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  1. Article ; Online: Identification of microRNAs as potential prognostic markers in ependymoma.

    Fabricio F Costa / Jared M Bischof / Elio F Vanin / Rishi R Lulla / Min Wang / Simone T Sredni / Veena Rajaram / Maria de Fátima Bonaldo / Deli Wang / Stewart Goldman / Tadanori Tomita / Marcelo B Soares

    PLoS ONE, Vol 6, Iss 10, p e

    2011  Volume 25114

    Abstract: Introduction We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression ... ...

    Abstract Introduction We have examined expression of microRNAs (miRNAs) in ependymomas to identify molecular markers of value for clinical management. miRNAs are non-coding RNAs that can block mRNA translation and affect mRNA stability. Changes in the expression of miRNAs have been correlated with many human cancers. Materials and methods We have utilized TaqMan Low Density Arrays to evaluate the expression of 365 miRNAs in ependymomas and normal brain tissue. We first demonstrated the similarity of expression profiles of paired frozen tissue (FT) and paraffin-embedded specimens (FFPE). We compared the miRNA expression profiles of 34 FFPE ependymoma samples with 8 microdissected normal brain tissue specimens enriched for ependymal cells. miRNA expression profiles were then correlated with tumor location, histology and other clinicopathological features. Results We have identified miRNAs that are over-expressed in ependymomas, such as miR-135a and miR-17-5p, and down-regulated, such as miR-383 and miR-485-5p. We have also uncovered associations between expression of specific miRNAs which portend a worse prognosis. For example, we have identified a cluster of miRNAs on human chromosome 14q32 that is associated with time to relapse. We also found that miR-203 is an independent marker for relapse compared to the parameters that are currently used. Additionally, we have identified three miRNAs (let-7d, miR-596 and miR-367) that strongly correlate to overall survival. Conclusion We have identified miRNAs that are differentially expressed in ependymomas compared with normal ependymal tissue. We have also uncovered significant associations of miRNAs with clinical behavior. This is the first report of clinically relevant miRNAs in ependymomas.
    Keywords Medicine ; R ; Science ; Q
    Subject code 500
    Language English
    Publishing date 2011-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article: Onset of rosette formation during spontaneous neural differentiation of hESC and hiPSC colonies

    Malchenko, Sergey / Abdelhak Belmadani / Bula J. Bhattacharyya / Elio F. Vanin / Guifa Xi / Jianping Xie / John Crispino / Marcelo B. Soares / Maria de Fatima Bonaldo / Martha C. Bohn / Mary J.C. Hendrix / Richard E.B. Seftor / Richard J. Miller / Tadanori Tomita / Vasily Galat / William Goossens

    Gene. 2014 Jan. 25, v. 534

    2014  

    Abstract: In vitro neural differentiation of human embryonic stem cells (hESCs) is an advantageous system for studying early neural development. The process of early neural differentiation in hESCs begins by initiation of primitive neuroectoderm, which is ... ...

    Abstract In vitro neural differentiation of human embryonic stem cells (hESCs) is an advantageous system for studying early neural development. The process of early neural differentiation in hESCs begins by initiation of primitive neuroectoderm, which is manifested by rosette formation, with consecutive differentiation into neural progenitors and early glial-like cells. In this study, we examined the involvement of early neural markers – OTX2, PAX6, Sox1, Nestin, NR2F1, NR2F2, and IRX2 – in the onset of rosette formation, during spontaneous neural differentiation of hESC and human induced pluripotent stem cell (hiPSC) colonies. This is in contrast to the conventional way of studying rosette formation, which involves induction of neuronal differentiation and the utilization of embryoid bodies. Here we show that OTX2 is highly expressed at the onset of rosette formation, when rosettes comprise no more than 3–5 cells, and that its expression precedes that of established markers of early neuronal differentiation. Importantly, the rise of OTX2 expression in these cells coincides with the down-regulation of the pluripotency marker OCT4. Lastly, we show that cells derived from rosettes that emerge during spontaneous differentiation of hESCs or hiPSCs are capable of differentiating into dopaminergic neurons in vitro, and into mature-appearing pyramidal and serotonergic neurons weeks after being injected into the motor cortex of NOD-SCID mice.
    Keywords embryonic stem cells ; humans ; mice ; motor cortex ; neurodevelopment ; neurons
    Language English
    Dates of publication 2014-0125
    Size p. 400-407.
    Publishing place Elsevier B.V.
    Document type Article
    ZDB-ID 391792-7
    ISSN 1879-0038 ; 0378-1119
    ISSN (online) 1879-0038
    ISSN 0378-1119
    DOI 10.1016/j.gene.2013.07.101
    Database NAL-Catalogue (AGRICOLA)

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  3. Article ; Online: Putative Multifunctional Signature of Lung Metastases in Dedifferentiated Chondrosarcoma

    Sergey Malchenko / Elisabeth A. Seftor / Yuri Nikolsky / Susan L. Hasegawa / Sean Kuo / Jeff W. Stevens / Stas Poyarkov / Tatiana Nikolskaya / Tamara Kucaba / Min Wang / Hakim Abdulkawy / Thomas Casavant / Jose Morcuende / Joseph Buckwalter / Raymond Hohl / Barry DeYoung / Kemp Kernstine / Maria de Fatima Bonaldo / Mary J. C. Hendrix /
    Marcelo B. Soares / Vera Maria F. C. Soares

    Sarcoma, Vol

    2012  Volume 2012

    Keywords Neoplasms. Tumors. Oncology. Including cancer and carcinogens ; RC254-282 ; Internal medicine ; RC31-1245 ; Medicine ; R ; DOAJ:Oncology ; DOAJ:Medicine (General) ; DOAJ:Health Sciences
    Language English
    Publishing date 2012-01-01T00:00:00Z
    Publisher Hindawi Publishing Corporation
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

    Tadashi Imanishi / Takeshi Itoh / Yutaka Suzuki / Claire O'Donovan / Satoshi Fukuchi / Kanako O Koyanagi / Roberto A Barrero / Takuro Tamura / Yumi Yamaguchi-Kabata / Motohiko Tanino / Kei Yura / Satoru Miyazaki / Kazuho Ikeo / Keiichi Homma / Arek Kasprzyk / Tetsuo Nishikawa / Mika Hirakawa / Jean Thierry-Mieg / Danielle Thierry-Mieg /
    Jennifer Ashurst / Libin Jia / Mitsuteru Nakao / Michael A Thomas / Nicola Mulder / Youla Karavidopoulou / Lihua Jin / Sangsoo Kim / Tomohiro Yasuda / Boris Lenhard / Eric Eveno / Yoshiyuki Suzuki / Chisato Yamasaki / Jun-ichi Takeda / Craig Gough / Phillip Hilton / Yasuyuki Fujii / Hiroaki Sakai / Susumu Tanaka / Clara Amid / Matthew Bellgard / Maria de Fatima Bonaldo / Hidemasa Bono / Susan K Bromberg / Anthony J Brookes / Elspeth Bruford / Piero Carninci / Claude Chelala / Christine Couillault / Sandro J de Souza / Marie-Anne Debily / Marie-Dominique Devignes / Inna Dubchak / Toshinori Endo / Anne Estreicher / Eduardo Eyras / Kaoru Fukami-Kobayashi / Gopal R Gopinath / Esther Graudens / Yoonsoo Hahn / Michael Han / Ze-Guang Han / Kousuke Hanada / Hideki Hanaoka / Erimi Harada / Katsuyuki Hashimoto / Ursula Hinz / Momoki Hirai / Teruyoshi Hishiki / Ian Hopkinson / Sandrine Imbeaud / Hidetoshi Inoko / Alexander Kanapin / Yayoi Kaneko / Takeya Kasukawa / Janet Kelso / Paul Kersey / Reiko Kikuno / Kouichi Kimura / Bernhard Korn / Vladimir Kuryshev / Izabela Makalowska / Takashi Makino / Shuhei Mano / Regine Mariage-Samson / Jun Mashima / Hideo Matsuda / Hans-Werner Mewes / Shinsei Minoshima / Keiichi Nagai / Hideki Nagasaki / Naoki Nagata / Rajni Nigam / Osamu Ogasawara / Osamu Ohara / Masafumi Ohtsubo / Norihiro Okada / Toshihisa Okido / Satoshi Oota / Motonori Ota / Toshio Ota / Tetsuji Otsuki / Dominique Piatier-Tonneau / Annemarie Poustka / Shuang-Xi Ren / Naruya Saitou / Katsunaga Sakai / Shigetaka Sakamoto / Ryuichi Sakate / Ingo Schupp / Florence Servant / Stephen Sherry / Rie Shiba / Nobuyoshi Shimizu / Mary Shimoyama / Andrew J Simpson / Bento Soares / Charles Steward / Makiko Suwa / Mami Suzuki / Aiko Takahashi / Gen Tamiya / Hiroshi Tanaka / Todd Taylor / Joseph D Terwilliger / Per Unneberg / Vamsi Veeramachaneni / Shinya Watanabe / Laurens Wilming / Norikazu Yasuda / Hyang-Sook Yoo / Marvin Stodolsky / Wojciech Makalowski / Mitiko Go / Kenta Nakai / Toshihisa Takagi / Minoru Kanehisa / Yoshiyuki Sakaki / John Quackenbush / Yasushi Okazaki / Yoshihide Hayashizaki / Winston Hide / Ranajit Chakraborty / Ken Nishikawa / Hideaki Sugawara / Yoshio Tateno / Zhu Chen / Michio Oishi / Peter Tonellato / Rolf Apweiler / Kousaku Okubo / Lukas Wagner / Stefan Wiemann / Robert L Strausberg / Takao Isogai / Charles Auffray / Nobuo Nomura / Takashi Gojobori / Sumio Sugano

    PLoS Biology, Vol 2, Iss 6, p e

    2004  Volume 162

    Abstract: The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation ... ...

    Abstract The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
    Keywords Biology (General) ; QH301-705.5
    Subject code 572
    Language English
    Publishing date 2004-06-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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