World Biomedical frontiers Breakthrought New Tech

8. Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution

N. Maherali, R. Sridharan, W. Xie, J. Utikal, S. Eminli, K. Arnold, M. Stadtfeld, R. Yachechko, J. Tchieu, R. Jaenisch, K. Plath and K. Hochedlinger

Cell Stem Cell.2007 Jul;1(1):55-70.

Abstract: Ectopic expression of the four transcription factors Oct4, Sox2, c-Myc, and Klf4 is sufficient to confer a pluripotent state upon the fibroblast genome, generating induced pluripotent stem (PS) cells. It remains unknown if nuclear reprogramming induced by these four factors globally resets epigenetic differences between differentiated and pluripotent cells. Here, using novel selection approaches, we have generated PS cells from fibroblasts to characterize their epigenetic state. Female PS cells showed reactivation of a somatically silenced X chromosome and underwent random X inactivation upon differentiation. Genome-wide analysis of two key histone modifications indicated that PS cells are highly similar to ES cells. Consistent with these observations, PS cells gave rise to viable high-degree chimeras with contribution to the germline. These data show that transcription factor-induced reprogramming leads to the global reversion of the somatic epigenome into an ES-like state. Our results provide a paradigm for studying the epigenetic modifications that accompany nuclear reprogramming and suggest that abnormal epigenetic reprogramming does not pose a problem for the potential therapeutic applications of PS cells.

Keywords: embryonic stem-cells, inactive x-chromosome, developmental regulators, somatic-cells, es cells, mouse, pluripotency, methylation, nanog, polycomb

*Times Cited: 741

PMID: 18371336

9. Effect of rosiglitazone on the risk of myocardial infarction and death from cardiovascular causes

S. E. Nissen and K. Wolski

N Engl J Med.2007 Jun;356(24):2457-2471.

Abstract: BACKGROUND: Rosiglitazone is widely used to treat patients with type 2 diabetes mellitus, but its effect on cardiovascular morbidity and mortality has not been determined. METHODS: We conducted searches of the published literature, the Web site of the Food and Drug Administration, and a clinical-trials registry maintained by the drug manufacturer (GlaxoSmithKline). Criteria for inclusion in our meta-analysis included a study duration of more than 24 weeks, the use of a randomized control group not receiving rosiglitazone, and the availability of outcome data for myocardial infarction and death from cardiovascular causes. Of 116 potentially relevant studies, 42 trials met the inclusion criteria. We tabulated all occurrences of myocardial infarction and death from cardiovascular causes. RESULTS: Data were combined by means of a fixed-effects model. In the 42 trials, the mean age of the subjects was approximately 56 years, and the mean baseline glycated hemoglobin level was approximately 8.2%. In the rosiglitazone group, as compared with the control group, the odds ratio for myocardial infarction was 1.43 (95% confidence interval [CI], 1.03 to 1.98; P=0.03), and the odds ratio for death from cardiovascular causes was 1.64 (95% CI, 0.98 to 2.74; P=0.06). CONCLUSIONS: Rosiglitazone was associated with a significant increase in the risk of myocardial infarction and with an increase in the risk of death from cardiovascular causes that had borderline significance. Our study was limited by a lack of access to original source data, which would have enabled time-to-event analysis. Despite these limitations, patients and providers should consider the potential for serious adverse cardiovascular effects of treatment with rosiglitazone for type 2 diabetes.

Keywords: type-2 diabetes-mellitus, randomized controlled-trial, improves glycemic, control, combination therapy, metformin, sulfonylurea, events, pioglitazone, monotherapy, glyburide

*Times Cited: 1619

PMID: 17517853

10. Effects of bariatric surgery on mortality in Swedish obese subjects

L. Sjostrom, K. Narbro, D. Sjostrom, K. Karason, B. Larsson, H. Wedel, T. Lystig, M. Sullivan, C. Bouchard, B. Carlsson, C. Bengtsson, S. Dahlgren, A. Gummesson, P. Jacobson, J. Karlsson, A. K. Lindroos, H. Lonroth, I. Naslund, T. Olbers, K. Stenlof, J. Torgerson, G. Agren, L. M. S. Carlsson and S. Swedish Obese Subjects

N Engl J Med.2007 Aug;357(8):741-752.

Abstract: Background: Obesity is associated with increased mortality. Weight loss improves cardiovascular risk factors, but no prospective interventional studies have reported whether weight loss decreases overall mortality. In fact, many observational studies suggest that weight reduction is associated with increased mortality. Methods: The prospective, controlled Swedish Obese Subjects study involved 4047 obese subjects. Of these subjects, 2010 underwent bariatric surgery (surgery group) and 2037 received conventional treatment (matched control group). We report on overall mortality during an average of 10.9 years of follow-up. At the time of the analysis (November 1, 2005), vital status was known for all but three subjects (follow-up rate, 99.9%). Results: The average weight change in control subjects was less than +/-2% during the period of up to 15 years during which weights were recorded. Maximum weight losses in the surgical subgroups were observed after 1 to 2 years: gastric bypass, 32%; vertical-banded gastroplasty, 25%; and banding, 20%. After 10 years, the weight losses from baseline were stabilized at 25%, 16%, and 14%, respectively. There were 129 deaths in the control group and 101 deaths in the surgery group. The unadjusted overall hazard ratio was 0.76 in the surgery group (P=0.04), as compared with the control group, and the hazard ratio adjusted for sex, age, and risk factors was 0.71 (P=0.01). The most common causes of death were myocardial infarction (control group, 25 subjects; surgery group, 13 subjects) and cancer (control group, 47; surgery group, 29). Conclusions: Bariatric surgery for severe obesity is associated with long-term weight loss and decreased overall mortality.

Keywords: body-mass index, intentional weight-loss, aged 40-64 years, united-states, subjects sos, older persons, follow-up, overweight, cohort, intervention

*Times Cited: 1055

PMID: 17715408

11. Effects of torcetrapib in patients at high risk for coronary events

P. J. Barter, M. Caulfield, M. Eriksson, S. M. Grundy, J. J. P. Kastelein, M. Komajda, J. Lopez-Sendon, L. Mosca, J. Tardif, D. D. Waters, C. L. Shear, J. H. Revkin, K. A. Buhr, M. R. Fisher, A. R. Tall, B. Brewer and I. Investigators

N Engl J Med.2007 Nov;357(21):2109-2122.

Abstract: Background Inhibition of cholesteryl ester transfer protein (CETP) has been shown to have a substantial effect on plasma lipoprotein levels. We investigated whether torcetrapib, a potent CETP inhibitor, might reduce major cardiovascular events. The trial was terminated prematurely because of an increased risk of death and cardiac events in patients receiving torcetrapib. Methods We conducted a randomized, double-blind study involving 15,067 patients at high cardiovascular risk. The patients received either torcetrapib plus atorvastatin or atorvastatin alone. The primary outcome was the time to the first major cardiovascular event, which was defined as death from coronary heart disease, nonfatal myocardial infarction, stroke, or hospitalization for unstable angina. Results At 12 months in patients who received torcetrapib, there was an increase of 72.1% in high-density lipoprotein cholesterol and a decrease of 24.9% in low-density lipoprotein cholesterol, as compared with baseline (P

Keywords: ester transfer protein, high-density-lipoprotein, cardiovascular-disease, hdl-cholesterol, atherosclerosis, target, inhibitor

*Times Cited: 767

PMID: 17984165

12. Erlotinib plus gemcitabine compared with gemcitabine alone in patients with advanced pancreatic cancer: A phase III trial of the National Cancer Institute of Canada clinical trials group

M. J. Moore, D. Goldstein, J. Hamm, A. Figer, J. R. Hecht, S. Gallinger, H. J. Au, P. Murawa, D. Walde, R. A. Wolff, D. Campos, R. Lim, K. Ding, G. Clark, T. Voskoglou-Nomikos, M. Ptasynski and W. Parulekar

Journal of Clinical Oncology.2007 May;25(15):1960-1966.

Abstract: Purpose Patients with advanced pancreatic cancer have a poor prognosis and there have been no improvements in survival since the introduction of gemcitabine in 1996. Pancreatic tumors often overexpress human epidermal growth factor receptor type 1 (HER1/EGFR) and this is associated with a worse prognosis. We studied the effects of adding the HER1/EGFR-targeted agent erlotinib to gemcitabine in patients with unresectable, locally advanced, or metastatic pancreatic cancer. Patients and Methods Patients were randomly assigned 1:1 to receive standard gemcitabine plus erlotinib (100 or 150 mg/d orally) or gemcitabine plus placebo in a double-blind, international phase III trial. The primary end point was overall survival. Results A total of 569 patients were randomly assigned. Overall survival based on an intent-to-treat analysis was significantly prolonged on the erlotinib/gemcitabine arm with a hazard ratio (HR) of 0.82 (95% Cl, 0.69 to 0.99; P=.038, adjusted for stratification factors; median 6.24 months v 5.91 months). One-year survival was also greater with erlotinib plus gemcitabine (23% v 17%; P =.023). Progression-free survival was significantly longer with erlotinib plus gemcitabine with an estimated HR of 0.77 (95% Cl, 0.64 to 0.92; P =.004). Objective response rates were not significantly different between the arms, although more patients on erlotinib had disease stabilization. There was a higher incidence of some adverse events with erlotinib plus gemcitabine, but most were grade 1 or 2. Conclusion To our knowledge, this randomized phase III trial is the first to demonstrate statistically significantly improved survival in advanced pancreatic cancer by adding any agent to gemcitabine. The recommended dose of erlotinib with gemcitabine for this indication is 100 mg/d.

Keywords: growth-factor receptor, tyrosine kinase inhibitor, cell lung-cancer, randomized-trial, therapy, chemotherapy, combination, osi-774, adenocarcinoma, expression

*Times Cited: 1010

PMID: 17452677

13. Exosome-mediated transfer of mRNAs and microRNAs is a novel mechanism of genetic exchange between cells

H. Valadi, K. Ekstrom, A. Bossios, M. Sjostrand, J. J. Lee and J. O. Lotvall

Nat Cell Biol.2007 Jun;9(6):654-U672.

Abstract: Exosomes are vesicles of endocytic origin released by many cells. These vesicles can mediate communication between cells, facilitating processes such as antigen presentation. Here, we show that exosomes from a mouse and a human mast cell line (MC/9 and HMC-1, respectively), as well as primary bone marrow-derived mouse mast cells, contain RNA. Microarray assessments revealed the presence of mRNA from approximately 1300 genes, many of which are not present in the cytoplasm of the donor cell. In vitro translation proved that the exosome mRNAs were functional. Quality control RNA analysis of total RNA derived from exosomes also revealed presence of small RNAs, including microRNAs. The RNA from mast cell exosomes is transferable to other mouse and human mast cells. After transfer of mouse exosomal RNA to human mast cells, new mouse proteins were found in the recipient cells, indicating that transferred exosomal mRNA can be translated after entering another cell. In summary, we show that exosomes contain both mRNA and microRNA, which can be delivered to another cell, and can be functional in this new location. We propose that this RNA is called “exosomal shuttle RNA” (esRNA).

Keywords: mast-cell, proteomic analysis, dendritic cells, animal development, microvesicles, vesicles, accumulation, activation, complex, surface

*Times Cited: 727

PMID: 17486113

14. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences

J. Chun, J. H. Lee, Y. Jung, M. Kim, S. Kim, B. K. Kim and Y. W. Lim

Int J Syst Evol Microbiol.2007 Oct;57:2259-2261.

Abstract: 16S rRNA gene sequences have been widely used for the identification of prokaryotes. However, the flood of sequences of non-type strains and the lack of a peer-reviewed database for 16S rRNA gene sequences of type strains have made routine identification of isolates difficult and labour-intensive. In the present study, we generated a database containing 16S rRNA gene sequences of all prokaryotic type strains. In addition, a web-based tool, named EzTaxon, for analysis of 16S rRNA gene sequences was constructed to achieve identification of isolates based on pairwise nucleoticle similarity values and phylogenetic inference methods. The system developed provides users with a similarity-based search, multiple sequence alignment and various phylogenetic analyses. All of these functions together with the 16S rRNA gene sequence database of type strains can be successfully used for automated and reliable identification of prokaryotic isolates.

Keywords: alignment, trees

*Times Cited: 964

PMID: 17911292

15. Genomewide association analysis of coronary artery disease

N. J. Samani, J. Erdmann, A. S. Hall, C. Hengstenberg, M. Mangino, B. Mayer, R. J. Dixon, T. Meitinger, P. Braund, H. E. Wichmann, J. H. Barrett, I. R. Konig, S. E. Stevens, S. Szymczak, D. Tregouet, M. M. Iles, F. Pahlke, H. Pollard, W. Lieb, F. Cambien, M. Fischer, W. Ouwehand, S. Blankenberg, A. J. Balmforth, A. Baessler, S. G. Ball, T. M. Strom, I. Braenne, C. Gieger, P. Deloukas, M. D. Tobin, A. Ziegler, J. R. Thompson, H. Schunkert, Wtccc and C. Cardiogenics

N Engl J Med.2007 Aug;357(5):443-453.

Abstract: Background Modern genotyping platforms permit a systematic search for inherited components of complex diseases. We performed a joint analysis of two genomewide association studies of coronary artery disease. Methods We first identified chromosomal loci that were strongly associated with coronary artery disease in the Wellcome Trust Case Control Consortium (WTCCC) study (which involved 1926 case subjects with coronary artery disease and 2938 controls) and looked for replication in the German MI [Myocardial Infarction] Family Study (which involved 875 case subjects with myocardial infarction and 1644 controls). Data on other single-nucleotide polymorphisms (SNPs) that were significantly associated with coronary artery disease in either study (P<0.001) were then combined to identify additional loci with a high probability of TRUE association. Genotyping in both studies was performed with the use of the GeneChip Human Mapping 500K Array Set (Affymetrix). Results Of thousands of chromosomal loci studied, the same locus had the strongest association with coronary artery disease in both the WTCCC and the German studies: chromosome 9p21.3 (SNP, rs1333049) (P=1.80×10(-14) and P=3.40×10(-6), respectively). Overall, the WTCCC study revealed nine loci that were strongly associated with coronary artery disease (P<1.2×10(-5) and less than a 50% chance of being falsely positive). In addition to chromosome 9p21.3, two of these loci were successfully replicated (adjusted P<0.05) in the German study: chromosome 6q25.1 (rs6922269) and chromosome 2q36.3 (rs2943634). The combined analysis of the two studies identified four additional loci significantly associated with coronary artery disease (P<1.3×10(-6)) and a high probability(>80%) of a TRUE association: chromosomes 1p13.3 (rs599839), 1q41 (rs17465637), 10q11.21 (rs501120), and 15q22.33 (rs17228212). Conclusions We identified several genetic loci that, individually and in aggregate, substantially affect the risk of development of coronary artery disease.

Keywords: mitochondrial c-1-tetrahydrofolate synthase, wide association, risk-factors, myocardial-infarction, gene, susceptibility, replication, expression, families, linkage

*Times Cited: 802

PMID: 17634449

16. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis

J. D. Rioux, R. J. Xavier, K. D. Taylor, M. S. Silverberg, P. Goyette, A. Huett, T. Green, P. Kuballa, M. M. Barmada, L. W. Datta, Y. Y. Shugart, A. M. Griffiths, S. R. Targan, A. F. Ippoliti, E. J. Bernard, L. Mei, D. L. Nicolae, M. Regueiro, L. P. Schumm, A. H. Steinhart, J. I. Rotter, R. H. Duerr, J. H. Cho, M. J. Daly and S. R. Brant

Nature Genetics.2007 May;39(5):596-604.

Abstract: We present a genome-wide association study of ileal Crohn disease and two independent replication studies that identify several new regions of association to Crohn disease. Specifically, in addition to the previously established CARD15 and IL23R associations, we identified strong and significantly replicated associations ( combined P < 10(-10)) with an intergenic region on 10q21.1 and a coding variant in ATG16L1, the latter of which was also recently reported by another group. We also report strong associations with independent replication to variation in the genomic regions encoding PHOX2B, NCF4 and a predicted gene on 16q24.1 (FAM92B). Finally, we demonstrate that ATG16L1 is expressed in intestinal epithelial cell lines and that functional knockdown of this gene abrogates autophagy of Salmonella typhimurium. Together, these findings suggest that autophagy and host cell responses to intracellular microbes are involved in the pathogenesis of Crohn disease.

Keywords: inflammatory-bowel-disease, dendritic cells, nadph oxidase, gene, complex, antigen, localization, concordance, expression, variants

*Times Cited: 729

PMID: 17435756

17. High-resolution profiling of histone methylations in the human genome

A. Barski, S. Cuddapah, K. R. Cui, T. Y. Roh, D. E. Schones, Z. B. Wang, G. Wei, I. Chepelev and K. J. Zhao

Cell.2007 May;129(4):823-837.

Abstract: Histone modifications are implicated in influencing gene expression. We have generated high-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology. Typical patterns of histone methylations exhibited at promoters, insulators, enhancers, and transcribed regions are identified. The monomethylations of H3K27, H3K9, H4K20, H3K79, and H2BK5 are all linked to gene activation, whereas trimethylations of H3K27, H3K9, and H3K79 are linked to repression. H2A.Z associates with functional regulatory elements, and CTCF marks boundaries of histone methylation domains. Chromosome banding patterns are correlated with unique patterns of histone modifications. Chromosome breakpoints detected in T cell cancers frequently reside in chromatin regions associated with H3K4 methylations. Our data provide new insights into the function of histone methylation and chromatin organization in genome function.

Keywords: embryonic stem-cells, active genes, t-cells, developmental regulators, saccharomyces-cerevisiae, mammalian chromatin, coding regions, wide, h2a.z, h3

*Times Cited: 1895

PMID: 17512414

18. Identification of pancreatic cancer stem cells

C. W. Li, D. G. Heidt, P. Dalerba, C. F. Burant, L. J. Zhang, V. Adsay, M. Wicha, M. F. Clarke and D. M. Simeone

Cancer research.2007 Feb;67(3):1030-1037.

Abstract: Emerging evidence has suggested that the capability of a tumor to grow and propagate is dependent on a small subset of cells within a tumor, termed cancer stem cells. Although data have been provided to support this theory in human blood, brain, and breast cancers, the identity of pancreatic cancer stem cells has not been determined. Using a xenograft model in which primary human pancreatic adenocarcinomas were grown in immunocompromised mice, we identified a highly tumorigenic subpopulation of pancreatic cancer cells expressing the cell surface markers CD44, CD24, and epithelial-specific antigen (ESA). Pancreatic cancer cells with the CD44(+)CD24(+)ESA(+) phenotype (0.2-0.8% of pancreatic cancer cells) had a 100-fold increased tumorigenic potential compared with nontumorigenic cancer cells, with 50% of animals injected with as few as 100 CD44(+)CD24(+)ESA(+) cells forming tumors that were histologically indistinguishable from the human tumors from which they originated. The enhanced ability of CD44(+)CD24(+)ESA(+) pancreatic cancer cells to form tumors was confirmed in an orthotopic pancreatic tail injection model. The CD44(+)CD24(+)ESA(+) pancreatic cancer cells showed the stem cell properties of self-renewal, the ability to produce differentiated progeny, and increased expression of the developmental signaling molecule sonic hedgehog. Identification of pancreatic cancer stem cells and further elucidation of the signaling pathways that regulate their growth and survival may provide novel therapeutic approaches to treat pancreatic cancer, which is notoriously resistant to standard chemotherapy and radiation.

Keywords: acute myeloid-leukemia, initiating cells, progenitor cells, brain-tumors, hedgehog, adenocarcinoma, apoptosis, survival, growth

*Times Cited: 992

PMID: 17283135

19. Induction of pluripotent stem cells from adult human fibroblasts by defined factors

K. Takahashi, K. Tanabe, M. Ohnuki, M. Narita, T. Ichisaka, K. Tomoda and S. Yamanaka

Cell.2007 Nov;131(5):861-872.

Abstract: Successful reprogramming of differentiated human somatic cells into a pluripotent state would allow creation of patient- and disease-specific stem cells. We previously reported generation of induced pluripotent stem (iPS) cells, capable of germline transmission, from mouse somatic cells by transduction of four defined transcription factors. Here, we demonstrate the generation of iPS cells from adult human dermal fibroblasts with the same four factors: Oct3/4, Sox2, Klf4, and c-Myc. Human iPS cells were similar to human embryonic stem (ES) cells in morphology, proliferation, surface antigens, gene expression, epigenetic status of pluripotent cell-specific genes, and telomerase activity. Furthermore, these cells could differentiate into cell types of the three germ layers in vitro and in teratomas. These findings demonstrate that iPS cells can be generated from adult human fibroblasts.

Keywords: self-renewal, human blastocysts, mouse embryos, es cells, lines, differentiation, activation, stat3, generation, maintain

*Times Cited: 3800

PMID: 18035408