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Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Wednesday, 2014 September 17
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

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PubMed Results

Items 1 - 3 of 3

1.	Nature. 2014 Jul 31;511(7511):606-10. doi: 10.1038/nature13544. Epub 2014 Jul 23. The DNA methylation landscape of human early embryos. Guo H1, Zhu P2, Yan L3, Li R3, Hu B4, Lian Y5, Yan J5, Ren X5, Lin S5, Li J5, Jin X5, Shi X5, Liu P5, Wang X6, Wang W6, Wei Y6, Li X4, Guo F4, Wu X4, Fan X4, Yong J7, Wen L4, Xie SX7, Tang F8, Qiao J5. Author information: 11] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2]. 21] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China [3]. 31] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China [3]. 4Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China. 51] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Key Laboratory of Assisted Reproduction, Ministry of Education, Beijing 100191, China. 6Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China. 71] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. 81] Biodynamic Optical Imaging Center &Center for Reproductive Medicine, College of Life Sciences, Third Hospital, Peking University, Beijing 100871, China [2] Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing 100871, China. Abstract DNA methylation is a crucial element in the epigenetic regulation of mammalian embryonic development. However, its dynamic patterns have not been analysed at the genome scale in human pre-implantation embryos due to technical difficulties and the scarcity of required materials. Here we systematically profile the methylome of human early embryos from the zygotic stage through to post-implantation by reduced representation bisulphite sequencing and whole-genome bisulphite sequencing. We show that the major wave of genome-wide demethylation is complete at the 2-cell stage, contrary to previous observations in mice. Moreover, the demethylation of the paternal genome is much faster than that of the maternal genome, and by the end of the zygotic stage the genome-wide methylation level in male pronuclei is already lower than that in female pronuclei. The inverse correlation between promoter methylation and gene expression gradually strengthens during early embryonic development, reaching its peak at the post-implantation stage. Furthermore, we show that active genes, with the trimethylation of histone H3 at lysine 4 (H3K4me3) mark at the promoter regions in pluripotent human embryonic stem cells, are essentially devoid of DNA methylation in both mature gametes and throughout pre-implantation development. Finally, we also show that long interspersed nuclear elements or short interspersed nuclear elements that are evolutionarily young are demethylated to a milder extent compared to older elements in the same family and have higher abundance of transcripts, indicating that early embryos tend to retain higher residual methylation at the evolutionarily younger and more active transposable elements. Our work provides insights into the critical features of the methylome of human early embryos, as well as its functional relation to the regulation of gene expression and the repression of transposable elements.
	PMID: 25079557 [PubMed - indexed for MEDLINE]
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2.	Nature. 2014 Jul 31;511(7511):543-50. doi: 10.1038/nature13385. Epub 2014 Jul 9. Comprehensive molecular profiling of lung adenocarcinoma. Cancer Genome Atlas Research Network. Collaborators: Collisson EA, Campbell JD, Brooks AN, Berger AH, Lee W, Chmielecki J, Beer DG, Cope L, Creighton CJ, Danilova L, Ding L, Getz G, Hammerman PS, Hayes DN, Hernandez B, Herman JG, Heymach JV, Jurisica I, Kucherlapati R, Kwiatkowski D, Ladanyi M, Robertson G, Schultz N, Shen R, Sinha R, Sougnez C, Tsao MS, Travis WD, Weinstein JN, Wigle DA, Wilkerson MD, Chu A, Cherniack AD, Hadjipanayis A, Rosenberg M, Weisenberger DJ, Laird PW, Radenbaugh A, Ma S, Stuart JM, Averett Byers L, Baylin SB, Govindan R, Meyerson M, Rosenberg M, Gabriel SB, Cibulskis K, Sougnez C, Kim J, Stewart C, Lichtenstein L, Lander ES, Lawrence MS, Getz, Kandoth C, Fulton R, Fulton LL, McLellan MD, Wilson RK, Ye K, Fronick CC, Maher CA, Miller CA, Wendl MC, Cabanski C, Ding L, Mardis E, Govindan R, Creighton CJ, Wheeler D, Balasundaram M, Butterfield YS, Carlsen R, Chu A, Chuah E, Dhalla N, Guin R, Hirst C, Lee D, Li HI, Mayo M, Moore RA, Mungall AJ, Schein JE, Sipahimalani P, Tam A, Varhol R, Robertson A, Wye N, Thiessen N, Holt RA, Jones SJ, Marra MA, Campbell JD, Brooks AN, Chmielecki J, Imielinski M, Onofrio RC, Hodis E, Zack T, Sougnez C, Helman E, Sekhar Pedamallu C, Mesirov J, Cherniack AD, Saksena G, Schumacher SE, Carter SL, Hernandez B, Garraway L, Beroukhim R, Gabriel SB, Getz G, Meyerson M, Hadjipanayis A, Lee S, Mahadeshwar HS, Pantazi A, Protopopov A, Ren X, Seth S, Song X, Tang J, Yang L, Zhang J, Chen PC, Parfenov M, Wei Xu A, Santoso N, Chin L, Park PJ, Kucherlapati R, Hoadley KA, Auman JT, Meng S, Shi Y, Buda E, Waring S, Veluvolu U, Tan D, Mieczkowski PA, Jones CD, Simons JV, Soloway MG, Bodenheimer T, Jefferys SR, Roach J, Hoyle AP, Wu J, Balu S, Singh D, Prins JF, Marron JS, Parker JS, Hayes DN, Perou CM, Liu J, Cope L, Danilova L, Weisenberger DJ, Maglinte DT, Lai PH, Bootwalla MS, Van Den Berg DJ, Triche T Jr, Baylin SB, Laird PW, Rosenberg M, Chin L, Zhang J, Cho J, DiCara D, Heiman D, Lin P, Mallard W, Voet D, Zhang H, Zou L, Noble MS, Lawrence MS, Saksena G, Gehlenborg N, Thorvaldsdottir H, Mesirov J, Nazaire MD, Robinson J, Getz G, Lee W, Aksoy BA, Ciriello G, Taylor BS, Dresdner G, Gao J, Gross B, Seshan VE, Ladanyi M, Reva B, Sinha R, Sumer SO, Weinhold N, Schultz N, Shen R, Sander C, Ng S, Ma S, Zhu J, Radenbaugh A, Stuart JM, Benz CC, Yau C, Haussler D, Spellman PT, Wilkerson MD, Parker JS, Hoadley KA, Kimes PK, Hayes DN, Perou CM, Broom BM, Wang J, Lu Y, Kwok Shing Ng P, Diao L, Averett Byers L, Liu W, Heymach JV, Amos CI, Weinstein JN, Akbani R, Mills GB, Curley E, Paulauskis J, Lau K, Morris S, Shelton T, Mallery D, Gardner J, Penny R, Saller C, Tarvin K, Richards WG, Cerfolio R, Bryant A, Raymond DP, Pennell NA, Farver C, Czerwinski C, Huelsenbeck-Dill L, Iacocca M, Petrelli N, Rabeno B, Brown J, Bauer T, Dolzhanskiy O, Potapova O, Rotin D, Voronina O, Nemirovich-Danchenko E, Fedosenko KV, Gal A, Behera M, Ramalingam SS, Sica G, Flieder D, Boyd J, Weaver J, Kohl B, Huy Quoc Thinh D, Sandusky G, Juhl H, Duhig E, Illei P, Gabrielson E, Shin J, Lee B, Rogers K, Trusty D, Brock MV, Williamson C, Burks E, Rieger-Christ K, Holway A, Sullivan T, Wigle DA, Asiedu MK, Kosari F, Travis WD, Rekhtman N, Zakowski M, Rusch VW, Zippile P, Suh J, Pass H, Goparaju C, Owusu-Sarpong Y, Bartlett JM, Kodeeswaran S, Parfitt J, Sekhon H, Albert M, Eckman J, Myers JB, Cheney R, Morrison C, Gaudioso C, Borgia JA, Bonomi P, Pool M, Liptay MJ, Moiseenko F, Zaytseva I, Dienemann H, Meister M, Schnabel PA, Muley TR, Peifer M, Gomez-Fernandez C, Herbert L, Egea S, Huang M, Thorne LB, Boice L, Hill Salazar A, Funkhouser WK, Rathmell WK, Dhir R, Yousem SA, Dacic S, Schneider F, Siegfried JM, Hajek R, Watson MA, McDonald S, Meyers B, Clarke B, Yang IA, Fong KM, Hunter L, Windsor M, Bowman RV, Peters S, Letovanec I, Khan KZ, Jensen MA, Snyder EE, Srinivasan D, Kahn AB, Baboud J, Pot DA, Mills Shaw KR, Sheth M, Davidsen T, Demchok JA, Yang L, Wang Z, Tarnuzzer R, Zenklusen JC, Ozenberger BA, Sofia HJ, Travis WD, Cheney R, Clarke B, Dacic S, Duhig E, Funkhouser WK, Illei P, Farver C, Rekhtman N, Sica G, Suh J, Tsao MS, Travis WD, Cheney R, Clarke B, Dacic S, Duhig E, Funkhouser WK, Illei P, Farver C, Rekhtman N, Sica G, Suh J, Tsao MS. Abstract Adenocarcinoma of the lung is the leading cause of cancer death worldwide. Here we report molecular profiling of 230 resected lung adenocarcinomas using messenger RNA, microRNA and DNA sequencing integrated with copy number, methylation and proteomic analyses. High rates of somatic mutation were seen (mean 8.9 mutations per megabase). Eighteen genes were statistically significantly mutated, including RIT1 activating mutations and newly described loss-of-function MGA mutations which are mutually exclusive with focal MYC amplification. EGFR mutations were more frequent in female patients, whereas mutations in RBM10 were more common in males. Aberrations in NF1, MET, ERBB2 and RIT1 occurred in 13% of cases and were enriched in samples otherwise lacking an activated oncogene, suggesting a driver role for these events in certain tumours. DNA and mRNA sequence from the same tumour highlighted splicing alterations driven by somatic genomic changes, including exon 14 skipping in MET mRNA in 4% of cases. MAPK and PI(3)K pathway activity, when measured at the protein level, was explained by known mutations in only a fraction of cases, suggesting additional, unexplained mechanisms of pathway activation. These data establish a foundation for classification and further investigations of lung adenocarcinoma molecular pathogenesis.
	PMID: 25079552 [PubMed - indexed for MEDLINE]
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3.	Nature. 2014 Jul 31;511(7511):540-1. doi: 10.1038/nature13648. Epub 2014 Jul 23. Epigenetics: Cellular memory erased in human embryos. Reik W1, Kelsey G2. Author information: 11] Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK, and at the Centre for Trophoblast Research, University of Cambridge. [2] Wellcome Trust Sanger Institute, Cambridge. 2Epigenetics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK, and at the Centre for Trophoblast Research, University of Cambridge.
	PMID: 25079550 [PubMed - indexed for MEDLINE]
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