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340 results on '"Stupka, Elia"'

1. The BioMart community portal: an innovative alternative to large, centralized data repositories.

Author

Smedley, Damian, Haider, Syed, Durinck, Steffen, Pandini, Luca, Provero, Paolo, Allen, James, Arnaiz, Olivier, Awedh, Mohammad Hamza, Baldock, Richard, Barbiera, Giulia, Bardou, Philippe, Beck, Tim, Blake, Andrew, Bonierbale, Merideth, Brookes, Anthony J, Bucci, Gabriele, Buetti, Iwan, Burge, Sarah, Cabau, Cédric, Carlson, Joseph W, Chelala, Claude, Chrysostomou, Charalambos, Cittaro, Davide, Collin, Olivier, Cordova, Raul, Cutts, Rosalind J, Dassi, Erik, Di Genova, Alex, Djari, Anis, Esposito, Anthony, Estrella, Heather, Eyras, Eduardo, Fernandez-Banet, Julio, Forbes, Simon, Free, Robert C, Fujisawa, Takatomo, Gadaleta, Emanuela, Garcia-Manteiga, Jose M, Goodstein, David, Gray, Kristian, Guerra-Assunção, José Afonso, Haggarty, Bernard, Han, Dong-Jin, Han, Byung Woo, Harris, Todd, Harshbarger, Jayson, Hastings, Robert K, Hayes, Richard D, Hoede, Claire, Hu, Shen, Hu, Zhi-Liang, Hutchins, Lucie, Kan, Zhengyan, Kawaji, Hideya, Keliet, Aminah, Kerhornou, Arnaud, Kim, Sunghoon, Kinsella, Rhoda, Klopp, Christophe, Kong, Lei, Lawson, Daniel, Lazarevic, Dejan, Lee, Ji-Hyun, Letellier, Thomas, Li, Chuan-Yun, Lio, Pietro, Liu, Chu-Jun, Luo, Jie, Maass, Alejandro, Mariette, Jerome, Maurel, Thomas, Merella, Stefania, Mohamed, Azza Mostafa, Moreews, Francois, Nabihoudine, Ibounyamine, Ndegwa, Nelson, Noirot, Céline, Perez-Llamas, Cristian, Primig, Michael, Quattrone, Alessandro, Quesneville, Hadi, Rambaldi, Davide, Reecy, James, Riba, Michela, Rosanoff, Steven, Saddiq, Amna Ali, Salas, Elisa, Sallou, Olivier, Shepherd, Rebecca, Simon, Reinhard, Sperling, Linda, Spooner, William, Staines, Daniel M, Steinbach, Delphine, Stone, Kevin, Stupka, Elia, Teague, Jon W, Dayem Ullah, Abu Z, Wang, Jun, and Ware, Doreen

Subjects
Humans, Neoplasms, Proteomics, Genomics, Internet, Database Management Systems, Developmental Biology, Environmental Sciences, Biological Sciences, Information and Computing Sciences
Abstract

The BioMart Community Portal (www.biomart.org) is a community-driven effort to provide a unified interface to biomedical databases that are distributed worldwide. The portal provides access to numerous database projects supported by 30 scientific organizations. It includes over 800 different biological datasets spanning genomics, proteomics, model organisms, cancer data, ontology information and more. All resources available through the portal are independently administered and funded by their host organizations. The BioMart data federation technology provides a unified interface to all the available data. The latest version of the portal comes with many new databases that have been created by our ever-growing community. It also comes with better support and extensibility for data analysis and visualization tools. A new addition to our toolbox, the enrichment analysis tool is now accessible through graphical and web service interface. The BioMart community portal averages over one million requests per day. Building on this level of service and the wealth of information that has become available, the BioMart Community Portal has introduced a new, more scalable and cheaper alternative to the large data stores maintained by specialized organizations.

Published
2015

2. The kinetochore protein, CENPF, is mutated in human ciliopathy and microcephaly phenotypes

Author

Waters, Aoife M, Asfahani, Rowan, Carroll, Paula, Bicknell, Louise, Lescai, Francesco, Bright, Alison, Chanudet, Estelle, Brooks, Anthony, Christou-Savina, Sonja, Osman, Guled, Walsh, Patrick, Bacchelli, Chiara, Chapgier, Ariane, Vernay, Bertrand, Bader, David M, Deshpande, Charu, O' Sullivan, Mary, Ocaka, Louise, Stanescu, Horia, Stewart, Helen S, Hildebrandt, Friedhelm, Otto, Edgar, Johnson, Colin A, Szymanska, Katarzyna, Katsanis, Nicholas, Davis, Erica, Kleta, Robert, Hubank, Mike, Doxsey, Stephen, Jackson, Andrew, Stupka, Elia, Winey, Mark, and Beales, Philip L

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Rare Diseases, Pediatric, Human Genome, Congenital Structural Anomalies, Aetiology, 2.1 Biological and endogenous factors, Animals, Centrioles, Chromosomal Proteins, Non-Histone, Cilia, Exome, Female, Fetus, Genetics, Medical, HEK293 Cells, High-Throughput Nucleotide Sequencing, Humans, Male, Mice, Microcephaly, Microfilament Proteins, Mutation, NIH 3T3 Cells, Pedigree, Pregnancy, Zebrafish, CENPF, Ciliopathy, Clinical genetics, Molecular genetics, Medical and Health Sciences, Genetics & Heredity, Clinical sciences
Abstract

BackgroundMutations in microtubule-regulating genes are associated with disorders of neuronal migration and microcephaly. Regulation of centriole length has been shown to underlie the pathogenesis of certain ciliopathy phenotypes. Using a next-generation sequencing approach, we identified mutations in a novel centriolar disease gene in a kindred with an embryonic lethal ciliopathy phenotype and in a patient with primary microcephaly.Methods and resultsWhole exome sequencing data from a non-consanguineous Caucasian kindred exhibiting mid-gestation lethality and ciliopathic malformations revealed two novel non-synonymous variants in CENPF, a microtubule-regulating gene. All four affected fetuses showed segregation for two mutated alleles [IVS5-2A>C, predicted to abolish the consensus splice-acceptor site from exon 6; c.1744G>T, p.E582X]. In a second unrelated patient exhibiting microcephaly, we identified two CENPF mutations [c.1744G>T, p.E582X; c.8692 C>T, p.R2898X] by whole exome sequencing. We found that CENP-F colocalised with Ninein at the subdistal appendages of the mother centriole in mouse inner medullary collecting duct cells. Intraflagellar transport protein-88 (IFT-88) colocalised with CENP-F along the ciliary axonemes of renal epithelial cells in age-matched control human fetuses but did not in truncated cilia of mutant CENPF kidneys. Pairwise co-immunoprecipitation assays of mitotic and serum-starved HEKT293 cells confirmed that IFT88 precipitates with endogenous CENP-F.ConclusionsOur data identify CENPF as a new centriolar disease gene implicated in severe human ciliopathy and microcephaly related phenotypes. CENP-F has a novel putative function in ciliogenesis and cortical neurogenesis.

Published
2015

4. Whole-Genome Shotgun Assembly and Analysis of the Genome of Fugu rubripes

Author

Aparicio, Samuel, Chapman, Jarrod, Stupka, Elia, Putnam, Nik, Chia, Jer-ming, Dehal, Paramvir, Christoffels, Alan, Rash, Sam, Hoon, Shawn, Smit, Arian, Roach, Jared, Oh, Tania, Ho, Isaac Y., Wong, Marie, Detter, Chris, Verhoef, Frans, Predki, Paul, Tay, Alice, Lucas, Susan, Richardson, Paul, Smith, Sarah F., Clark, Melody S., Doggett, Norman, Zharkikh, Andrey, Tavtigian, Sean V., Pruss, Dmitry, Barnstead, Mary, Evans, Cheryl, Baden, Holly, Powell, Justin, Glusman, Gustavo, Rowen, Lee, Hood, Leroy, Tan, Y. H., Elgar, Greg, Hawkins, Trevor, Venkatesh, Byrappa, Rokhsar, Daniel, and Brenner, Sydney

Published
2002

5. The case of an APDS patient: Defects in maturation and function and decreased in vitro anti-mycobacterial activity in the myeloid compartment

Author

Chiriaco, Maria, Brigida, Immacolata, Ariganello, Paola, Di Cesare, Silvia, Di Matteo, Gigliola, Taus, Francesco, Cittaro, Davide, Lazarevic, Dejan, Scarselli, Alessia, Santilli, Veronica, Attardi, Enrico, Stupka, Elia, Giannelli, Stefania, Fraziano, Maurizio, Finocchi, Andrea, Rossi, Paolo, Aiuti, Alessandro, Palma, Paolo, and Cancrini, Caterina

Published
2017
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6. BASC: an integrated bioinformatics system for Brassica research

Author

Erwin, Timothy A, Jewell, Erica G, Love, Christopher G, Lim, Geraldine AC, Li, Xi, Chapman, Ross, Batley, Jacqueline, Stajich, Jason E, Mongin, Emmanuel, Stupka, Elia, Ross, Bruce, Spangenberg, German, and Edwards, David

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Arabidopsis, Brassica, Chromosome Mapping, Computational Biology, Databases, Genetic, Expressed Sequence Tags, Gene Expression Profiling, Genetic Markers, Genome, Plant, Genomics, Internet, Phenotype, Quantitative Trait Loci, Software, Systems Integration, User-Computer Interface, Environmental Sciences, Information and Computing Sciences, Developmental Biology, Biological sciences, Chemical sciences, Environmental sciences
Abstract

The BASC system provides tools for the integrated mining and browsing of genetic, genomic and phenotypic data. This public resource hosts information on Brassica species supporting the Multinational Brassica Genome Sequencing Project, and is based upon five distinct modules, ESTDB, Microarray, MarkerQTL, CMap and EnsEMBL. ESTDB hosts expressed gene sequences and related annotation derived from comparison with GenBank, UniRef and the genome sequence of Arabidopsis. The Microarray module hosts gene expression information related to genes annotated within ESTDB. MarkerQTL is the most complex module and integrates information on genetic markers, maps, individuals, genotypes and traits. Two further modules include an Arabidopsis EnsEMBL genome viewer and the CMap comparative genetic map viewer for the visualization and integration of genetic and genomic data. The database is accessible at http://bioinformatics.pbcbasc.latrobe.edu.au.

Published
2007

8. A Whole-Genome Sequencing Study Implicates GRAMD1B in Multiple Sclerosis Susceptibility

Author

Esposito, Federica, primary, Osiceanu, Ana Maria, additional, Sorosina, Melissa, additional, Ottoboni, Linda, additional, Bollman, Bryan, additional, Santoro, Silvia, additional, Bettegazzi, Barbara, additional, Zauli, Andrea, additional, Clarelli, Ferdinando, additional, Mascia, Elisabetta, additional, Calabria, Andrea, additional, Zacchetti, Daniele, additional, Capra, Ruggero, additional, Ferrari, Maurizio, additional, Provero, Paolo, additional, Lazarevic, Dejan, additional, Cittaro, Davide, additional, Carrera, Paola, additional, Patsopoulos, Nikolaos, additional, Toniolo, Daniela, additional, Sadovnick, A Dessa, additional, Martino, Gianvito, additional, De Jager, Philip L., additional, Comi, Giancarlo, additional, Stupka, Elia, additional, Vilariño-Güell, Carles, additional, Piccio, Laura, additional, and Martinelli Boneschi, Filippo, additional

Published
2022
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12. Lentiviral Hematopoietic Stem Cell Gene Therapy Benefits Metachromatic Leukodystrophy

Author

Biffi, Alessandra, Montini, Eugenio, Lorioli, Laura, Cesani, Martina, Fumagalli, Francesca, Plati, Tiziana, Baldoli, Cristina, Martino, Sabata, Calabria, Andrea, Canale, Sabrina, Benedicenti, Fabrizio, Vallanti, Giuliana, Biasco, Luca, Leo, Simone, Kabbara, Nabil, Zanetti, Gianluigi, Rizzo, William B., Mehta, Nalini A. L., Cicalese, Maria Pia, Casiraghi, Miriam, Boelens, Jaap J., Del Carro, Ubaldo, Dow, David J., Schmidt, Manfred, Assanelli, Andrea, Neduva, Victor, Di Serio, Clelia, Stupka, Elia, Gardner, Jason, von Kalle, Christof, Bordignon, Claudio, Ciceri, Fabio, Rovelli, Attilio, Roncarolo, Maria Grazia, Aiuti, Alessandro, Sessa, Maria, and Naldini, Luigi

Published
2013

15. Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma

Author

Okosun, Jessica, Bödör, Csaba, Wang, Jun, Araf, Shamzah, Yang, Cheng-Yuan, Pan, Chenyi, Boller, Sören, Cittaro, Davide, Bozek, Monika, Iqbal, Sameena, Matthews, Janet, Wrench, David, Marzec, Jacek, Tawana, Kiran, Popov, Nikolay, O'Riain, Ciaran, O'Shea, Derville, Carlotti, Emanuela, Davies, Andrew, Lawrie, Charles H, Matolcsy, András, Calaminici, Maria, Norton, Andrew, Byers, Richard J, Mein, Charles, Stupka, Elia, Lister, T Andrew, Lenz, Georg, Montoto, Silvia, Gribben, John G, Fan, Yuhong, Grosschedl, Rudolf, Chelala, Claude, and Fitzgibbon, Jude

Published
2014
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18. Genome-wide signatures of convergent evolution in echolocating mammals

Author

Parker, Joe, Tsagkogeorga, Georgia, Cotton, James A., Liu, Yuan, Provero, Paolo, Stupka, Elia, and Rossiter, Stephen J.

Subjects
Delphinidae -- Physiological aspects -- Genetic aspects -- Research, Dolphins -- Physiological aspects -- Genetic aspects -- Research, Echolocation (Physiology) -- Analysis -- Physiological aspects -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Evolution is typically thought to proceed through divergence of genes, proteins and ultimately phenotypes (1-3). However, similar traits might also evolve convergently in unrelated taxa owing to similar selection pressures (4,5). Adaptive phenotypic convergence is widespread in nature, and recent results from several genes have suggested that this phenomenon is powerful enough to also drive recurrent evolution at the sequence level (6-9). Where homoplasious substitutions do occur these have long been considered the result of neutral processes. However, recent studies have demonstrated that adaptive convergent sequence evolution can be detected in vertebrates using statistical methods that model parallel evolution (9,10), although the extent to which sequence convergence between genera occurs across genomes is unknown. Here we analyse genomic sequence data in mammals that have independently evolved echolocation and show that convergence is not a rare process restricted to several loci but is instead widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Systematic analyses of convergent sequence evolution in 805,053 amino acids within 2,326 orthologous coding gene sequences compared across 22 mammals (including four newly sequenced bat genomes) revealed signatures consistent with convergence in nearly 200 loci. Strong and significant support for convergence among bats and the bottlenose dolphin was seen in numerous genes linked to hearing or deafness, consistent with an involvement in echolocation. Unexpectedly, we also found convergence in many genes linked to vision: the convergent signal of many sensory genes was robustly correlated with the strength of natural selection. This first attempt to detect genome-wide convergent sequence evolution across divergent taxa reveals the phenomenon to be much more pervasive than previously recognized., Echolocation is a complex phenotypic trait that has evolved independently in bats and whales, and which involves the production, reception and auditory processing of ultrasonic pulses for obstacle avoidance, orientation [...]

Published
2013

20. The combination of transcriptomics and informatics identifies pathways targeted by miR-204 during neurogenesis and axon guidance

Author

Conte, Ivan, Merella, Stefania, Garcia-Manteiga, Jose Manuel, Migliore, Chiara, Lazarevic, Dejan, Carrella, Sabrina, Marco-Ferreres, Raquel, Avellino, Raffaella, Davidson, Nathan Paul, Emmett, Warren, Sanges, Remo, Bockett, Nicholas, Van Heel, David, Meroni, Germana, Bovolenta, Paola, Stupka, Elia, and Banfi, Sandro

Published
2014
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21. Mutation of SALL2 causes recessive ocular coloboma in humans and mice

Author

Kelberman, Daniel, Islam, Lily, Lakowski, Jörn, Bacchelli, Chiara, Chanudet, Estelle, Lescai, Francesco, Patel, Aara, Stupka, Elia, Buck, Anja, Wolf, Stephan, Beales, Philip L., Jacques, Thomas S., Bitner-Glindzicz, Maria, Liasis, Alki, Lehmann, Ordan J., Kohlhase, Jürgen, Nischal, Ken K., and Sowden, Jane C.

Published
2014
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23. ARNT2 mutation causes hypopituitarism, post-natal microcephaly, visual and renal anomalies

Author

Webb, Emma A., AlMutair, Angham, Kelberman, Daniel, Bacchelli, Chiara, Chanudet, Estelle, Lescai, Francesco, Andoniadou, Cynthia L., Banyan, Abdul, Alsawaid, Al, Alrifai, Muhammad T., Alahmesh, Mohammed A., Balwi, M., Mousavy-Gharavy, Seyedeh N., Lukovic, Biljana, Burke, Derek, McCabe, Mark J., Kasia, Tessa, Kleta, Robert, Stupka, Elia, Beales, Philip L., Thompson, Dorothy A., Chong, W. Kling, Alkuraya, Fowzan S., Martinez-Barbera, Juan-Pedro, Sowden, Jane C., and Dattani, Mehul T.

Published
2013
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24. Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

Author

Sanges, Remo, Hadzhiev, Yavor, Gueroult-Bellone, Marion, Roure, Agnes, Ferg, Marco, Meola, Nicola, Amore, Gabriele, Basu, Swaraj, Brown, Euan R., De Simone, Marco, Petrera, Francesca, Licastro, Danilo, Strähle, Uwe, Banfi, Sandro, Lemaire, Patrick, Birney, Ewan, Müller, Ferenc, and Stupka, Elia

Published
2013
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26. Initial sequencing and analysis of the human genome

Author

Lander, Eric S., Linton, Lauren M., Birren, Bruce, Nusbaum, Chad, Zody, Michael C., Baldwin, Jennifer, Devon, Keri, Dewar, Ken, Doyle, Michael, FitzHugh, William, Funke, Roel, Gage, Diane, Harris, Katrina, Heaford, Andrew, Howland, John, Kann, Lisa, Lehoczky, Jessica, LeVine, Rosie, McEwan, Paul, McKernan, Kevin, Meldrim, James, Mesirov, Jill P., Miranda, Cher, Morris, William, Naylor, Jerome, Raymond, Christina, Rosetti, Mark, Santos, Ralph, Sheridan, Andrew, Sougnez, Carrie, Stange-Thomann, Nicole, Stojanovic, Nikola, Subramanian, Aravind, Wyman, Dudley, Rogers, Jane, Sulston, John, Ainscough, Rachael, Beck, Stephan, Bentley, David, Burton, John, Clee, Christopher, Carter, Nigel, Coulson, Alan, Deadman, Rebecca, Deloukas, Panos, Dunham, Andrew, Dunham, Ian, Durbin, Richard, French, Lisa, Grafham, Darren, Gregory, Simon, Hubbard, Tim, Humphray, Sean, Hunt, Adrienne, Jones, Matthew, Lloyd, Christine, McMurray, Amanda, Matthews, Lucy, Mercer, Simon, Milne, Sarah, Mullikin, James C., Mungall, Andrew, Plumb, Robert, Ross, Mark, Shownkeen, Ratna, Sims, Sarah, Waterston, Robert H., Wilson, Richard K., Hillier, LaDeana W., McPherson, John D., Marra, Marco A., Mardis, Elaine R., Fulton, Lucinda A., Chinwalla, Asif T., Pepin, Kymberlie H., Gish, Warren R., Chissoe, Stephanie L., Wendl, Michael C., Delehaunty, Kim D., Miner, Tracie L., Delehaunty, Andrew, Kramer, Jason B., Cook, Lisa L., Fulton, Robert S., Johnson, Douglas L., Minx, Patrick J., Clifton, Sandra W., Hawkins, Trevor, Branscomb, Elbert, Predki, Paul, Richardson, Paul, Wenning, Sarah, Slezak, Tom, Doggett, Norman, Cheng, Jan-Fang, Olsen, Anne, Lucas, Susan, Elkin, Christopher, Uberbacher, Edward, Frazier, Marvin, Gibbs, Richard A., Muzny, Donna M., Scherer, Steven E., Bouck, John B., Sodergren, Erica J., Worley, Kim C., Rives, Catherine M., Gorrell, James H., Metzker, Michael L., Naylor, Susan L., Kucherlapati, Raju S., Nelson, David L., Weinstock, George M., Sakaki, Yoshiyuki, Fujiyama, Asao, Hattori, Masahira, Yada, Tetsushi, Toyoda, Atsushi, Itoh, Takehiko, Kawagoe, Chiharu, Watanabe, Hidemi, Totoki, Yasushi, Taylor, Todd, Weissenbach, Jean, Heilig, Roland, Saurin, William, Artiguenave, Francois, Brottier, Philippe, Bruls, Thomas, Pelletier, Eric, Robert, Catherine, Wincker, Patrick, Rosenthal, Andre, Platzer, Matthias, Nyakatura, Gerald, Taudien, Stefan, Rump, Andreas, Smith, Douglas R., Doucette-Stamm, Lynn, Rubenfield, Marc, Weinstock, Keith, Lee, Hong Mei, Dubois, JoAnn, Yang, Huanming, Yu, Jun, Wang, Jian, Huang, Guyang, Gu, Jun, Hood, Leroy, Rowen, Lee, Madan, Anup, Qin, Shizen, Davis, Ronald W., Federspiel, Nancy A., Abola, A. Pia, Proctor, Michael J., Roe, Bruce A., Chen, Feng, Pan, Huaqin, Ramser, Juliane, Lehrach, Hans, Reinhardt, Richard, McCombie, W. Richard, de la Bastide, Melissa, Dedhia, Neilay, Blocker, Helmut, Hornischer, Klaus, Nordsiek, Gabriele, Agarwala, Richa, Aravind, L., Bailey, Jeffrey A., Bateman, Alex, Batzoglou, Serafim, Birney, Ewan, Bork, Peer, Brown, Daniel G., Burge, Christopher B., Cerutti, Lorenzo, Chen, Hsiu-Chuan, Church, Deanna, Clamp, Michele, Copley, Richard R., Doerks, Tobias, Eddy, Sean R., Eichler, Evan E., Furey, Terrence S., Galagan, James, Gilbert, James G. R., Harmon, Cyrus, Hayashizaki, Yoshihide, Haussler, David, Hermjakob, Henning, Hokamp, Karsten, Jang, Wonhee, Johnson, L. Steven, Jones, Thomas A., Kasif, Simon, Kaspryzk, Arek, Kennedy, Scot, Kent, W. James, Kitts, Paul, Koonin, Eugene V., Korf, Ian, Kulp, David, Lancet, Doron, Lowe, Todd M., McLysaght, Aoife, Mikkelsen, Tarjei, Moran, John V., Mulder, Nicola, Pollara, Victor J., Ponting, Chris P., Schuler, Greg, Schultz, Jorg, Slater, Guy, Smit, Arian F. A., Stupka, Elia, Szustakowki, Joseph, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Wallis, John, Wheeler, Raymond, Williams, Alan, Wolf, Yuri I., Wolfe, Kenneth H., Yang, Shiaw-Pyng, Yeh, Ru-Fang, Collins, Francis, Guyer, Mark S., Peterson, Jane, Felsenfeld, Adam, Wetterstrand, Kris A., Myers, Richard M., Schmutz, Jeremy, Dickson, Mark, Grimwood, Jane, Cox, David R., Olson, Maynard V., Kaul, Rajinder, Raymond, Christopher, Shimizu, Nobuyoshi, Kawasaki, Kazuhiko, Minoshima, Shinsei, Evans, Glen A., Athanasiou, Maria, Schultz, Roger, Patrinos, Aristides, and Morgan, Michael J.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): International Human Genome Sequencing Consortium; Whitehead Institute for Biomedical Research, Center for Genome Research:; Eric S. Lander [1]; Lauren M. Linton [1]; Bruce Birren [1]; Chad Nusbaum [1]; Michael [...]

Published
2001
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28. Abstract 28: Identification of multisite real-world patient cohorts to enable immunotherapy utilization and safety assessment

Author

Del Vecchio Fitz, Catherine, primary, Eldridge, Elizabeth, additional, Antonopoulos, Alyssa, additional, Petrone, Paula, additional, Caldwell, Will, additional, Corbett, Ed, additional, Flaster, Amy, additional, Rimmasch, Holly, additional, Albayrak, Adem, additional, Sanders, Dale, additional, Mahmood, Sadiqa, additional, and Stupka, Elia, additional

Published
2020
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31. Mixed lineage kinase 3 gene mutations in mismatch repair deficient gastrointestinal tumours

Author

Velho, Sérgia, Oliveira, Carla, Paredes, Joana, Sousa, Sónia, Leite, Marina, Matos, Paulo, Milanezi, Fernanda, Ribeiro, Ana Sofia, Mendes, Nuno, Licastro, Danilo, Karhu, Auli, Oliveira, Maria José, Ligtenberg, Marjolijn, Hamelin, Richard, Carneiro, Fátima, Lindblom, Annika, Peltomaki, Paivi, Castedo, Sérgio, Schwartz, Simó, Jr, Jordan, Peter, Aaltonen, Lauri A., Hofstra, Robert M.W., Suriano, Gianpaolo, Stupka, Elia, Fialho, Arsenio M., and Seruca, Raquel

Published
2010

33. Germline CDH1 deletions in hereditary diffuse gastric cancer families

Author

Oliveira, Carla, Senz, Janine, Kaurah, Pardeep, Pinheiro, Hugo, Sanges, Remo, Haegert, Anne, Corso, Giovanni, Schouten, Jan, Fitzgerald, Rebecca, Vogelsang, Holger, Keller, Gisela, Dwerryhouse, Sarah, Grimmer, Donna, Chin, Suet-Feung, Yang, Han-Kwang, Jackson, Charles E., Seruca, Raquel, Roviello, Franco, Stupka, Elia, Caldas, Carlos, and Huntsman, David

Published
2009

35. Additional file 5: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Figure S2. (a) Boxplots showing the expression levels of FOXM1 mRNA in breast cancer samples with high and low expression of HMGA1 (b) Schematic representation of the pGL3-5BS reporter vector. The 5 binding elements of FOXM1 are represented with white boxes. (c) Western blot analysis of HEK293T transfected with pEGFP-FOXM1 (600 ng) and increasing amounts (200, 400 and 600 ng) of pEGFP-HMGA1, using an α-GFP as primary antibody. pRL-CMV Renilla luciferase expression vector was used to normalize for transfection efficiencies. (d) Confirmation of gene silencing. qRT-PCR of HMGA1 and FOXM1 levels after 72 h of HMGA1 (grey bar), FOXM1 (light blue bar) and HMGA1/FOXM1 (purple bar) silencing in MDA-MB-231 cell line. GAPDH was used for normalization. The data are compared to siCTRL and are presented as the mean ± SD (n = 3), ***p

Published
2019
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36. Additional file 4: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Table S4. List of differentially expressed genes after HMGA1-silencing at 24 (a) and 72 (b) hours in common with FOXM1-gene network. (PDF 35 kb)

Published
2019
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37. Additional file 1: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Subjects
body regions, nervous system, fungi
Abstract

Table S1. List of primers used in qRT-PCR analyses. (PDF 44 kb)

Published
2019
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38. Additional file 2: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Figure S1. Clustering of gene expression data showing expression levels at different time points before and after silencing of HMGA1. Color intensity corresponds to the row Z-Score. (PDF 1107 kb)

Published
2019
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39. Additional file 6: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Figure S3. (a) Representative immunofluorescence images of the translocation of FOXM1 (green) and its colocalization with the Subunit β5 of the proteasome (red) in MDA-MB-231 control cells versus cells silenced for HMGA1. Images were taken at 60X magnification. (b) and (c) Representative immunofluorescence images of the translocation of FOXM1 (green) and its colocalization with the Subunit β2 (b) and β5 (c) of the proteasome (red) in MDA-MB-157 control cells versus cells silenced for HMGA1. Images were taken at 60X magnification. (d) Representative images of FOXM1-GFP after HMGA1 silencing and pEGFP-FOXM1 transfection in MDA-MB-231 cells. White arrows indicate the translocation of FOXM1 after HMGA1 silencing. (e) Representative images of FOXM1-GFP after HMGA1 silencing and pEGFP-FOXM1 transfection in HEK293T cells. White arrows indicate the cellular localization of FOXM1 after HMGA1 silencing. (PDF 1197 kb)

Published
2019
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40. Additional file 7: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Figure S4. (a) Boxplots showing the expression levels of VEGFA mRNA in breast cancer samples. The samples were stratified based on HMGA1 (left) and FOXM1 (right) mRNA expression levels. (b) and (c) Luciferase assays on HEK293T cells transiently co-transfected with the luciferase reporter plasmid pGL4.10-VEGFprom (− 1000–1) with increasing quantities of either the expression plasmid pEGFP-FOXM1 (b) or pEGFP-HMGA1 (c). pRL-CMV Renilla luciferase expression vector was included to normalize for transfection efficiencies. Values are reported as relative luciferase activity comparing to cells transfected with the expression control vector pEGFP. The data are represented as the mean ± SD (n = 3). **p

Published
2019
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41. Additional file 8: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Figure S5. (a) Schematic representation of the bioinformatic analysis of the 1000 bp VEGFA promoter sequence cloned upstream the luciferase sequence in pGL4.10-VEGFprom (− 1000–1) used in reporter experiments. FOXM1 binding sites are represented with light blue ovals, whereas the AT-enriched sequences bound by HMGA1 are figured as grey boxes. In detailed, we found several AT-rich sequences in the region from – 979 to 907 bp, from − 641 to − 521 bp, from − 355 to − 322 bp, from − 169 to − 75 bp, where the AT stretches are particularly long, and from − 17 to − 13 bp from the TSS of the VEGFA promoter. In addition, we found 9 putative FOXM1 binding sites from − 993 to − 922 bp, from − 643 to – 638 bp, from − 326 to − 322 bp, from − 124 to − 104 bp, where it is located the FOXM1 preferential binding sequence TAAACA, and from − 17 to − 13 bp from the TSS of the VEGFA promoter. (b) Schematic representation of deletion reporter vectors pGL4.10-VEGF (− 1000–500) and pGL4.10-VEGF (− 500–1) obtained from pGL4.10-VEGFprom (− 1000–1). (c) Luciferase assay on HEK293T cells transiently co-transfected with the luciferase reporter plasmid pVEGFprom (− 1000–1), the deletion mutants pVEGFprom (− 1000–500) or pVEGFprom (− 500–1) with the expression plasmids pEGFP-HMGA1 and pEGFP-FOXM1. pRL-CMV Renilla luciferase expression vector was included to normalize for transfection efficiencies. Values are reported as relative luciferase activity comparing to cells transfected with the expression plasmid pEGFP. The data are represented as the mean ± SD (n = 3). NS: not significant; two-tailed Student’s t-test. An example of western blot validations is reported. (d) and (e) Representative images of western blot validations of experiments presented in Fig. 5b and d respectively. (PDF 2000 kb)

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2019
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42. Additional file 9: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Figure S6. HUVEC cells were treated with MDA-MB-231 cells supernatants, who had been previously silenced for HMGA1, FOXM1 or co-silenced for HMGA1 and FOXM1. Serum-free medium and normal human serum (NHS) were used as negative and positive controls respectively. (a) The proliferation of HUVEC cells was investigated by the positivity to the Ki67 marker and expressed in terms of relative % of fluorescence respect to negative control (CTRL-). The data are represented as the mean ± SD (n > 3); **p 3). *p

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2019
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43. Additional file 3: of HMGA1 promotes breast cancer angiogenesis supporting the stability, nuclear localization and transcriptional activity of FOXM1

Author

Zanin, Rossella, Pegoraro, Silvia, Ros, Gloria, Yari Ciani, Piazza, Silvano, Bossi, Fleur, Bulla, Roberta, Zennaro, Cristina, Tonon, Federica, Lazarevic, Dejan, Stupka, Elia, Sgarra, Riccardo, and Guidalberto Manfioletti

Abstract

Tables S2. and S3. GSEA analysis on 24 and 72â h siHMGA1-regulated genes. (PDF 72 kb)

Published
2019
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44. Immune signature drives leukemia escape and relapse after hematopoietic cell transplantation

Author

Toffalori, Cristina, primary, Zito, Laura, additional, Gambacorta, Valentina, additional, Riba, Michela, additional, Oliveira, Giacomo, additional, Bucci, Gabriele, additional, Barcella, Matteo, additional, Spinelli, Orietta, additional, Greco, Raffaella, additional, Crucitti, Lara, additional, Cieri, Nicoletta, additional, Noviello, Maddalena, additional, Manfredi, Francesco, additional, Montaldo, Elisa, additional, Ostuni, Renato, additional, Naldini, Matteo M., additional, Gentner, Bernhard, additional, Waterhouse, Miguel, additional, Zeiser, Robert, additional, Finke, Jurgen, additional, Hanoun, Maher, additional, Beelen, Dietrich W., additional, Gojo, Ivana, additional, Luznik, Leo, additional, Onozawa, Masahiro, additional, Teshima, Takanori, additional, Devillier, Raynier, additional, Blaise, Didier, additional, Halkes, Constantijn J. M., additional, Griffioen, Marieke, additional, Carrabba, Matteo G., additional, Bernardi, Massimo, additional, Peccatori, Jacopo, additional, Barlassina, Cristina, additional, Stupka, Elia, additional, Lazarevic, Dejan, additional, Tonon, Giovanni, additional, Rambaldi, Alessandro, additional, Cittaro, Davide, additional, Bonini, Chiara, additional, Fleischhauer, Katharina, additional, Ciceri, Fabio, additional, and Vago, Luca, additional

Published
2019
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46. Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

Author

Sanges Remo, Petrera Francesca, Gennarino Vincenzo A, Licastro Danilo, Banfi Sandro, and Stupka Elia

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Ultraconserved elements (UCEs) are highly constrained elements of mammalian genomes, whose functional role has not been completely elucidated yet. Previous studies have shown that some of them act as enhancers in mouse, while some others are expressed in both normal and cancer-derived human tissues. Only one UCE element so far was shown to present these two functions concomitantly, as had been observed in other isolated instances of single, non ultraconserved enhancer elements. Results We used a custom microarray to assess the levels of UCE transcription during mouse development and integrated these data with published microarray and next-generation sequencing datasets as well as with newly produced PCR validation experiments. We show that a large fraction of non-exonic UCEs is transcribed across all developmental stages examined from only one DNA strand. Although the nature of these transcripts remains a mistery, our meta-analysis of RNA-Seq datasets indicates that they are unlikely to be short RNAs and that some of them might encode nuclear transcripts. In the majority of cases this function overlaps with the already established enhancer function of these elements during mouse development. Utilizing several next-generation sequencing datasets, we were further able to show that the level of expression observed in non-exonic UCEs is significantly higher than in random regions of the genome and that this is also seen in other regions which act as enhancers. Conclusion Our data shows that the concurrent presence of enhancer and transcript function in non-exonic UCE elements is more widespread than previously shown. Moreover through our own experiments as well as the use of next-generation sequencing datasets, we were able to show that the RNAs encoded by non-exonic UCEs are likely to be long RNAs transcribed from only one DNA strand.

Published
2010
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47. BATLAS: Deconvoluting Brown Adipose Tissue

Author

Perdikari, Aliki, primary, Leparc, Germán Gastón, additional, Balaz, Miroslav, additional, Pires, Nuno D., additional, Lidell, Martin E., additional, Sun, Wenfei, additional, Fernandez-Albert, Francesc, additional, Müller, Sebastian, additional, Akchiche, Nassila, additional, Dong, Hua, additional, Balazova, Lucia, additional, Opitz, Lennart, additional, Röder, Eva, additional, Klein, Holger, additional, Stefanicka, Patrik, additional, Varga, Lukas, additional, Nuutila, Pirjo, additional, Virtanen, Kirsi A., additional, Niemi, Tarja, additional, Taittonen, Markku, additional, Rudofsky, Gottfried, additional, Ukropec, Jozef, additional, Enerbäck, Sven, additional, Stupka, Elia, additional, Neubauer, Heike, additional, and Wolfrum, Christian, additional

Published
2018
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50. 738. Evidence from Gene-Environment Mouse Models that Amygdala Oligodendropathy Contributes to Emotional Pathology

Author

Cathomas, Flurin, primary, Azzinnari, Damiano, additional, Bergamini, Giorgio, additional, Sigrist, Hannes, additional, Buerge, Michaela, additional, Hoop, Vanessa, additional, Wicki, Benedikt, additional, Goetze, Lea, additional, Seifritz, Erich, additional, Goebbels, Sandra, additional, Nave, Klaus-Armin, additional, Ghandour, Said, additional, Seoighe, Cathal, additional, Hildebrandt, Tobias, additional, Leparc, German, additional, Klein, Holger, additional, Stupka, Elia, additional, Hengerer, Bastian, additional, and Pryce, Christopher R., additional

Published
2017
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