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Mutations in human induced pluripotent stem cells (iPSCs) pose a risk for their clinical use due to preferential reprogramming of mutated founder cell and selection of mutations during maintenance of iPSCs in cell culture. It is unknown,however,if mutations in iPSCs are due to stress associated with oncogene expression during reprogramming. We performed whole exome sequencing of human foreskin fibroblasts and their derived iPSCs at two different passages. We found that in vitro passaging contributed 7% to the iPSC coding point mutation load,and ultradeep amplicon sequencing revealed that 19% of the mutations preexist as rare mutations in the parental fibroblasts suggesting that the remaining 74% of the mutations were acquired during cellular reprogramming. Simulation suggests that the mutation intensity during reprogramming is ninefold higher than the background mutation rate in culture. Thus the factor induced reprogramming stress contributes to a significant proportion of the mutation load of iPSCs. View Publication

Recent reports link Kaposi sarcoma-associated herpesvirus (KSHV) infection of bone marrow cells to bone marrow failure and lymphoproliferative syndromes. The identity of the infected marrow cells,however,remains unclear. Other work has demonstrated that circulating mononuclear cells can harbor KSHV where its detection predicts the onset and severity of Kaposi sarcoma. In either setting,bone marrow precursors may serve as viral reservoirs. Since mesenchymal stem cells (MSCs) in human bone marrow regulate the differentiation and proliferation of adjacent hematopoietic precursors,we investigated their potential role in KSHV infection. Our results indicate that primary MSCs are susceptible to both cell-free and cell-associated KSHV in culture. Moreover,infection persisted within nearly half of the cells for up to 6 weeks. Thus,MSCs possess a clear capacity to support KSHV infection and warrant further exploration into their potential role in KSHV-related human disease. View Publication

Current sources of mesenchymal cells,including bone marrow,fat and muscle,all require invasive procurement procedures,and provide relatively low frequencies of progenitors. Here,we describe the non-invasive isolation,and characterization,of a rich source of mesenchymal progenitor cells,which we call human umbilical cord perivascular cells (HUCPVCs). HUCPVCs show a similar immunological phenotype to bone marrow-derived mesenchymal stromal cells (BM-MSCs),since they are non-alloreactive,exhibit immunosuppression,and significantly reduce lymphocyte activation,in vitro. They present a non-hematopoietic myofibroblastic mesenchymal phenotype (CD45-,CD34-,CD105+,CD73+,CD90+,CD44+,CD106+,3G5+,CD146+); with a 1:300 frequency at harvest,a short-doubling time,and a clonogenic frequency of textgreater1:3 in culture. Furthermore,in addition to robust quinti-potential differentiation capacity in vitro,HUCPVCs have been shown to contribute to both musculo-skeletal and dermal wound healing in vivo. View Publication

The use of induced pluripotent stem cells (iPSCs) is an exciting frontier in the study and treatment of human diseases through the generation of specific cell types. Here we show the derivation of iPSCs from human nonmobilized peripheral blood (PB) and bone marrow (BM) mononuclear cells (MNCs) by retroviral transduction of OCT3/4,SOX2,KLF4,and c-MYC. The PB- and BM-derived iPSCs were quite similar to human embryonic stem cells with regard to morphology,expression of surface antigens and pluripotency-associated transcription factors,global gene expression profiles,and differentiation potential in vitro and in vivo. Infected PB and BM MNCs gave rise to iPSCs in the presence of several cytokines,although transduction efficiencies were not high. We found that 5 × 10(5) PB MNCs,which corresponds to less than 1 mL of PB,was enough for the generation of several iPSC colonies. Generation of iPSCs from MNCs of nonmobilized PB,with its relative efficiency and ease of harvesting,could enable the therapeutic use of patient-specific pluripotent stem cells. View Publication

Ring chromosomes are structural aberrations commonly associated with birth defects,mental disabilities and growth retardation. Rings form after fusion of the long and short arms of a chromosome,and are sometimes associated with large terminal deletions. Owing to the severity of these large aberrations that can affect multiple contiguous genes,no possible therapeutic strategies for ring chromosome disorders have been proposed. During cell division,ring chromosomes can exhibit unstable behaviour leading to continuous production of aneuploid progeny with low viability and high cellular death rate. The overall consequences of this chromosomal instability have been largely unexplored in experimental model systems. Here we generated human induced pluripotent stem cells (iPSCs) from patient fibroblasts containing ring chromosomes with large deletions and found that reprogrammed cells lost the abnormal chromosome and duplicated the wild-type homologue through the compensatory uniparental disomy (UPD) mechanism. The karyotypically normal iPSCs with isodisomy for the corrected chromosome outgrew co-existing aneuploid populations,enabling rapid and efficient isolation of patient-derived iPSCs devoid of the original chromosomal aberration. Our results suggest a fundamentally different function for cellular reprogramming as a means of /`chromosome therapy/' to reverse combined loss-of-function across many genes in cells with large-scale aberrations involving ring structures. In addition,our work provides an experimentally tractable human cellular system for studying mechanisms of chromosomal number control,which is of critical relevance to human development and disease. View Publication

Therapeutic and industrial applications of pluripotent stem cells and their derivatives require large cell quantities generated in defined conditions. To this end,we have translated single cell-inoculated suspension cultures of human pluripotent stem cells (hPSCs; including human induced pluripotent stem cells [hiPS] and human embryonic stem cells [hESC]) to stirred tank bioreactors. These systems that are widely used in biopharmaceutical industry allow straightforward scale up and detailed online monitoring of key process parameters. To ensure minimum medium consumption,but in parallel functional integration of all probes mandatory for process monitoring,that is,for pO₂ and pH,experiments were performed in 100 mL culture volume in a mini reactor platform" consisting of four independently controlled vessels. By establishing defined parameters for tightly controlled cell inoculation and aggregate formation up to 2×10�?� hiPSCs/100 mL were generated in a single process run in 7 days. Expression of pluripotency markers and ability of cells to differentiate into derivates of all three germ layers in vitro was maintained� View Publication

PURPOSE This study aimed to develop a feasible and efficient method for generating embryonic stem cell (ESC)-like induced pluripotent stem (iPS) cells from human Tenon's capsule fibroblasts (HTFs) through the expression of a defined set of transcription factors,which will have significant application value for ophthalmic personalized regenerative medicine. METHODS HTFs were harvested from fresh samples,and reprogramming was induced by the exogenous expression of the four classic transcription factors,OCT-3/4,SOX-2,KLF-4,and C-MYC. The HTF-derived iPS (TiPS) cells were analyzed with phase contrast microscopy,real-time PCR,immunofluorescence,FACS analysis,alkaline phosphatase activity analysis,and a teratoma formation assay. Human ESC colonies were used as the positive control. RESULTS The resulting HTF-derived iPS cell colonies were indistinguishable from human ESC colonies regarding morphology,gene expression levels,pluripotent gene expression,alkaline phosphatase activity,and the ability to generate all three embryonic germ layers. CONCLUSIONS This study presents a simple,efficient,practical procedure for generating patient-tailored iPS cells from HTFs. These cells will serve as a valuable and preferred candidate donor cell population for ophthalmological regenerative medicine. View Publication

textlessptextgreater Induced pluripotent stem cells (iPSC) are a most promising approach to the development of a hepatocyte transplantable mass sufficient to induce long-term correction of inherited liver metabolic diseases,thus avoiding liver transplantation. Their intrinsic self-renewal ability and potential to differentiate into any of the three germ layers identify iPSC as the most promising cell-based therapeutics,but also as drivers of tumor development. Teratoma development currently represents the gold standard to assess iPSC pluripotency. We analyzed the tumorigenic potential of iPSC generated from human hepatocytes (HEP-iPSC) and compared their immunohistochemical profiles to that of tumors developed from fibroblast and hematopoietic stem cell-derived iPSC. HEP-iPSC generated tumors significantly presented more malignant morphological features than reprogrammed fibroblasts or CD34+ iPSC. Moreover,the protooncogene textlessitalictextgreatermyctextless/italictextgreater showed the strongest expression in HEP-iPSC,compared to only faint expression in the other cell subsets. Random integration of transgenes and the use of potent protooncogenes such as textlessitalictextgreatermyctextless/italictextgreater might be a risk factor for malignant tumor development if hepatocytes are used for reprogramming. Nonviral vector delivery systems or reprogramming of cells obtained from less invasive harvesting methods would represent interesting options for future developments in stem cell-based approaches for liver metabolic diseases. textless/ptextgreater View Publication

BACKGROUND The Activin A and bone morphogenetic protein (BMP) pathways are critical regulators of the immune system and of bone formation. Inappropriate activation of these pathways,as in conditions of congenital heterotopic ossification,are thought to activate an osteogenic program in endothelial cells. However,if and how this occurs in human endothelial cells remains unclear. METHODS We used a new directed differentiation protocol to create human induced pluripotent stem cell (hiPSC)-derived endothelial cells (iECs) from patients with fibrodysplasia ossificans progressiva (FOP),a congenital disease of heterotopic ossification caused by an activating R206H mutation in the Activin A type I receptor (ACVR1). This strategy allowed the direct assay of the cell-autonomous effects of ACVR1 R206H in the endogenous locus without the use of transgenic expression. These cells were challenged with BMP or Activin A ligand,and tested for their ability to activate osteogenesis,extracellular matrix production,and differential downstream signaling in the BMP/Activin A pathways. RESULTS We found that FOP iECs could form in conditions with low or absent BMP4. These conditions are not normally permissive in control cells. FOP iECs cultured in mineralization media showed increased alkaline phosphatase staining,suggesting formation of immature osteoblasts,but failed to show mature osteoblastic features. However,FOP iECs expressed more fibroblastic genes and Collagen 1/2 compared to control iECs,suggesting a mechanism for the tissue fibrosis seen in early heterotopic lesions. Finally,FOP iECs showed increased SMAD1/5/8 signaling upon BMP4 stimulation. Contrary to FOP hiPSCs,FOP iECs did not show a significant increase in SMAD1/5/8 phosphorylation upon Activin A stimulation,suggesting that the ACVR1 R206H mutation has a cell type-specific effect. In addition,we found that the expression of ACVR1 and type II receptors were different in hiPSCs and iECs,which could explain the cell type-specific SMAD signaling. CONCLUSIONS Our results suggest that the ACVR1 R206H mutation may not directly increase the formation of mature chondrogenic or osteogenic cells by FOP iECs. Our results also show that BMP can induce endothelial cell dysfunction,increase expression of fibrogenic matrix proteins,and cause differential downstream signaling of the ACVR1 R206H mutation. This iPSC model provides new insight into how human endothelial cells may contribute to the pathogenesis of heterotopic ossification. View Publication

We demonstrate a highly efficient method for gene delivery into clinically relevant human cell types,such as induced pluripotent stem cells (iPSCs) and fibroblasts,reducing the protocol time by one full day. To preserve cell physiology during gene transfer,we designed a microfluidic strategy,which facilitates significant gene delivery in a short transfection time (textless1 min) for several human cell types. This fast,optimized and generally applicable cell transfection method can be used for rapid screening of different delivery systems and has significant potential for high-throughput cell therapy applications. View Publication

Since their derivation 11 years ago,human embryonic stem (hES) cells have become a powerful tool in both basic biomedical research and developmental biology. Their capacity for self-renewal and differentiation into any tissue type has also brought interest from fields such as cell therapy and drug screening. We conducted an extensive analysis of 750 papers (51% of the total published about hES cells between 1998 and 2008) to present a spectrum of hES cell research including culture protocols developed worldwide. This review may stimulate discussions about the importance of having unvarying methods to culture hES cells,in order to facilitate comparisons among data obtained by research groups elsewhere,especially concerning preclinical studies. Moreover,the description of the most widely used cell lines,reagents,and procedures adopted internationally will help newcomers on deciding the best strategies for starting their own studies. Finally,the results will contribute with the efforts of stem cell researchers on comparing the performance of different aspects related to hES cell culture methods. View Publication

BACKGROUND: Human pluripotent stem cells have the ability to generate all cell types present in the adult organism,therefore harboring great potential for the in vitro study of differentiation and for the development of cell-based therapies. Nonetheless their use may prove challenging as incomplete differentiation of these cells might lead to tumoregenicity. Interestingly,many cancer types have been reported to display metabolic modifications with features that might be similar to stem cells. Understanding the metabolic properties of human pluripotent stem cells when compared to their differentiated counterparts can thus be of crucial importance. Furthermore recent data has stressed distinct features of different human pluripotent cells lines,namely when comparing embryo-derived human embryonic stem cells (hESCs) and induced pluripotent stem cells (IPSCs) reprogrammed from somatic cells.backslashnbackslashnMETHODOLOGY/PRINCIPAL FINDINGS: We compared the energy metabolism of hESCs,IPSCs,and their somatic counterparts. Focusing on mitochondria,we tracked organelle localization and morphology. Furthermore we performed gene expression analysis of several pathways related to the glucose metabolism,including glycolysis,the pentose phosphate pathway and the tricarboxylic acid (TCA) cycle. In addition we determined oxygen consumption rates (OCR) using a metabolic extracellular flux analyzer,as well as total intracellular ATP levels by high performance liquid chromatography (HPLC). Finally we explored the expression of key proteins involved in the regulation of glucose metabolism.backslashnbackslashnCONCLUSIONS/FINDINGS: Our results demonstrate that,although the metabolic signature of IPSCs is not identical to that of hESCs,nonetheless they cluster with hESCs rather than with their somatic counterparts. ATP levels,lactate production and OCR revealed that human pluripotent cells rely mostly on glycolysis to meet their energy demands. Furthermore,our work points to some of the strategies which human pluripotent stem cells may use to maintain high glycolytic rates,such as high levels of hexokinase II and inactive pyruvate dehydrogenase (PDH). View Publication