Induced pluripotent stem cells and human disease

Taming Human Genetic Variability: Transcriptomic Meta-Analysis Guides the Experimental Design and Interpretation of iPSC-Based Disease Modeling

Both the promises and pitfalls of the cell reprogramming research platform rest on human genetic variation, making the measurement of its impact one of the most urgent issues in the field. Harnessing large transcriptomics datasets of induced pluripotent stem cells (iPSC), we investigate the implications of this variability for iPSC-based disease modeling. In particular, we show that the widespread use of more than one clone per individual in combination with current analytical practices is detrimental to the robustness of the findings. We then proceed to identify methods to address this challenge and leverage multiple clones per individual. Finally, we evaluate the specificity and sensitivity of different sample sizes and experimental designs, presenting computational tools for power analysis. These findings and tools reframe the nature of replicates used in disease modeling and provide important resources for the design, analysis, and interpretation of iPSC-based studies.

Application of biomaterials to in vitro pluripotent stem cell disease modeling of the skeletal system

Disease-specific pluripotent stem cells can be derived through genetic manipulation of embryonic stem cells or by reprogramming somatic cells (induced pluripotent stem cells).

Human induced pluripotent stem cells as a tool to model a form of Leber congenital amaurosis

Our purpose was to investigate genes and molecular mechanisms involved in patients with Leber congenital amaurosis (LCA) and to model this type of LCA for drug screening. Fibroblasts from two unrelated clinically identified patients with a yet undetermined gene mutation were reprogrammed to pluripotency by retroviral transduction. These human induced pluripotent stem cells (hiPSCs) were differentiated into neural stem cells (NSCs) that mimicked the neural tube stage and retinal pigmented epithelial (RPE) cells that could be targeted by the disease. A genome-wide transcriptome analysis was performed with Affymetrix Exon Array GeneChip(®), comparing LCA-hiPSCs derivatives to controls. A genomic search for alteration in all genes known to be involved in LCA revealed a common polymorphism on the GUCY2D gene, referenced as the LCA type I (OMIM *600179 and #204000), but the causative gene remained unknown. The hiPSCs expressed the key pluripotency factors and formed embryoid bodies in vitro containing cells originating from all three germ layers. They were successfully differentiated into NSC and RPE cells. One gene, NNAT, was upregulated in LCA cell populations, and three genes were downregulated, GSTT1, TRIM61 and ZNF558, with potential correlates for molecular mechanisms of this type of LCA, in particular for protein degradation and oxidative stress. The two LCA patient-specific iPSC lines will contribute to modeling LCA phenotypes and screening candidate drugs.

Bioreactor engineering of stem cell environments

Stem cells hold promise to revolutionize modern medicine by the development of new therapies, disease models and drug screening systems. Standard cell culture systems have limited biological relevance because they do not recapitulate the complex 3-dimensional interactions and biophysical cues that characterize the in vivo environment. In this review, we discuss the current advances in engineering stem cell environments using novel biomaterials and bioreactor technologies. We also reflect on the challenges the field is currently facing with regard to the translation of stem cell based therapies into the clinic.

Human-induced pluripotent stem cells: in quest of clinical applications

In the field of regenerative medicine, the development of induced pluripotent stem (iPS) cells may represent a potential strategy to overcome the limitations of human embryonic stem cells (ESCs). iPS cells have the potential to mimic human disease, since they carry the genome of the donor. Hypothetically, with iPS cell technology it is possible to screen patients for a genetic cause of disease (genetic mutation), develop cell lines, reprogram them back to iPS cells, finally differentiate them into one or more cell types that develop the disease. Although the creation of multiple lineages with iPS cells can seem limitless, a number of challenges need to be addressed in order to effectively use these cell lines for disease modeling. These include the low efficiency of iPS cell generation without genetic alterations, the possibility of tumor formation in vivo, the random integration of retroviral-based delivery vectors into the genome, and unregulated growth of the remaining cells that are partially reprogrammed and refractory to differentiation. The establishment of protein or RNA-based reprogramming strategies will help generate human iPS cells without permanent genetic alterations. Finally, direct reprogramming strategies can provide rapid production of models of human "diseases in a dish", without first passing the cells through a pluripotent state, so avoiding the challenges of time-consumming and labor-intensive iPS cell line generation. This review will overview methods to develop iPS cells, current strategies for direct reprogramming, and main applications of iPS cells as human disease model, focusing on human cardiovascular diseases, with the aim to be a potential information resource for biomedical scientists and clinicians who exploit or intend to exploit iPS cell technology in a range of applications.

Suicide gene-mediated ablation of tumor-initiating mouse pluripotent stem cells

Pluripotent stem cells, including embryonic stem (ES) and induced pluripotent stem (iPS) cells, serve as unlimited resources for cell replacement therapy and tissue engineering because such cells are capable of extensive proliferation in vitro and can give rise to lineages that represent any of the three embryonic germ layers. However, in the context of the in vivo behavior of cell transplants, key challenges need to be addressed and essential strategies should be developed before stem cells can be used in clinical practice. In the present study, we modified mouse ES/iPS cells to contain a suicide gene, deltaTK or CodA, under the transcriptional control of the EF1α or Nanog promoter. The suicide gene was introduced via lentivirus transduction without interfering with their self-renewal and pluripotency characteristics. We found that EF1α promoter-controlled deltaTK/CodA expression efficiently eliminated pluripotent stem cells and their derivatives both in vitro and in vivo. When the suicide gene was under the control of the Nanog promoter, tumor-initiating undifferentiated pluripotent stem cells were selectively ablated in vitro after prodrug treatment. These results indicate that modification of pluripotent stem cells with a suicide gene prior to transplantation offers a safe manner by which wayward stem cells, and their progeny, can be controlled in vivo. Our approach will render the clinical application of human pluripotent stem cells increasingly possible.

Derivation of human embryonic stem cell lines after blastocyst microsurgery

Embryonic stem cells (ESCs) are derived from the inner cell mass (ICM) of the blastocyst. Because of their ability to differentiate into a variety of cell types, human embryonic stem cells (hESCs) provide an unlimited source of cells for clinical medicine and have begun to be used in clinical trials. Presently, although several hundred hESC lines are available in the word, only few have been widely used in basic and applied research. More and more hESC lines with differing genetic backgrounds are required for establishing a bank of hESCs. Here, we report the first Canadian hESC lines to be generated from cryopreserved embryos and we discuss how we navigated through the Canadian regulatory process. The cryopreserved human zygotes used in this study were cultured to the blastocyst stage, and used to isolate ICM via microsurgery. Unlike previous microsurgery methods, which use specialized glass or steel needles, our method conveniently uses syringe needles for the isolation of ICM and subsequent hESC lines. ICM were cultured on MEF feeders in medium containing FBS or serum replacer (SR). Resulting outgrowths were isolated, cut into several cell clumps, and transferred onto fresh feeders. After more than 30 passages, the two hESC lines established using this method exhibited normal morphology, karyotype, and growth rate. Moreover, they stained positively for a variety of pluripotency markers and could be differentiated both in vitro and in vivo. Both cell lines could be maintained under a variety of culture conditions, including xeno-free conditions we have previously described. We suggest that this microsurgical approach may be conducive to deriving xeno-free hESC lines when outgrown on xeno-free human foreskin fibroblast feeders.

Perspectives on human stem cell research

Human stem cell research draws not only scientists' but the public's attention. Human stem cell research is considered to be able to identify the mechanism of human development and change the paradigm of medical practices. However, there are heated ethical and legal debates about human stem cell research. The core issue is that of human dignity and human life. Some prefer human adult stem cell research or iPS cell research, others hES cell research. We do not need to exclude any type of stem cell research because each has its own merits and issues, and they can facilitate the scientific revolution when working together.