The Journal of experimental medicine, 2007
Authors
Leong, Kevin G, Niessen, Kyle, Kulic, Iva, Raouf, Afshin, Eaves, Connie, Pollet, Ingrid, Karsan, Aly
Publication Abstract
Aberrant expression of Jagged1 and Notch1 are associated with poor outcome in breast cancer. However, the reason that Jagged1 and/or Notch overexpression portends a poor prognosis is unknown. We identify Slug, a transcriptional repressor, as a novel Notch target and show that elevated levels of Slug correlate with increased expression of Jagged1 in various human cancers. Slug was essential for Notch-mediated repression of E-cadherin, which resulted in beta-catenin activation and resistance to anoikis. Inhibition of ligand-induced Notch signaling in xenografted Slug-positive/E-cadherin-negative breast tumors promoted apoptosis and inhibited tumor growth and metastasis. This response was associated with down-regulated Slug expression, reexpression of E-cadherin, and suppression of active beta-catenin. Our findings suggest that ligand-induced Notch activation, through the induction of Slug, promotes tumor growth and metastasis characterized by epithelial-to-mesenchymal transition and inhibition of anoikis.

Molecular systems biology, 2007
Authors
Ewing, Rob M, Chu, Peter, Elisma, Fred, Li, Hongyan, Taylor, Paul, Climie, Shane, McBroom-Cerajewski, Linda, Robinson, Mark D, O'Connor, Liam, Li, Michael, Taylor, Rod, Dharsee, Moyez, Ho, Yuen, Heilbut, Adrian, Moore, Lynda, Zhang, Shudong, Ornatsky, Olga, Bukhman, Yury V, Ethier, Martin, Sheng, Yinglun, Vasilescu, Julian, Abu-Farha, Mohamed, Lambert, Jean-Philippe, Duewel, Henry S, Stewart, Ian I, Kuehl, Bonnie, Hogue, Kelly, Colwill, Karen, Gladwish, Katharine, Muskat, Brenda, Kinach, Robert, Adams, Sally-Lin, Moran, Michael F, Morin, Gregg B, Topaloglou, Thodoros, Figeys, Daniel
Publication Abstract
Mapping protein-protein interactions is an invaluable tool for understanding protein function. Here, we report the first large-scale study of protein-protein interactions in human cells using a mass spectrometry-based approach. The study maps protein interactions for 338 bait proteins that were selected based on known or suspected disease and functional associations. Large-scale immunoprecipitation of Flag-tagged versions of these proteins followed by LC-ESI-MS/MS analysis resulted in the identification of 24,540 potential protein interactions. False positives and redundant hits were filtered out using empirical criteria and a calculated interaction confidence score, producing a data set of 6463 interactions between 2235 distinct proteins. This data set was further cross-validated using previously published and predicted human protein interactions. In-depth mining of the data set shows that it represents a valuable source of novel protein-protein interactions with relevance to human diseases. In addition, via our preliminary analysis, we report many novel protein interactions and pathway associations.

Blood, 2006
Authors
Leong, Kevin G, Karsan, Aly
Publication Abstract
Members of the Notch family of transmembrane receptors play an important role in cell fate determination. Over the past decade, a role for Notch in the pathogenesis of hematologic and solid malignancies has become apparent. Numerous cellular functions and microenvironmental cues associated with tumorigenesis are modulated by Notch signaling, including proliferation, apoptosis, adhesion, epithelial-to-mesenchymal transition, and angiogenesis. It is becoming increasingly evident that Notch signaling can be both oncogenic and tumor suppressive. This review highlights recent findings regarding the molecular and functional aspects of Notch-mediated neoplastic transformation. In addition, cellular mechanisms that potentially explain the complex role of Notch in tumorigenesis are discussed.

Current treatment options in oncology, 2005
Authors
Caron, Nadine R, Clark, Orlo H
Publication Abstract
Papillary thyroid cancer (PTC), the most common thyroid malignancy, is associated with cervical lymph node metastases in 30% to 90% of patients. While surgery is the primary treatment modality for PTC, radioactive iodine and thyroid hormone suppression often complement the treatment plan. Although thyroid hormone suppression may decrease the incidence of recurrent disease and radioactive iodine may diagnose and treat metastases, lymph node dissection (LND) is the mainstay treatment for clinically evident cervical lymph node metastases. The surgical treatment options published in the literature include the traditional radical LND, the modified radical LND, the selective LND (compartment-based resection based on documented lymph node metastases), and a 'berry picking' resection (in which only the grossly abnormal lymph nodes are excised). At the University of California, San Francisco, we prefer the modified radical LND with preservation of the cervical sensory nerves for the first lymph node dissection with the 'berry picking' procedure limited to surgical treatment of recurrent nodal metastases in previously resected lymph node basins. Some centers are evaluating the potential role of sentinel lymph node biopsies for PTC. While the extent of lymphadenectomy is debated, most physicians treating patients with PTC agree that clinical evidence of lymphatic metastases should be surgically exercised and there is no role for prophylactic LND.

CMAJ : Canadian Medical Association journal = journal de l'Association medicale canadienne, 2005
Authors
Caron, Nadine R

Science (New York, N.Y.), 2003
Authors
Marra, Marco A, Jones, Steven J M, Astell, Caroline R, Holt, Robert A, Brooks-Wilson, Angela, Butterfield, Yaron S N, Khattra, Jaswinder, Asano, Jennifer K, Barber, Sarah A, Chan, Susanna Y, Cloutier, Alison, Coughlin, Shaun M, Freeman, Doug, Girn, Noreen, Griffith, Obi L, Leach, Stephen R, Mayo, Michael, McDonald, Helen, Montgomery, Stephen B, Pandoh, Pawan K, Petrescu, Anca S, Robertson, A Gordon, Schein, Jacqueline E, Siddiqui, Asim, Smailus, Duane E, Stott, Jeff M, Yang, George S, Plummer, Francis, Andonov, Anton, Artsob, Harvey, Bastien, Nathalie, Bernard, Kathy, Booth, Timothy F, Bowness, Donnie, Czub, Martin, Drebot, Michael, Fernando, Lisa, Flick, Ramon, Garbutt, Michael, Gray, Michael, Grolla, Allen, Jones, Steven, Feldmann, Heinz, Meyers, Adrienne, Kabani, Amin, Li, Yan, Normand, Susan, Stroher, Ute, Tipples, Graham A, Tyler, Shaun, Vogrig, Robert, Ward, Diane, Watson, Brynn, Brunham, Robert C, Krajden, Mel, Petric, Martin, Skowronski, Danuta M, Upton, Chris, Roper, Rachel L
Publication Abstract
We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.

Science (New York, N.Y.), 2002
Authors
Holt, Robert A, Subramanian, G Mani, Halpern, Aaron, Sutton, Granger G, Charlab, Rosane, Nusskern, Deborah R, Wincker, Patrick, Clark, Andrew G, Ribeiro, José M C, Wides, Ron, Salzberg, Steven L, Loftus, Brendan, Yandell, Mark, Majoros, William H, Rusch, Douglas B, Lai, Zhongwu, Kraft, Cheryl L, Abril, Josep F, Anthouard, Veronique, Arensburger, Peter, Atkinson, Peter W, Baden, Holly, de Berardinis, Veronique, Baldwin, Danita, Benes, Vladimir, Biedler, Jim, Blass, Claudia, Bolanos, Randall, Boscus, Didier, Barnstead, Mary, Cai, Shuang, Center, Angela, Chaturverdi, Kabir, Christophides, George K, Chrystal, Mathew A, Clamp, Michele, Cravchik, Anibal, Curwen, Val, Dana, Ali, Delcher, Art, Dew, Ian, Evans, Cheryl A, Flanigan, Michael, Grundschober-Freimoser, Anne, Friedli, Lisa, Gu, Zhiping, Guan, Ping, Guigo, Roderic, Hillenmeyer, Maureen E, Hladun, Susanne L, Hogan, James R, Hong, Young S, Hoover, Jeffrey, Jaillon, Olivier, Ke, Zhaoxi, Kodira, Chinnappa, Kokoza, Elena, Koutsos, Anastasios, Letunic, Ivica, Levitsky, Alex, Liang, Yong, Lin, Jhy-Jhu, Lobo, Neil F, Lopez, John R, Malek, Joel A, McIntosh, Tina C, Meister, Stephan, Miller, Jason, Mobarry, Clark, Mongin, Emmanuel, Murphy, Sean D, O'Brochta, David A, Pfannkoch, Cynthia, Qi, Rong, Regier, Megan A, Remington, Karin, Shao, Hongguang, Sharakhova, Maria V, Sitter, Cynthia D, Shetty, Jyoti, Smith, Thomas J, Strong, Renee, Sun, Jingtao, Thomasova, Dana, Ton, Lucas Q, Topalis, Pantelis, Tu, Zhijian, Unger, Maria F, Walenz, Brian, Wang, Aihui, Wang, Jian, Wang, Mei, Wang, Xuelan, Woodford, Kerry J, Wortman, Jennifer R, Wu, Martin, Yao, Alison, Zdobnov, Evgeny M, Zhang, Hongyu, Zhao, Qi, Zhao, Shaying, Zhu, Shiaoping C, Zhimulev, Igor, Coluzzi, Mario, della Torre, Alessandra, Roth, Charles W, Louis, Christos, Kalush, Francis, Mural, Richard J, Myers, Eugene W, Adams, Mark D, Smith, Hamilton O, Broder, Samuel, Gardner, Malcolm J, Fraser, Claire M, Birney, Ewan, Bork, Peer, Brey, Paul T, Venter, J Craig, Weissenbach, Jean, Kafatos, Fotis C, Collins, Frank H, Hoffman, Stephen L
Publication Abstract
Anopheles gambiae is the principal vector of malaria, a disease that afflicts more than 500 million people and causes more than 1 million deaths each year. Tenfold shotgun sequence coverage was obtained from the PEST strain of A. gambiae and assembled into scaffolds that span 278 million base pairs. A total of 91% of the genome was organized in 303 scaffolds; the largest scaffold was 23.1 million base pairs. There was substantial genetic variation within this strain, and the apparent existence of two haplotypes of approximately equal frequency ("dual haplotypes") in a substantial fraction of the genome likely reflects the outbred nature of the PEST strain. The sequence produced a conservative inference of more than 400,000 single-nucleotide polymorphisms that showed a markedly bimodal density distribution. Analysis of the genome sequence revealed strong evidence for about 14,000 protein-encoding transcripts. Prominent expansions in specific families of proteins likely involved in cell adhesion and immunity were noted. An expressed sequence tag analysis of genes regulated by blood feeding provided insights into the physiological adaptations of a hematophagous insect.

Science (New York, N.Y.), 2001
Authors
Venter, J C, Adams, M D, Myers, E W, Li, P W, Mural, R J, Sutton, G G, Smith, H O, Yandell, M, Evans, C A, Holt, R A, Gocayne, J D, Amanatides, P, Ballew, R M, Huson, D H, Wortman, J R, Zhang, Q, Kodira, C D, Zheng, X H, Chen, L, Skupski, M, Subramanian, G, Thomas, P D, Zhang, J, Gabor Miklos, G L, Nelson, C, Broder, S, Clark, A G, Nadeau, J, McKusick, V A, Zinder, N, Levine, A J, Roberts, R J, Simon, M, Slayman, C, Hunkapiller, M, Bolanos, R, Delcher, A, Dew, I, Fasulo, D, Flanigan, M, Florea, L, Halpern, A, Hannenhalli, S, Kravitz, S, Levy, S, Mobarry, C, Reinert, K, Remington, K, Abu-Threideh, J, Beasley, E, Biddick, K, Bonazzi, V, Brandon, R, Cargill, M, Chandramouliswaran, I, Charlab, R, Chaturvedi, K, Deng, Z, Di Francesco, V, Dunn, P, Eilbeck, K, Evangelista, C, Gabrielian, A E, Gan, W, Ge, W, Gong, F, Gu, Z, Guan, P, Heiman, T J, Higgins, M E, Ji, R R, Ke, Z, Ketchum, K A, Lai, Z, Lei, Y, Li, Z, Li, J, Liang, Y, Lin, X, Lu, F, Merkulov, G V, Milshina, N, Moore, H M, Naik, A K, Narayan, V A, Neelam, B, Nusskern, D, Rusch, D B, Salzberg, S, Shao, W, Shue, B, Sun, J, Wang, Z, Wang, A, Wang, X, Wang, J, Wei, M, Wides, R, Xiao, C, Yan, C, Yao, A, Ye, J, Zhan, M, Zhang, W, Zhang, H, Zhao, Q, Zheng, L, Zhong, F, Zhong, W, Zhu, S, Zhao, S, Gilbert, D, Baumhueter, S, Spier, G, Carter, C, Cravchik, A, Woodage, T, Ali, F, An, H, Awe, A, Baldwin, D, Baden, H, Barnstead, M, Barrow, I, Beeson, K, Busam, D, Carver, A, Center, A, Cheng, M L, Curry, L, Danaher, S, Davenport, L, Desilets, R, Dietz, S, Dodson, K, Doup, L, Ferriera, S, Garg, N, Gluecksmann, A, Hart, B, Haynes, J, Haynes, C, Heiner, C, Hladun, S, Hostin, D, Houck, J, Howland, T, Ibegwam, C, Johnson, J, Kalush, F, Kline, L, Koduru, S, Love, A, Mann, F, May, D, McCawley, S, McIntosh, T, McMullen, I, Moy, M, Moy, L, Murphy, B, Nelson, K, Pfannkoch, C, Pratts, E, Puri, V, Qureshi, H, Reardon, M, Rodriguez, R, Rogers, Y H, Romblad, D, Ruhfel, B, Scott, R, Sitter, C, Smallwood, M, Stewart, E, Strong, R, Suh, E, Thomas, R, Tint, N N, Tse, S, Vech, C, Wang, G, Wetter, J, Williams, S, Williams, M, Windsor, S, Winn-Deen, E, Wolfe, K, Zaveri, J, Zaveri, K, Abril, J F, Guigó, R, Campbell, M J, Sjolander, K V, Karlak, B, Kejariwal, A, Mi, H, Lazareva, B, Hatton, T, Narechania, A, Diemer, K, Muruganujan, A, Guo, N, Sato, S, Bafna, V, Istrail, S, Lippert, R, Schwartz, R, Walenz, B, Yooseph, S, Allen, D, Basu, A, Baxendale, J, Blick, L, Caminha, M, Carnes-Stine, J, Caulk, P, Chiang, Y H, Coyne, M, Dahlke, C, Mays, A, Dombroski, M, Donnelly, M, Ely, D, Esparham, S, Fosler, C, Gire, H, Glanowski, S, Glasser, K, Glodek, A, Gorokhov, M, Graham, K, Gropman, B, Harris, M, Heil, J, Henderson, S, Hoover, J, Jennings, D, Jordan, C, Jordan, J, Kasha, J, Kagan, L, Kraft, C, Levitsky, A, Lewis, M, Liu, X, Lopez, J, Ma, D, Majoros, W, McDaniel, J, Murphy, S, Newman, M, Nguyen, T, Nguyen, N, Nodell, M, Pan, S, Peck, J, Peterson, M, Rowe, W, Sanders, R, Scott, J, Simpson, M, Smith, T, Sprague, A, Stockwell, T, Turner, R, Venter, E, Wang, M, Wen, M, Wu, D, Wu, M, Xia, A, Zandieh, A, Zhu, X
Publication Abstract
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Science (New York, N.Y.), 1997
Authors
Nakamura, T M, Morin, G B, Chapman, K B, Weinrich, S L, Andrews, W H, Lingner, J, Harley, C B, Cech, T R
Publication Abstract
Catalytic protein subunits of telomerase from the ciliate Euplotes aediculatus and the yeast Saccharomyces cerevisiae contain reverse transcriptase motifs. Here the homologous genes from the fission yeast Schizosaccharomyces pombe and human are identified. Disruption of the S. pombe gene resulted in telomere shortening and senescence, and expression of mRNA from the human gene correlated with telomerase activity in cell lines. Sequence comparisons placed the telomerase proteins in the reverse transcriptase family but revealed hallmarks that distinguish them from retroviral and retrotransposon relatives. Thus, the proposed telomerase catalytic subunits are phylogenetically conserved and represent a deep branch in the evolution of reverse transcriptases.
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