying the non-mutated form of laminin-322. The integration sites of the virus used for gene delivery provide a tracing tool ex vivo and in vivo and demonstrate that the human epidermis is sustained by a limited number of long-lived stem cells.

Article | | Nature

Three-dimensional cellular models of the human brain, or organoids, enable the in vitro study of cerebral development and disease, but exactly which cells are generated and how much of the brain's complexity they recreate is undefined. To investigate in depth the nature of cells in human cerebral organoids differentiated from pluripotent stem cells, Paola Arlotta and colleagues carried out droplet-based single-cell expression analysis on cells isolated from over 30 organoids at developmental stages ranging from 3 to 9 months and beyond. They identify a wide diversity of neurons and progenitors and show that the more mature organoids formed dendritic spines as well as electrically active networks, which responded to light stimulation. The authors suggest that organoids may facilitate the study of circuit function using physiological sensory mechanisms. Elsewhere in this issue, Sergiu Paşca and colleagues show that re-assembling ventral and dorsal forebrain spheroids obtained separately in vitro allows the migration of human interneurons and the formation of functional synapses.

Article | | Nature

GABAergic neurons play important roles in brain function and are implicated in numerous psychiatric disorders. They migrate long distances from the ventral to the dorsal forebrain before integrating to cortical circuits. In vitro modelling of GABAergic neuronal differentiation during this interaction would allow us to investigate the cause of human brain disorders associated with defects in neuronal migration, but this has so far been difficult. Sergiu Paşca and colleagues have developed an approach for generating neural three-dimensional spheroids resembling either the ventral or dorsal forebrain. They show that assembling the two types of spheroids separately in vitro allows the saltatory migration of human interneurons into the cortex, as seen in human development, and the formation of functional synapses with the dorsally derived cortical glutamatergic neurons. In this context, they find that interneurons from Timothy syndrome patients exhibit perturbation in migration patterns. Elsewhere in this issue, Paola Arlotta and colleagues carried out single cell expression analysis on cells from human brain organoids to investigate the nature of cells generated by these three-dimensional models.

Article | | Nature

Restoring neuronal function by implanting dopaminergic (DA) neurons derived from pluripotent stem cells in patients suffering from Parkinson's disease is a long-term goal in regenerative medicine. In a preclinical study using primate models, Jun Takahashi and colleagues show that such DA progenitors derived from human induced pluripotent stem cells exhibit long-term survival, extended neurites in the host brain and function as midbrain DA neurons when implanted in a monkey model for Parkinson's disease. The implanted cells restored a range of movements and no tumours were observed after two years.

Letter | | Nature

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.

Review Article | | Nature Reviews Genetics

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.

Article | | Nature Neuroscience

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.

Article | Open Access | | Nature Communications

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.

Review Article | | Nature Reviews Gastroenterology & Hepatology

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.

Review Article | | Nature Reviews Cardiology

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.

Review Article | | Nature Reviews Cardiology

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.

Review Article | | Nature Reviews Cancer

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.

Article | Open Access | | Nature Communications

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.

Review Article | | Nature Reviews Molecular Cell Biology

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.

Science and Society | | Nature Reviews Molecular Cell Biology

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.

Review Article | | Nature Reviews Molecular Cell Biology

Macrophages, a type of white blood cell, when derived from embryonic stem cells in the laboratory reduce fibrosis in chronic liver disease. Lesley Forrester and colleagues from the University of Edinburgh found murine embryonic stem-cell-derived macrophages (ESDM) were morphologically similar to bone marrow-derived macrophages (BMDM), previously found to reduce fibrosis and improve liver function in mice with induced liver injury. Using a novel technique, the team found ESDM engulfed fewer particles at a slower rate than BMDM, indicating ESDM were less inflammatory. A higher dose of ESDM was required to have the same effect of BMDM to help liver fibrosis regression. However, they were more efficient in repopulating mouse livers depleted of liver-specific macrophages and also significantly improved liver function, indicating ESDM were similar to resident macrophages in the liver and had therapeutic potential.

Article | Open Access | | npj Regenerative Medicine

Adult stem cells

Transplantation-based assays of haematopoietic stem cells (HSCs) and progenitors isolated on the basis of the expression of their surface markers have inferred that the haematopoietic lineage follows a tree-like structure that starts from a long-term multipotent HSC at its base and splits into a few major branches. However, recent data question the existence of this structure, instead supporting the idea that the blood lineage is sustained by several fate-restricted progenitors. Hans-Reimer Rodewald and colleagues have developed a DNA recombination locus based on the Cre–loxP system that can tag single cells using several hundred thousand barcodes. They introduce the labelling in mouse embryos and track HSCs during their life. Surprisingly, the adult HSC compartment is a mosaic of HSC clones derived from embryos and contributes with different proportion to blood lineage, some multilineage and others of restricted fates, according to a pattern that is consistent within clones. However, they define an early split of fate between myeloid erythroid and lymphocyte development which agrees with the tree-like structure.

Letter | | Nature

It is generally believed that a very small number of haematopoietic stem cells (HSCs) maintain multilineage haematopoiesis by stably producing a hierarchy of short-lived progenitor cells. This theory is historically based on transplantation experiments in lethally irradiated hosts. Using a new transposon-based labelling technique that enables unique tagging of individual cells and their progeny in vivo, Fernando Camargo and colleagues now show that this might not be the case during native non-transplant haematopoiesis. The authors found that the main drivers of steady state haematopoiesis during most of adulthood are a large number of long-lived progenitors, rather than classically defined haematopoietic stem cells.

Article | | Nature

Many blood disorders can be treated with haematopoietic (blood-generating) stem cell (HSC) transplants, but such treatment does not always lead to efficient replenishment of all blood lineages. Through single-cell transplantation of HSCs in mice, Sten Eirik Jacobsen and colleagues define lineage-restricted fates of long-term self-renewing cells. They identify a class of HSC that effectively replenishes the megakaryocyte and platelet lineages over other lineages, and other HSCs that are more able to participate in megakaryocyte, erythroid and myeloid lineages despite being able to sustain lymphoid potential. Genetic lineage tracing also shows that platelet-biased HSCs are able to support unperturbed adult haematopoiesis.

Letter | | Nature

Allon Klein, Merav Socolovsky and colleagues examine the emergence of distinct blood cell lineages from mouse haematopoietic progenitors. Their approach combines single-cell transcriptomics, cell fate potential assays and population balance analysis—a computational method for predicting cell fate probabilities from population snapshots. They use a new flow-cytometry strategy to sort cells with newly defined markers of erythroid differentiation and validate the findings at the single-cell level. The results show that differentiation is a continuous, albeit hierarchical, process. They also reveal that erythroid and mast cell fates are coupled, and that remodelling the expression of cell cycle regulators is very important as erythroid cells proceed to terminal differentiation.

Article | | Nature

The effect of changes in metabolite levels on stem-cell fate in vivo has been unclear. Sean Morrison and colleagues survey the metabolites of haematopoietic stem cells (HSCs) and progenitors. They show that each type of blood cell has a specific signature and that human and mouse HSCs have high levels of ascorbate, which drop during differentiation. Depletion of ascorbate in mice increases the number and function of HSCs and cooperates with a mutation associated with leukaemia to accelerate tumorigenesis. Analysis of the phenotypes indicates that ascorbate can act in a non-cell-autonomous fashion, partly by modulating the function of the tumour suppressor Tet2.

Article | | Nature

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.

Article | | Nature Genetics

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.

Article | | Nature Genetics

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.

Article | | Nature Medicine

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.

Article | | Nature Medicine

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.

Article | Open Access | | Nature Communications

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.

Review Article | | Nature Reviews Molecular Cell Biology

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.

Review Article | | Nature Reviews Molecular Cell Biology

A select group of bone marrow cells (BMCs) with the capacity to regenerate the heart are not all the same. Working with mouse cells, a team led by Annarosa Leri used single cell-based analytical techniques to test whether all BMCs that express a cell surface marker called c-kit possess the ability to form new heart tissue. They found that these BMCs, despite their shared expression of c-kit, were not a uniform population. Only a subset could give rise to various cell lineages in the heart. Others remained in an undifferentiated state and retained their bone marrow identity, even within the damaged heart. The findings could help explain why researchers have reported such disparate results in the past when assessing the heart repairing potential of c-kit-positive BMCs.

Article | Open Access | | npj Regenerative Medicine

Co-culture of meniscal cartilage-forming cells with fat-derived stem cells can lead to enhanced cartilage matrix production when cultured under simulated microgravity. Adetola Adesida from the University of Alberta in Edmonton, Canada, and colleagues cultured two types of cells found together in the knee—cartilage-forming chondrocyte cells (taken from the meniscus) and mesenchymal stem cells (isolated from the infrapatellar fat pad)—in a rotary cell culture system designed to model weightlessness on Earth. Simulated microgravity enhanced the synergistic interaction between the two types of cells in culture, resulting in more matrix production, but it also prompted the cartilage-forming cells to differentiate towards bone-forming cells, as evidenced by gene expression analysis. These findings suggest that microgravity and simulated microgravity-based culture technologies could help bioengineers grow knee replacements for people with meniscus tears, but increased bone-directed differentiation could pose a possible problem for astronauts on prolonged missions.

Article | Open Access | | npj Microgravity

Signals from a protein that regulates cell division are essential to maintain the stem cells that regenerate hair follicles. Jeff Biernaskie and colleagues at Canada’s University of Calgary found signals from platelet-derived growth factor (PDGF) promote self-renewal of ‘hair follicle dermal stem cells’ (hfDSCs)—cells present at the bottom of hair follicles important for their regeneration. They ‘turned off’ the gene responsible for PDGF production in hfDSCs in mice. This led to a significant reduction in the stem cells with successive hair cycles. They also tested the effects of PDGF signaling molecules on isolated hfDSCs and found they improved their ability to proliferate and to induce follicle regeneration. The results suggest disruption to PDGF signaling may contribute to hair loss. PDGF could be an important additive to rapidly expand hfDSCs ex vivo for cell-based therapies.

Article | Open Access | | npj Regenerative Medicine

Reprogramming & Pluripotency

Copy number variants at particular genomic locations have been shown to arise in human pluripotent stem cells (hPSCs) under certain culture conditions, but the extent of acquired mutations in such culture remains to be determined. Kevin Eggan and colleagues surveyed the exomes of 140 human embryonic stem cell (hESC) lines, some of which are in the pipeline for clinical use.They identified mosaic mutations in the TP53 gene in a subset of cells for five unrelated hESC lines and show that the cells carrying the mutations outcompeted the non-mutant cells and could readily differentiate. Similar mutations were also identified by mining published datasets for an additional 14 hESC lines and more than 100 human induced PSC lines. The study highlights the need for in-depth characterization of cells derived from hPSCs before their use in the clinic.

Letter | | Nature

The Human Induced Pluripotent Stem Cells Initiative (HipSci) has resulted in the generation, genotyping and phenotyping of more than 700 human induced pluripotent stem (iPS) cell lines derived from 300 healthy individuals. Although analysis of these data indicates that most of the variations in phenotypes between cells arise from variations between individuals, the authors also assess the consequences of the rare genetic defects that are recurrently seen in iPS cells after reprogramming and provide a map of the common regulatory variants that can change the transcriptome of human pluripotent cells. This resource will be useful for genetic studies of complex traits and cancer.

Article | | Nature

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.

Article | | Nature

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.

Article | | Nature Genetics

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.

Article | | Nature Genetics

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.

Article | | Nature Genetics

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.

Technical Report | | Nature Neuroscience

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.

Review Article | | Nature Reviews Genetics

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.

Review Article | | Nature Reviews Molecular Cell Biology

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.

Timeline | | Nature Reviews Molecular Cell Biology

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.

Review Article | | Nature Cell Biology

Stem cells in development

The molecular mechanisms that direct early cell fate decisions in human embryos are currently unclear. Kathy Niakan and colleagues have used CRISPR–Cas9-mediated genome editing to analyse the role of the pluripotency transcription factor OCT4 during human embryogenesis, and uncover some unexpected functions. They first defined the most efficient OCT4-targeting single-cell RNA and delivery method using a combination of analysis in human embryonic stem cells and mouse embryos, before moving to donated diploid human zygotes. They find that OCT4 is required early in development to regulate the expression of genes in extra-embryonic trophectoderm, which makes up the placenta, and of pluripotent genes such as NANOG, which define the pluripotent epiblast.

Article | | Nature

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.

Letter | | Nature

During mammalian development, embryonic pluripotent stem cells form a cavitated epithelium at the time of implantation. Magdalena Zernicka-Goetz and colleagues show that, in spheroids made from mouse embryonic stem cells, the cells must leave their unrestricted naive pluripotent state for the events leading to cavity formation. The transcription factor Oct4 activates this exit and the expression of genes that code for proteins involved in lumenogenesis. The authors also show that these events are conserved in spheroids from human embryonic stem cells.

Letter | | Nature

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.

Article | | Nature Genetics

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.

Article | | Nature Genetics

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.

Article | | Nature Genetics

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.

Review Article | | Nature Reviews Molecular Cell Biology

Previous lines of evidence have suggested that neural precursors are present in adult humans and continue to generate new neurons in the hippocampus even after full maturation. Here, Arturo Alvarez-Buylla and colleagues re-visit that concept and come to a different conclusion. Using a more comprehensive and larger set of samples of human hippocampus than those analysed in previous studies, the authors find evidence for the production of new neurons early in life, but note that hippocampal neurogenesis rates decline rapidly within the first few years of childhood. The authors were unable to detect the production of any new neurons in adults. The same patterns of neurogenesis were observed in rhesus macaques.

Letter | | Nature

The mechanisms by which interactions between different cell types influence lineage identity and cell maturation during human development are unknown. Barbara Treutlein and colleagues use single-cell RNA-sequencing to analyse the emergence of hepatocytes lineages in a three-dimensional organoid system that is based on the reconstitution of hepatic, stromal and endothelial interactions. They compare their findings in vitro with data they obtain from fetal and adult human livers, and show that hepatocytes from the organoids closely resemble fetal liver cells. Through a chemical screen, they show that the three-dimensional system can be used to explore how signalling pathways influence endothelial network and hepatoblast formation.

Letter | | Nature

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.

Article | Open Access | | Nature Communications

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.

Article | Open Access | | Communications Biology