S.J Lee

Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture

Genomic stability is critical for the clinical use of human embryonic and induced pluripotent stem cells. We performed high-resolution SNP (single-nucleotide polymorphism) analysis on 186 pluripotent and 119 nonpluripotent samples. We report a higher frequency of subchromosomal copy number variations in pluripotent samples compared to nonpluripotent samples, with variations enriched in specific genomic regions. The distribution of these variations differed between hESCs and hiPSCs, characterized by large numbers of duplications found in a few hESC samples and moderate numbers of deletions distributed across many hiPSC samples. For hiPSCs, the reprogramming process was associated with deletions of tumor-suppressor genes, whereas time in culture was associated with duplications of oncogenic genes. We also observed duplications that arose during a differentiation protocol. Our results illustrate the dynamic nature of genomic abnormalities in pluripotent stem cells and the need for frequent genomic monitoring to assure phenotypic stability and clinical safety.

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives

Human pluripotent stem cells (hPSCs) are potential sources of cells for modeling disease and development, drug discovery, and regenerative medicine. However, it is important to identify factors that may impact the utility of hPSCs for these applications. In an unbiased analysis of 205 hPSC and 130 somatic samples, we identified hPSC-specific epigenetic and transcriptional aberrations in genes subject to X chromosome inactivation (XCI) and genomic imprinting, which were not corrected during directed differentiation. We also found that specific tissue types were distinguished by unique patterns of DNA hypomethylation, which were recapitulated by DNA demethylation during in vitro directed differentiation. Our results suggest that verification of baseline epigenetic status is critical for hPSC-based disease models in which the observed phenotype depends on proper XCI or imprinting and that tissue-specific DNA methylation patterns can be accurately modeled during directed differentiation of hPSCs, even in the presence of variations in XCI or imprinting.

Human Cytomegalovirus Inhibits Tapasin-Dependent Peptide Loading and Optimization of the MHC Class I Peptide Cargo for Immune Evasion

The immune evasion protein US3 of human cytomegalovirus binds to and arrests MHC class I molecules in the endoplasmic reticulum (ER). However, substantial amounts of class I molecules still escape US3-mediated ER retention, suggesting that not all class I alleles are affected equally by US3. Here, we identify tapasin inhibition as the mechanism of MHC retention by US3. US3 directly binds tapasin and inhibits tapasin-dependent peptide loading, thereby preventing the optimization of the peptide repertoire presented by class I molecules. Due to the allelic specificity of tapasin toward class I molecules, US3 affects only class I alleles that are dependent on tapasin for peptide loading and surface expression. Accordingly, tapasin-independent class I alleles selectively escape to the cell surface.

Prohibitin interacts with RNF2 and regulates E2F1 function via dual pathways

Prohibitin, a tumor suppresser protein, plays an important role in the transcriptional regulation of various genes involved in cell-cycle control and proliferation. Recent studies have reported that the growth-suppressive property of the prohibitin protein is exhibited in its physical interaction with E2F family proteins and its subsequent repression of their transcriptional activity. Herein, we report that prohibitin interacts with RING finger protein 2 (RNF2), a member of the PcG (polycomb-group) family of proteins, and that the two proteins regulate the activity of E2F1 via dual pathways: the direct, prohibitin-mediated pathway and the indirect, p16-mediated pathway of E2F1 transcriptional regulation. Co-immunoprecipitation experiments showed that endogenous prohibitin interacts with endogenous RNF2. Interestingly, the expressed amounts of RNF2 and prohibitin were interdependently affected at the post-translational level. Furthermore, the depletion of either endogenous RNF2 or prohibitin using the RNA interference technique increased the level of p16 protein expression, resulting in a decrease in the transcriptional activity of E2F1 via the p16–CDK4–Rb pathway. In addition, chromatin immunoprecipitation assays showed that RNF2 was recruited to E2F1-response promoters along with prohibitin to inhibit the transcriptional activity of E2F1. Cell proliferation was also regulated by the prohibitin–RNF2 interaction. These results suggest that the RNF2–prohibitin complex regulates the activity of E2F1 via dual pathways.

The effects of the physical properties of culture substrates on the growth and differentiation of human embryonic stem cells

The physical factors of cell-culture environment have received little attention despite their anticipated significant role in human embryonic stem cell (hESC) culture optimization. Here we show that hESC culture conditions can be optimized by utilizing polyethylene terephthalate (PET) membranes whose defined pore densities (PDs) determine membrane surface hardness. The PET membranes with 1-4 × 10(6) pores/cm(2) (0.291-0.345 GPa) supported the adherence and survival of hESCs without matrix coating. Furthermore, PET membrane with 4 × 10(6) pores/cm(2) (0.345 GPa) supported optimal hESC self renewal as well as by the increase in cell proliferation. The expression level and activity of Rho-associated kinase (ROCK) were specifically down-regulated in hESCs cultured on the optimal PET membrane. We suggest that PET membranes of a defined PD/hardness provide an excellent culture substrate for the maintenance of uniform and undifferentiated hESCs.

Comparison of mesenchymal-like stem/progenitor cells derived from supernumerary teeth with stem cells from human exfoliated deciduous teeth

AIMS Dental tissue has been the focus of attention as an easily accessible postnatal tissue source of high-quality stem cells. Since the first report on the dental pulp stem cells (DPSCs) from permanent third molar teeth, stem cells from human exfoliated deciduous teeth (SHED) were identified as a population distinct from DPSCs. In this study, we compared DPSCs from supernumerary teeth and SHED in three age- and sex-matched patients. PATIENTS & METHODS Dental samples were obtained from the three patients, who were 6 years old and male, with the parental consent of the three donors, and then isolated cells from dental pulp for comparative analysis between supernumerary DPSCs and SHED. RESULTS Colony-forming unit fibroblast levels and the proliferation rate of supernumerary DPSCs were slightly lower than that of SHED. The expression of cell surface antigens in supernumerary DPSCs and SHED were almost identical. Cells were mainly expressing endogenous mesodermal and ectodermal lineage markers. Differentiation capacity to osteogenic, adipogenic and chondrogenic lineage was similar in the SHED and supernumerary DPSCs. Migration assay revealed that both supernumerary DPSCs and SHED rapidly migrated toward wounded areas. Supernumerary DPSCs were altered in cell growth after storage for 2 years. Specially, the population doubling time of supernumerary DPSCs increased while that of SHED remained nearly unchanged. CONCLUSION Both supernumerary teeth and deciduous teeth share many characteristics, such as highly proliferative clonogenic cells with a similar immunophenotype to that of mesenchymal stem cells, although they are inferior to SHED for long-term banking. Our findings suggest that supernumerary teeth are also easily accessible and noninvasive sources of postnatal stem cells with multipotency and regenerative capacity.

Establishment of stably expandable induced myogenic stem cells by four transcription factors

Life-long regeneration of healthy muscle by cell transplantation is an ideal therapy for patients with degenerative muscle diseases. Yet, obtaining muscle stem cells from patients is very limited due to their exhaustion in disease condition. Thus, development of a method to obtain healthy myogenic stem cells is required. Here, we showed that the four transcription factors, Six1, Eya1, Esrrb, and Pax3, converts fibroblasts into induced myogenic stem cells (iMSCs). The iMSCs showed effective differentiation into multinucleated myotubes and also higher proliferation capacity than muscle derived stem cells both in vitro and in vivo. The iMSCs do not lose their proliferation capacity though the passaging number is increased. We further isolated CD106-negative and α7-integrin-positive iMSCs (sort-iMSCs) showing higher myogenic differentiation capacity than iMSCs. Moreover, genome-wide transcriptomic analysis of iMSCs and sort-iMSCs, followed by network analysis, revealed the genes and signaling pathways associated with enhanced proliferation and differentiation capacity of iMSCs and sort-iMSCs, respectively. The stably expandable iMSCs provide a new source for drug screening and muscle regenerative therapy for muscle wasting disease.

DNA capturing machinery through spore-displayed proteins

Aims:  The purpose of this study was to develop a general method for the facile development of a new DNA biosensor which utilizes streptavidin‐displayed spores as a molecular machinery.