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1.  From Stealing Fire to Cellular Reprogramming: A Scientific History Leading to the 2012 Nobel Prize 
Stem Cell Reports  2013;1(1):5-17.
Cellular reprogramming was recently “crowned” with the award of the Nobel Prize to two of its groundbreaking researchers, Sir John Gurdon and Shinya Yamanaka. The recent link between reprogramming and stem cells makes this appear almost a new field of research, but its historical roots have actually spanned more than a century. Here, the Nobel Prize in Physiology or Medicine 2012 is placed in its historical context.
doi:10.1016/j.stemcr.2013.05.001
PMCID: PMC3757737  PMID: 24052937
2.  Genome editing of human pluripotent stem cells to generate human cellular disease models 
Disease Models & Mechanisms  2013;6(4):896-904.
Disease modeling with human pluripotent stem cells has come into the public spotlight with the awarding of the Nobel Prize in Physiology or Medicine for 2012 to Drs John Gurdon and Shinya Yamanaka for the discovery that mature cells can be reprogrammed to become pluripotent. This discovery has opened the door for the generation of pluripotent stem cells from individuals with disease and the differentiation of these cells into somatic cell types for the study of disease pathophysiology. The emergence of genome-editing technology over the past few years has made it feasible to generate and investigate human cellular disease models with even greater speed and efficiency. Here, recent technological advances in genome editing, and its utility in human biology and disease studies, are reviewed.
doi:10.1242/dmm.012054
PMCID: PMC3701209  PMID: 23751357
3.  Cell transplantation therapies for spinal cord injury focusing on induced pluripotent stem cells 
Cell Research  2012;23(1):70-80.
Stimulated by the 2012 Nobel Prize in Physiology or Medicine awarded for Shinya Yamanaka and Sir John Gurdon, there is an increasing interest in the induced pluripotent stem (iPS) cells and reprograming technologies in medical science. While iPS cells are expected to open a new era providing enormous opportunities in biomedical sciences in terms of cell therapies and regenerative medicine, safety-related concerns for iPS cell-based cell therapy should be resolved prior to the clinical application of iPS cells. In this review, the pre-clinical investigations of cell therapy for spinal cord injury (SCI) using neural stem/progenitor cells derived from iPS cells, and their safety issues in vivo, are outlined. We also wish to discuss the strategy for the first human trails of iPS cell-based cell therapy for SCI patients.
doi:10.1038/cr.2012.171
PMCID: PMC3541652  PMID: 23229514
neural stem/progenitor cell; induced pluripotnet stem cell; spinal cord injury; transplantation
4.  Brain H2A.Z: the long and the short 
BMC Biology  2013;11:84.
The role of histone variants and their specific post-translational modifications (PTMs) in the epigenetic regulation of gene expression is still poorly understood. A paper published by Simonet and colleagues in Epigenetics and Chromatin describes a new H2A.Z subtype that is specific for brain and pituitary in the carp and provides additional information about the functional epigenetic complexity of the PTMs associated with histone H2A.Z.
See research article: http://www.epigeneticsandchromatin.com/content/6/1/22
doi:10.1186/1741-7007-11-84
PMCID: PMC3716961  PMID: 23866047
5.  Identifying Candidate Oocyte Reprogramming Factors Using Cross-Species Global Transcriptional Analysis 
Cellular Reprogramming  2013;15(2):126-133.
Abstract
There is mounting evidence to suggest that the epigenetic reprogramming capacity of the oocyte is superior to that of the current factor-based reprogramming approaches and that some factor-reprogrammed induced pluripotent stem cells (iPSCs) retain a degree of epigenetic memory that can influence differentiation capacity and may be linked to the observed expression of immunogenicity genes in iPSC derivatives. One hypothesis for this differential reprogramming capacity is the “chromatin loosening/enhanced reprogramming” concept, as previously described by John Gurdon and Ian Wilmut, as well as others, which postulates that the oocyte possesses factors that loosen the somatic cell chromatin structure, providing the epigenetic and transcriptional regulatory factors more ready access to repressed genes and thereby significantly increasing epigenetic reprogramming. However, to empirically test this hypothesis a list of candidate oocyte reprogramming factors (CORFs) must be ascertained that are significantly expressed in metaphase II oocytes. Previous studies have focused on intraspecies or cross-species transcriptional analysis of up to two different species of oocytes. In this study, we have identified eight CORFs (ARID2, ASF1A, ASF1B, DPPA3, ING3, MSL3, H1FOO, and KDM6B) based on unbiased global transcriptional analysis of oocytes from three different species (human, rhesus monkey, and mouse) that both demonstrate significant (p<0.05, FC>3) expression in oocytes of all three species and have well-established roles in loosening/opening up chromatin structure. We also identified an additional 15 CORFs that fit within our proposed “chromatin opening/fate transformative” (COFT) model. These CORFs may be able to augment Shinya Yamanaka's previously identified reprogramming factors (OCT4, SOX2, KLF4, and cMYC) and potentially facilitate the removal of epigenetic memory in iPSCs and/or reduce the expression of immunogenicity genes in iPSC derivatives, and may have applications in future personalized pluripotent stem cell based therapeutics.
doi:10.1089/cell.2012.0060
PMCID: PMC3616412  PMID: 23458164
6.  Histone variant macroH2A confers resistance to nuclear reprogramming 
The EMBO Journal  2011;30(12):2373-2387.
Histone variant macroH2A confers resistance to nuclear reprogramming
Gurdon and collaborators report reversible X chromosome inactivation in epiblast stem cells (EpiSCs) that seems to be determined by macroH2A1 deposition. These findings are of rather general interest as they highlight the epigenetic state of repressed loci as determinant for reprogramming efficiency.
How various layers of epigenetic repression restrict somatic cell nuclear reprogramming is poorly understood. The transfer of mammalian somatic cell nuclei into Xenopus oocytes induces transcriptional reprogramming of previously repressed genes. Here, we address the mechanisms that restrict reprogramming following nuclear transfer by assessing the stability of the inactive X chromosome (Xi) in different stages of inactivation. We find that the Xi of mouse post-implantation-derived epiblast stem cells (EpiSCs) can be reversed by nuclear transfer, while the Xi of differentiated or extraembryonic cells is irreversible by nuclear transfer to oocytes. After nuclear transfer, Xist RNA is lost from chromatin of the Xi. Most epigenetic marks such as DNA methylation and Polycomb-deposited H3K27me3 do not explain the differences between reversible and irreversible Xi. Resistance to reprogramming is associated with incorporation of the histone variant macroH2A, which is retained on the Xi of differentiated cells, but absent from the Xi of EpiSCs. Our results uncover the decreased stability of the Xi in EpiSCs, and highlight the importance of combinatorial epigenetic repression involving macroH2A in restricting transcriptional reprogramming by oocytes.
doi:10.1038/emboj.2011.144
PMCID: PMC3116279  PMID: 21552206
epiblast stem cells; inactive X chromosome; macroH2A; nuclear reprogramming; Xenopus oocytes
7.  Epigenetic factors influencing resistance to nuclear reprogramming 
Trends in genetics : TIG  2011;27(12):10.1016/j.tig.2011.08.002.
Patient-specific somatic cell reprogramming is likely to have a large impact on medicine by providing a source of cells for disease modelling and regenerative medicine. Several strategies can be used to reprogram cells yet they are generally characterised by a low reprogramming efficiency, reflecting the remarkable stability of the differentiated state. Transcription factors, chromatin modifications, and non-coding RNAs can increase the efficiency of reprogramming. However, the success of nuclear reprogramming is limited by epigenetic mechanisms that stabilise the state of gene expression in somatic cells and thereby resist efficient reprogramming. We review here the factors that influence reprogramming efficiency, and especially those that restrict the natural reprogramming mechanisms of eggs and oocytes. We see this as a step towards understanding the mechanisms by which nuclear reprogramming takes place.
doi:10.1016/j.tig.2011.08.002
PMCID: PMC3814186  PMID: 21940062
efficiency of nuclear reprogramming; resistance to nuclear reprogramming; epigenetic reprogramming; nuclear transfer; cell fusion; induced pluripotency
8.  Excellence in cell signaling research recognized with major new award 
The newly installed Life Sciences Breakthrough Prize (http://www.breakthroughprizeinlifesciences.org/), which comes with more than double the financial reward of the Nobel Prize, has been awarded to several world-leaders in the field of cancer-related cell signaling and therapy research: Lewis C. Cantley (PI3 kinase), Hans Clevers (Wnt signaling), Charles L. Sawyers (signaling-targeted cancer therapy), Bert Vogelstein (colorectal cancer signaling) and Robert Weinberg (Ras & other cancer-relevant genes). They have all made remarkable contributions to our understanding of cell communication and malignancies over the last decades. Needless to say that virtually all other awardees of the 11 scientists honored in 2013 have also, in one way or another, touched upon signaling molecules, highlighting the fundamental interdisciplinarity and significance of signal transduction for living cells in general. For example, Shinya Yamanaka’s exciting work was built on the four transcriptional signaling proteins, Oct3/4, Sox2, Klf4 and c-Myc.
doi:10.1186/1478-811X-11-17
PMCID: PMC3599230  PMID: 23497077
9.  IFPA Senior Award Lecture: Reproductive immunology in perspective – reprogramming at the maternal-fetal interface 
Placenta  2013;34(0):S52-S55.
Involvement of the maternal and fetal immune systems in the events of pregnancy was generally overlooked by reproductive biologists until the mid-twentieth century when many landmark explorations were reported. Now, more than half a century later, it is well understood that with the initiation of pregnancy, immune cells in mammalian uteri are reprogrammed, losing their cytotoxic potential and providing an immunosuppressive environment suitable for harboring the genetically different fetus. We propose that it is the placenta that is mainly responsible for this conversion and maintenance throughout pregnancy. Studies in our laboratory indicate that trophoblast-derived soluble HLA-G has a subtle but well defined role in programming uterine placental macrophages, a potentially destructive immune cell population. Thus, placental HLA-G plays a critical role in assuring that the developing fetus emerges unscathed at parturition.
doi:10.1016/j.placenta.2012.12.005
PMCID: PMC3700590  PMID: 23294570
Placenta; Trophoblast; Macrophage; HLA-G
10.  Nuclear reprogramming in cell-free extracts. 
Methods for directly turning a somatic cell type into another type (a process referred to as transdifferentiation) would be beneficial for producing replacement cells for therapeutic applications. Adult stem cells have been shown to display a broader differentiation potential than anticipated and may contribute to tissues other than those in which they reside. In addition, novel transdifferentiation strategies are being developed. I report recent results on the functional reprogramming of a somatic cell using a nuclear and cytoplasmic extract derived from another somatic cell type. The reprogramming of 293T fibroblasts in an extract from T cells is evidenced by nuclear uptake and the assembly of transcription factors, induction of activity of a chromatin remodelling complex, changes in chromatin composition and activation of lymphoid cell-specific genes. The reprogrammed cells express T-cell-specific surface molecules and a complex regulatory function. Reprogramming cells in cell-free extracts may create possibilities for producing replacement cells for therapeutic applications. The system may also constitute a powerful tool to examine the mechanisms of nuclear reprogramming, at least as they occur in vitro.
doi:10.1098/rstb.2003.1334
PMCID: PMC1693229  PMID: 14511486
11.  The John Insall Award: Gender-specific Total Knee Replacement: Prospectively Collected Clinical Outcomes 
Gender-specific total knee replacement design is a recent and debated topic. We determined the survivorship and clinical outcomes of a large primary total knee arthroplasty cohort, specifically assessing any differences between gender groups. A consecutive cohort of 3817 patients with 5279 primary total knee replacements (3100 female, 2179 male) with a minimum of 2 years followup were evaluated. Preoperative, latest, and change in clinical outcome scores (WOMAC, SF-12, KSCRS) were compared. While men had higher raw scores preoperatively, women had greater improvement in all WOMAC domains including pain (29.87 versus 27.3), joint stiffness (26.78 versus 24.26), function (27.21 versus 23.09), and total scores (28.35 versus 25.09). There were no gender differences in improvements of the SF-12 physical scores. Men had greater improvement in Knee Society function (22.1 versus 18.63) and total scores (70.01 versus 65.42), but not the Knee Society knee score (47.83 versus 46.64). Revision rates were 10.2% for men and 8% for women. Women demonstrated greater implant survivorship, greater improvement in WOMAC scores, equal improvements in SF-12 scores, and less improvement in only the Knee Society function and total scores. The data refute the hypothesis of inferior clinical outcome for women following total knee arthroplasty when using standard components.
Level of Evidence: Level II, prognostic study. See the Guidelines for Authors for a complete description of levels of evidence.
doi:10.1007/s11999-008-0430-1
PMCID: PMC2565048  PMID: 18800216
12.  Reprogramming to pluripotency: stepwise resetting of the epigenetic landscape 
Cell Research  2011;21(3):486-501.
In 2006, the “wall came down” that limited the experimental conversion of differentiated cells into the pluripotent state. In a landmark report, Shinya Yamanaka's group described that a handful of transcription factors (Oct4, Sox2, Klf4 and c-Myc) can convert a differentiated cell back to pluripotency over the course of a few weeks, thus reprograming them into induced pluripotent stem (iPS) cells. The birth of iPS cells started off a rush among researchers to increase the efficiency of the reprogramming process, to reveal the underlying mechanistic events, and allowed the generation of patient- and disease-specific human iPS cells, which have the potential to be converted into relevant specialized cell types for replacement therapies and disease modeling. This review addresses the steps involved in resetting the epigenetic landscape during reprogramming. Apparently, defined events occur during the course of the reprogramming process. Immediately, upon expression of the reprogramming factors, some cells start to divide faster and quickly begin to lose their differentiated cell characteristics with robust downregulation of somatic genes. Only a subset of cells continue to upregulate the embryonic expression program, and finally, pluripotency genes are upregulated establishing an embryonic stem cell-like transcriptome and epigenome with pluripotent capabilities. Understanding reprogramming to pluripotency will inform mechanistic studies of lineage switching, in which differentiated cells from one lineage can be directly reprogrammed into another without going through a pluripotent intermediate.
doi:10.1038/cr.2011.28
PMCID: PMC3193418  PMID: 21321600
reprogramming; pluripotency; epigenetic
14.  Zscan4 promotes genomic stability during reprogramming and dramatically improves the quality of iPS cells as demonstrated by tetraploid complementation 
Cell Research  2012;23(1):92-106.
Induced pluripotent stem (iPS) cells generated using Yamanaka factors have great potential for use in autologous cell therapy. However, genomic abnormalities exist in human iPS cells, and most mouse iPS cells are not fully pluripotent, as evaluated by the tetraploid complementation assay (TCA); this is most likely associated with the DNA damage response (DDR) occurred in early reprogramming induced by Yamanaka factors. In contrast, nuclear transfer can faithfully reprogram somatic cells into embryonic stem (ES) cells that satisfy the TCA. We thus hypothesized that factors involved in oocyte-induced reprogramming may stabilize the somatic genome during reprogramming, and improve the quality of the resultant iPS cells. To test this hypothesis, we screened for factors that could decrease DDR signals during iPS cell induction. We determined that Zscan4, in combination with the Yamanaka factors, not only remarkably reduced the DDR but also markedly promoted the efficiency of iPS cell generation. The inclusion of Zscan4 stabilized the genomic DNA, resulting in p53 downregulation. Furthermore, Zscan4 also enhanced telomere lengthening as early as 3 days post-infection through a telomere recombination-based mechanism. As a result, iPS cells generated with addition of Zscan4 exhibited longer telomeres than classical iPS cells. Strikingly, more than 50% of iPS cell lines (11/19) produced via this “Zscan4 protocol” gave rise to live-borne all-iPS cell mice as determined by TCA, compared to 1/12 for lines produced using the classical Yamanaka factors. Our findings provide the first demonstration that maintaining genomic stability during reprogramming promotes the generation of high quality iPS cells.
doi:10.1038/cr.2012.157
PMCID: PMC3541664  PMID: 23147797
somatic reprogramming; genomic stability; telomere; Zscan4; tetraploid complementation; iPS cells
15.  Sirtuin 1 Facilitates Generation of Induced Pluripotent Stem Cells from Mouse Embryonic Fibroblasts through the miR-34a and p53 Pathways 
PLoS ONE  2012;7(9):e45633.
Forced-expression of transcription factors can reprogram somatic cells into induced pluripotent stem cells (iPSC). Recent studies show that the reprogramming efficiency can be improved by inclusion of small molecules that regulate chromatin modifying enzymes. We report here that sirtuin 1 (SIRT1), a member of the sirtuin family of NAD+-dependent protein deacetylases, is involved in iPSC formation. By using an efficient mouse secondary fibroblast reprogramming system with doxycycline (DOX) inducible Yamanaka’s transcription factors delivered by piggyBac (PB) transposition (2°F/1B MEF), we show that SIRT1 knockdown decreased while resveratrol (RSV) increased the efficiency of iPSC formation. The treatments were associated with altered acetylated p53 and its downstream Nanog but not p21 expression. The stimulatory effect was also confirmed by SIRT1 over-expression, which stimulated the formation of colonies with induced Nanog and reduced p21 expression. Furthermore, the effects of RSV and SIRT1 knockdown on reprogramming were most pronounced during the initiation phase of reprogramming. MicroRNA-34a is a known regulator of SIRT1. Its inhibitor increased, while its mimics reduced iPSC formation. The stimulatory effect of SIRT1 during reprogramming was also confirmed in the primary MEF. RSV increased while tenovin-6, a small molecule that activates p53 through SIRT1 inhibition, suppressed reprogramming. In conclusion, SIRT1 enhances iPSC generation, in part, through deacetylation of p53, inhibition of p21 and enhancement of Nanog expression.
doi:10.1371/journal.pone.0045633
PMCID: PMC3448677  PMID: 23029150
16.  Appetite for destruction: the inhibition of glycolysis as a therapy for tuberous sclerosis complex-related tumors 
BMC Biology  2011;9:69.
The elevated metabolic requirements of cancer cells reflect their rapid growth and proliferation and are met through mutations in oncogenes and tumor suppressor genes that reprogram cellular processes. For example, in tuberous sclerosis complex (TSC)-related tumors, the loss of TSC1/2 function causes constitutive mTORC1 activity, which stimulates glycolysis, resulting in glucose addiction in vitro. In research published in Cell and Bioscience, Jiang and colleagues show that pharmacological restriction of glucose metabolism decreases tumor progression in a TSC xenograft model.
See research article: http://www.cellandbioscience.com/content/1/1/34
doi:10.1186/1741-7007-9-69
PMCID: PMC3198763  PMID: 22018140
18.  Nobel prize in medicine awarded to MRI pioneers 
BMJ : British Medical Journal  2003;327(7419):827.
PMCID: PMC214010  PMID: 14551069
20.  Human genome pioneers are awarded Nobel prize 
BMJ : British Medical Journal  2002;325(7368):791.
PMCID: PMC1124318  PMID: 12376428
21.  SECOND AWARD OF MACCABAEN PRIZE AND MEDAL 
Medical History  1962;6(4):388.2-389.
Images
PMCID: PMC1034763

Results 1-25 (103404)