Technical Challenges in Using Human Induced Pluripotent Stem Cells to Model Disease

Reprogramming of human somatic cells uses readily accessible tissue, such as skin or blood, to generate embryonic-like induced pluripotent stem cells (iPSCs). This procedure has been applied to somatic cells from patients who are classified into a disease group, thus creating “disease-specific” iPSCs. Here, we examine the challenges and assumptions in creating a disease model from a single cell of the patient. Both the kinetics of disease onset and progression as well as the spatial localization of disease in the patient's body are challenges to disease modeling. New tools in genetic modification, reprogramming, biomaterials, and animal models can be used for addressing these challenges.National Institutes of Health (U.S.) (Grant RO1-HD045022)National Institutes of Health (U.S.) (Grant R37-CA084198)National Institutes of Health (U.S.). (Grant RO1-CA087869

Induced Pluripotent Stem Cells Meet Genome Editing

It is extremely rare for a single experiment to be so impactful and timely that it shapes and forecasts the experiments of the next decade. Here, we review how two such experiments - the generation of human induced pluripotent stem cells (iPSCs) and the development of CRISPR/Cas9 technology - have fundamentally reshaped our approach to biomedical research, stem cell biology, and human genetics. We will also highlight the previous knowledge that iPSC and CRISPR/Cas9 technologies were built on as this groundwork demonstrated the need for solutions and the benefits that these technologies provided and set the stage for their success.National Institutes of Health (U.S.) (Grant 1R01NS088538-01)National Institutes of Health (U.S.) (Grant 2R01MH104610-15

Dissecting Risk Haplotypes in Sporadic Alzheimer's Disease

Understanding how genetic risk variants contribute to complex diseases is crucial for predicting disease susceptibility and developing patient-tailored therapies. In this issue of Cell Stem Cell, Young et al. (2015) dissect the function of common non-coding risk haplotypes in the SORL1 locus in the pathogenesis of sporadic Alzheimer's disease using patient-derived induced pluripotent stem cells

Pluripotency and Cellular Reprogramming: Facts, Hypotheses, Unresolved Issues

Direct reprogramming of somatic cells to induced pluripotent stem cells by ectopic expression of defined transcription factors has raised fundamental questions regarding the epigenetic stability of the differentiated cell state. In addition, evidence has accumulated that distinct states of pluripotency can interconvert through the modulation of both cell-intrinsic and exogenous factors. To fully realize the potential of in vitro reprogrammed cells, we need to understand the molecular and epigenetic determinants that convert one cell type into another. Here we review recent advances in this rapidly moving field and emphasize unresolved and controversial questions.Genzyme Corporation (Fellowship)Helen Hay Whitney Foundation (Fellowship)Swiss Federal Institute of Technology Zurich (Society in Science: Branco-Weiss fellowship

Genome Editing in Neurosciences

Innovations in molecular biology are allowing neuroscientists to study the brain with unprecedented resolution, from the level of single molecules to integrated gene circuits. Chief among these innovations is the CRISPR-Cas genome editing technology, which has the precision and scalability to tackle the complexity of the brain. This Colloque Médecine et Recherche has brought together experts from around the world that are applying genome editing to address important challenges in neuroscience, including basic biology in model organisms that has the power to reveal systems-level insight into how the nervous system develops and functions as well as research focused on understanding and treating human neurological disorders

Matched Developmental Timing of Donor Cells with the Host Is Crucial for Chimera Formation

Chimeric mice have been generated by injecting pluripotent stem cells into morula-to-blastocyst stage mouse embryo or by introducing more mature cells into later stage embryos that correspond to the differentiation stage of the donor cells. It has not been rigorously tested, however, whether successful chimera formation requires the developmental stage of host embryo and donor cell to be matched. Here, we compared the success of chimera formation following injection of primary neural crest cells (NCCs) into blastocysts or of embryonic stem cells (ESCs) into E8.5 embryos (heterochronic injection) with that of injecting ESCs cells into the blastocyst or NCCs into the E8.5 embryos (isochronic injection). Chimera formation was efficient when donor and host were matched, but no functional chimeric contribution was found in heterochronic injections. This suggests that matching the developmental stage of donor cells with the host embryo is crucial for functional engraftment of donor cells into the developing embryo. Cohen at al. compares the efficiency of chimera formation in heterochronic and isochronic injections of ESCs and NCCs. Using two distinct and well-characterized pre- and post-implantation chimeric platforms, they show that matching of developmental age of donor cells and the host is essential for chimera formation.National Institutes of Health (U.S.) (Grant R37HD045022)National Institutes of Health (U.S.) (Grant R01-NS088538)National Institutes of Health (U.S.) (Grant R01- MH104610

New Advances in iPS Cell Research Do Not Obviate the Need for Human Embryonic Stem Cells

SummaryRecently three different studies were published demonstrating that mouse fibroblast (skin) cells can be directly reprogrammed to behave like embryonic stem cells (Okita et al., 2007; Wernig et al., 2007; Maherali et al., 2007). These studies advanced a breakthrough announced last year in which a quartet of genes (Oct-3/4, Sox2, c-Myc, and Klf4) were discovered to induce pluripotency in mouse cells, albeit incompletely (Takahashi and Yamanaka, 2006). Now a second generation of these induced pluripotent stem cells (called iPS cells) has been made to do almost everything mouse embryonic stem cells can do. When mouse iPS cells were injected into mouse blastocysts, they contributed to all tissue types in the resulting adult mice, including sperm and oocytes (Okita et al., 2007; Wernig et al., 2007; Maherali et al., 2007). And one research team produced fetal mice derived entirely from iPS cells—a key criterion for embryonic stem cells (Wernig et al., 2007)

A stochastic model dissects cell states in biological transition processes

Many biological processes, including differentiation, reprogramming, and disease transformations, involve transitions of cells through distinct states. Direct, unbiased investigation of cell states and their transitions is challenging due to several factors, including limitations of single-cell assays. Here we present a stochastic model of cellular transitions that allows underlying single-cell information, including cell-state-specific parameters and rates governing transitions between states, to be estimated from genome-wide, population-averaged time-course data. The key novelty of our approach lies in specifying latent stochastic models at the single-cell level, and then aggregating these models to give a likelihood that links parameters at the single-cell level to observables at the population level. We apply our approach in the context of reprogramming to pluripotency. This yields new insights, including profiles of two intermediate cell states, that are supported by independent single-cell studies. Our model provides a general conceptual framework for the study of cell transitions, including epigenetic transformations