[ { "key": "TQ6W2CVG", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/TQ6W2CVG", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/TQ6W2CVG", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Dunlop et al.", "parsedDate": "2012-07", "numChildren": 0 }, "data": { "key": "TQ6W2CVG", "version": 7693, "itemType": "journalArticle", "title": "Common variation near CDKN1A, POLD3 and SHROOM2 influences colorectal cancer risk", "creators": [ { "creatorType": "author", "firstName": "Malcolm G.", "lastName": "Dunlop" }, { "creatorType": "author", "firstName": "Sara E.", "lastName": "Dobbins" }, { "creatorType": "author", "firstName": "Susan Mary", "lastName": "Farrington" }, { "creatorType": "author", "firstName": "Angela M.", "lastName": "Jones" }, { "creatorType": "author", "firstName": "Claire", "lastName": "Palles" }, { "creatorType": "author", "firstName": "Nicola", "lastName": "Whiffin" }, { "creatorType": "author", "firstName": "Albert", "lastName": "Tenesa" }, { "creatorType": "author", "firstName": "Sarah", "lastName": "Spain" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Broderick" }, { "creatorType": "author", "firstName": "Li-Yin", "lastName": "Ooi" }, { "creatorType": "author", "firstName": "Enric", "lastName": "Domingo" }, { "creatorType": "author", "firstName": "Claire", "lastName": "Smillie" }, { "creatorType": "author", "firstName": "Marc", "lastName": "Henrion" }, { "creatorType": "author", "firstName": "Matthew", "lastName": "Frampton" }, { "creatorType": "author", "firstName": "Lynn", "lastName": "Martin" }, { "creatorType": "author", "firstName": "Graeme", "lastName": "Grimes" }, { "creatorType": "author", "firstName": "Maggie", "lastName": "Gorman" }, { "creatorType": "author", "firstName": "Colin", "lastName": "Semple" }, { "creatorType": "author", "firstName": "Yusanne P.", "lastName": "Ma" }, { "creatorType": "author", "firstName": "Ella", "lastName": "Barclay" }, { "creatorType": "author", "firstName": "James", "lastName": "Prendergast" }, { "creatorType": "author", "firstName": "Jean-Baptiste", "lastName": "Cazier" }, { "creatorType": "author", "firstName": "Bianca", "lastName": "Olver" }, { "creatorType": "author", "firstName": "Steven", "lastName": "Penegar" }, { "creatorType": "author", "firstName": "Steven", "lastName": "Lubbe" }, { "creatorType": "author", "firstName": "Ian", "lastName": "Chander" }, { "creatorType": "author", "firstName": "Luis G.", "lastName": "Carvajal-Carmona" }, { "creatorType": "author", "firstName": "Stephane", "lastName": "Ballereau" }, { "creatorType": "author", "firstName": "Amy", "lastName": "Lloyd" }, { "creatorType": "author", "firstName": "Jayaram", "lastName": "Vijayakrishnan" }, { "creatorType": "author", "firstName": "Lina", "lastName": "Zgaga" }, { "creatorType": "author", "firstName": "Igor", "lastName": "Rudan" }, { "creatorType": "author", "firstName": "Evropi", "lastName": "Theodoratou" }, { "creatorType": "author", "firstName": "John M.", "lastName": "Starr" }, { "creatorType": "author", "firstName": "Ian", "lastName": "Deary" }, { "creatorType": "author", "firstName": "Iva", "lastName": "Kirac" }, { "creatorType": "author", "firstName": "Dujo", "lastName": "Kovacevic" }, { "creatorType": "author", "firstName": "Lauri A.", "lastName": "Aaltonen" }, { "creatorType": "author", "firstName": "Laura", "lastName": "Renkonen-Sinisalo" }, { "creatorType": "author", "firstName": "Jukka-Pekka", "lastName": "Mecklin" }, { "creatorType": "author", "firstName": "Koichi", "lastName": "Matsuda" }, { "creatorType": "author", "firstName": "Yusuke", "lastName": "Nakamura" }, { "creatorType": "author", "firstName": "Yukinori", "lastName": "Okada" }, { "creatorType": "author", "firstName": "Steven", "lastName": "Gallinger" }, { "creatorType": "author", "firstName": "David J.", "lastName": "Duggan" }, { "creatorType": "author", "firstName": "David", "lastName": "Conti" }, { "creatorType": "author", "firstName": "Polly", "lastName": "Newcomb" }, { "creatorType": "author", "firstName": "John", "lastName": "Hopper" }, { "creatorType": "author", "firstName": "Mark A.", "lastName": "Jenkins" }, { "creatorType": "author", "firstName": "Fredrick", "lastName": "Schumacher" }, { "creatorType": "author", "firstName": "Graham", "lastName": "Casey" }, { "creatorType": "author", "firstName": "Douglas", "lastName": "Easton" }, { "creatorType": "author", "firstName": "Mitul", "lastName": "Shah" }, { "creatorType": "author", "firstName": "Paul", "lastName": "Pharoah" }, { "creatorType": "author", "firstName": "Annika", "lastName": "Lindblom" }, { "creatorType": "author", "firstName": "Tao", "lastName": "Liu" }, { "creatorType": "author", "firstName": "Christopher G.", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Hannah", "lastName": "West" }, { "creatorType": "author", "firstName": "Jeremy P.", "lastName": "Cheadle" }, { "creatorType": "author", "firstName": "Rachel", "lastName": "Midgley" }, { "creatorType": "author", "firstName": "David J.", "lastName": "Kerr" }, { "creatorType": "author", "firstName": "Harry", "lastName": "Campbell" }, { "creatorType": "author", "firstName": "Ian P.", "lastName": "Tomlinson" }, { "creatorType": "author", "firstName": "Richard S.", "lastName": "Houlston" } ], "abstractNote": "We performed a meta-analysis of five genome-wide association studies to identify common variants influencing colorectal cancer (CRC) risk comprising 8,682 cases and 9,649 controls. Replication analysis was performed in case-control sets totaling 21,096 cases and 19,555 controls. We identified three new CRC risk loci at 6p21 (rs1321311, near CDKN1A; P = 1.14 x 10(-10)), 11q13.4 (rs3824999, intronic to POLD3; P = 3.65 x 10(-10)) and Xp22.2 (rs5934683, near SHROOM2; P = 7.30 x 10(-10)) This brings the number of independent loci associated with CRC risk to 20 and provides further insight into the genetic architecture of inherited susceptibility to CRC.", "publicationTitle": "Nature Genetics", "publisher": "", "place": "", "date": "JUL 2012", "volume": "44", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "770-U197", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature Genet.", "DOI": "10.1038/ng.2293", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1061-4036", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000305886900010", "tags": [ { "tag": "carriers", "type": 1 }, { "tag": "gene-expression", "type": 1 }, { "tag": "genome-wide association", "type": 1 }, { "tag": "metaanalysis", "type": 1 }, { "tag": "microsatellite instability", "type": 1 }, { "tag": "mutations", "type": 1 }, { "tag": "retinal-pigment epithelium", "type": 1 }, { "tag": "susceptibility loci", "type": 1 }, { "tag": "variants", "type": 1 }, { "tag": "x-chromosome inactivation", "type": 1 } ], "collections": [ "P5BTA2PX" ], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "UMHIUU98", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/UMHIUU98", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/UMHIUU98", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Lubbe et al.", "parsedDate": "2012-08", "numChildren": 0 }, "data": { "key": "UMHIUU98", "version": 7693, "itemType": "journalArticle", "title": "The 14q22.2 colorectal cancer variant rs4444235 shows cis-acting regulation of BMP4", "creators": [ { "creatorType": "author", "firstName": "S. J.", "lastName": "Lubbe" }, { "creatorType": "author", "firstName": "A. M.", "lastName": "Pittman" }, { "creatorType": "author", "firstName": "B.", "lastName": "Olver" }, { "creatorType": "author", "firstName": "A.", "lastName": "Lloyd" }, { "creatorType": "author", "firstName": "J.", "lastName": "Vijayakrishnan" }, { "creatorType": "author", "firstName": "S.", "lastName": "Naranjo" }, { "creatorType": "author", "firstName": "S.", "lastName": "Dobbins" }, { "creatorType": "author", "firstName": "P.", "lastName": "Broderick" }, { "creatorType": "author", "firstName": "J. L.", "lastName": "Gomez-Skarmeta" }, { "creatorType": "author", "firstName": "R. S.", "lastName": "Houlston" } ], "abstractNote": "Common genetic variation at human 14q22.2 tagged by rs4444235 is significantly associated with colorectal cancer (CRC) risk. Re-sequencing was used to comprehensively annotate the 17kb region of strong linkage disequilibrium encompassing rs4444235. Through bioinformatic analyses using H3K4Me1, H3K4Me3, and DNase-I hypersensitivity chromatin signatures and evolutionary conservation we identified seven candidate disease-causing single-nucleotide polymorphisms mapping to six regions within the 17-kb region predicted to have regulatory potential. Reporter gene studies of these regions demonstrated that the element to which rs4444235 maps acts as an allele-specific transcriptional enhancer. Allele-specific expression studies in CRC cell lines heterozygous for rs4444235 showed significantly increased expression of bone morphogenetic protein-4 (BMP4) associated with the risk allele (P<0.001). These data provide evidence for a functional basis for the non-coding risk variant rs4444235 at 14q22.2 and emphasizes the importance of genetic variation in the BMP pathway genes as determinants of CRC risk. Oncogene (2012) 31, 3777-3784; doi:10.1038/onc.2011.564; published online 12 December 2011", "publicationTitle": "Oncogene", "publisher": "", "place": "", "date": "AUG 2012", "volume": "31", "issue": "33", "section": "", "partNumber": "", "partTitle": "", "pages": "3777-3784", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Oncogene", "DOI": "10.1038/onc.2011.564", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0950-9232", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000307924900004", "tags": [ { "tag": "8q24", "type": 1 }, { "tag": "bone morphogenetic protein-4", "type": 1 }, { "tag": "chromosomal instability", "type": 1 }, { "tag": "cis-regulatory", "type": 1 }, { "tag": "colorectal cancer", "type": 1 }, { "tag": "common", "type": 1 }, { "tag": "gel-electrophoresis", "type": 1 }, { "tag": "gene-expression", "type": 1 }, { "tag": "genome-wide association", "type": 1 }, { "tag": "predisposition", "type": 1 }, { "tag": "risk", "type": 1 }, { "tag": "scan", "type": 1 }, { "tag": "susceptibility loci", "type": 1 } ], "collections": [ "P5BTA2PX" ], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "EZ3EFZXI", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/EZ3EFZXI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/EZ3EFZXI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Wingender et al.", "parsedDate": "2013-01", "numChildren": 1 }, "data": { "key": "EZ3EFZXI", "version": 7693, "itemType": "journalArticle", "title": "TFClass: an expandable hierarchical classification of human transcription factors", "creators": [ { "creatorType": "author", "firstName": "Edgar", "lastName": "Wingender" }, { "creatorType": "author", "firstName": "Torsten", "lastName": "Schoeps" }, { "creatorType": "author", "firstName": "Juergen", "lastName": "Doenitz" } ], "abstractNote": "TFClass (http://tfclass.bioinf.med.uni-goettingen.de/) provides a comprehensive classification of human transcription factors based on their DNA-binding domains. Transcription factors constitute a large functional family of proteins directly regulating the activity of genes. Most of them are sequence-specific DNA-binding proteins, thus reading out the information encoded in cis-regulatory DNA elements of promoters, enhancers and other regulatory regions of a genome. TFClass is a database that classifies human transcription factors by a six-level classification schema, four of which are abstractions according to different criteria, while the fifth level represents TF genes and the sixth individual gene products. Altogether, nine superclasses have been identified, comprising 40 classes and 111 families. Counted by genes, 1558 human TFs have been classified so far or > 2900 different TFs when including their isoforms generated by alternative splicing or protein processing events. With this classification, we hope to provide a basis for deciphering protein-DNA recognition codes; moreover, it can be used for constructing expanded transcriptional networks by inferring additional TF-target gene relations.", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "JAN 2013", "volume": "41", "issue": "D1", "section": "", "partNumber": "", "partTitle": "", "pages": "D165-D170", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucleic Acids Res.", "DOI": "10.1093/nar/gks1123", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0305-1048", "archive": "", "archiveLocation": "", "shortTitle": "TFClass", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000312893300023", "tags": [ { "tag": "database", "type": 1 }, { "tag": "expression", "type": 1 }, { "tag": "recognition", "type": 1 }, { "tag": "sequences", "type": 1 }, { "tag": "system", "type": 1 } ], "collections": [ "P5BTA2PX" ], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "T67JFXSX", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/T67JFXSX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/T67JFXSX", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/28561/items/J978BCU4", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "T67JFXSX", "version": 7693, "parentItem": "J978BCU4", "itemType": "note", "note": "

Free PMC Article

", "tags": [], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "K23VZCRX", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/K23VZCRX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/K23VZCRX", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/28561/items/EZ3EFZXI", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "K23VZCRX", "version": 7693, "parentItem": "EZ3EFZXI", "itemType": "note", "note": "

Free Article

", "tags": [], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "J978BCU4", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/J978BCU4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/J978BCU4", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Gabdoulline et al.", "parsedDate": "2012-07", "numChildren": 1 }, "data": { "key": "J978BCU4", "version": 7693, "itemType": "journalArticle", "title": "3DTF: a web server for predicting transcription factor PWMs using 3D structure-based energy calculations", "creators": [ { "creatorType": "author", "firstName": "R.", "lastName": "Gabdoulline" }, { "creatorType": "author", "firstName": "D.", "lastName": "Eckweiler" }, { "creatorType": "author", "firstName": "A.", "lastName": "Kel" }, { "creatorType": "author", "firstName": "P.", "lastName": "Stegmaier" } ], "abstractNote": "We present the webserver 3D transcription factor (3DTF) to compute position-specific weight matrices (PWMs) of transcription factors using a knowledge-based statistical potential derived from crystallographic data on protein-DNA complexes. Analysis of available structures that can be used to construct PWMs shows that there are hundreds of 3D structures from which PWMs could be derived, as well as thousands of proteins homologous to these. Therefore, we created 3DTF, which delivers binding matrices given the experimental or modeled protein-DNA complex. The webserver can be used by biologists to derive novel PWMs for transcription factors lacking known binding sites and is freely accessible at http://www.gene-regulation.com/pub/programs/3dtf/.", "publicationTitle": "Nucleic Acids Research", "publisher": "", "place": "", "date": "JUL 2012", "volume": "40", "issue": "W1", "section": "", "partNumber": "", "partTitle": "", "pages": "W180-W185", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nucleic Acids Res.", "DOI": "10.1093/nar/gks551", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0305-1048", "archive": "", "archiveLocation": "", "shortTitle": "3DTF", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000306670900029", "tags": [ { "tag": "factor-binding sites", "type": 1 }, { "tag": "protein-dna interactions", "type": 1 }, { "tag": "recognition", "type": 1 } ], "collections": [ "P5BTA2PX" ], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "BV4U63JV", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/BV4U63JV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/BV4U63JV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Dallosso et al.", "parsedDate": "2012-10", "numChildren": 0 }, "data": { "key": "BV4U63JV", "version": 7693, "itemType": "journalArticle", "title": "Long-range epigenetic silencing of chromosome 5q31 protocadherins is involved in early and late stages of colorectal tumorigenesis through modulation of oncogenic pathways", "creators": [ { "creatorType": "author", "firstName": "A. R.", "lastName": "Dallosso" }, { "creatorType": "author", "firstName": "B.", "lastName": "Oster" }, { "creatorType": "author", "firstName": "A.", "lastName": "Greenhough" }, { "creatorType": "author", "firstName": "K.", "lastName": "Thorsen" }, { "creatorType": "author", "firstName": "T. J.", "lastName": "Curry" }, { "creatorType": "author", "firstName": "C.", "lastName": "Owen" }, { "creatorType": "author", "firstName": "A. L.", "lastName": "Hancock" }, { "creatorType": "author", "firstName": "M.", "lastName": "Szemes" }, { "creatorType": "author", "firstName": "C.", "lastName": "Paraskeva" }, { "creatorType": "author", "firstName": "M.", "lastName": "Frank" }, { "creatorType": "author", "firstName": "C. L.", "lastName": "Andersen" }, { "creatorType": "author", "firstName": "K.", "lastName": "Malik" } ], "abstractNote": "Loss of tumour suppressor gene function can occur as a result of epigenetic silencing of large chromosomal regions, referred to as long-range epigenetic silencing (LRES), and genome-wide analyses have revealed that LRES is present in many cancer types. Here we utilize Illumina Beadchip methylation array analysis to identify LRES across 800 kb of chromosome 5q31 in colorectal adenomas and carcinomas (n = 34) relative to normal colonic epithelial DNA (n = 6). This region encompasses 53 individual protocadherin (PCDH) genes divided among three gene clusters. Hypermethylation within these gene clusters is asynchronous; while most PCDH hypermethylation occurs early, and is apparent in adenomas, PCDHGC3 promoter methylation occurs later in the adenoma-carcinoma transition. PCDHGC3 was hypermethylated in 17/28 carcinomas (60.7%) according to methylation array analysis. Quantitative real-time reverse transcription-polymerase chain reaction showed that PCDHGC3 is the highest expressed PCDH in normal colonic epithelium, and that there was a strong reciprocal relationship between PCDHGC3 methylation and expression in carcinomas (R = -0.84). PCDH LRES patterns are reflected in colorectal tumour cell lines; adenoma cell lines are not methylated at PCDHGC3 and show abundant expression at the mRNA and protein level, while the expression is suppressed in hypermethylated carcinoma cell lines (R = -0.73). Short-interfering RNA-mediated reduction of PCDHGC3 led to a decrease of apoptosis in RG/C2 adenoma cells, and overexpression of PCDHGC3 in HCT116 cells resulted in the reduction of colony formation, consistent with tumour suppressor capabilities for PCDHGC3. Further functional analysis showed that PCDHGC3 can suppress Wnt and mammalian target of rapamycin signalling in colorectal cancer cell lines. Taken together, our data suggest that the PCDH LRES is an important tumour suppressor locus in colorectal cancer, and that PCDHGC3 may be a strong marker and driver for the adenoma-carcinoma transition. Oncogene (2012) 31, 4409-4419; doi: 10.1038/onc.2011.609; published online 16 January 2012", "publicationTitle": "Oncogene", "publisher": "", "place": "", "date": "OCT 2012", "volume": "31", "issue": "40", "section": "", "partNumber": "", "partTitle": "", "pages": "4409-4419", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Oncogene", "DOI": "10.1038/onc.2011.609", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0950-9232", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000309591300007", "tags": [ { "tag": "Wnt", "type": 1 }, { "tag": "adenoma-carcinoma sequence", "type": 1 }, { "tag": "cancer-cells", "type": 1 }, { "tag": "cell-lines", "type": 1 }, { "tag": "colorectal cancer", "type": 1 }, { "tag": "cytoplasmic domain", "type": 1 }, { "tag": "dna methylation", "type": 1 }, { "tag": "epigenetic silencing", "type": 1 }, { "tag": "gamma-protocadherins", "type": 1 }, { "tag": "homophilic interaction", "type": 1 }, { "tag": "human breast", "type": 1 }, { "tag": "mTOR", "type": 1 }, { "tag": "microsatellite instability", "type": 1 }, { "tag": "protocadherin", "type": 1 }, { "tag": "tumor-suppressor", "type": 1 } ], "collections": [ "P5BTA2PX" ], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "GA2MRIW9", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/GA2MRIW9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/GA2MRIW9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Palles et al.", "parsedDate": "2013-02", "numChildren": 0 }, "data": { "key": "GA2MRIW9", "version": 7693, "itemType": "journalArticle", "title": "Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas", "creators": [ { "creatorType": "author", "firstName": "Claire", "lastName": "Palles" }, { "creatorType": "author", "firstName": "Jean-Baptiste", "lastName": "Cazier" }, { "creatorType": "author", "firstName": "Kimberley M.", "lastName": "Howarth" }, { "creatorType": "author", "firstName": "Enric", "lastName": "Domingo" }, { "creatorType": "author", "firstName": "Angela M.", "lastName": "Jones" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Broderick" }, { "creatorType": "author", "firstName": "Zoe", "lastName": "Kemp" }, { "creatorType": "author", "firstName": "Sarah L.", "lastName": "Spain" }, { "creatorType": "author", "firstName": "Estrella Guarino", "lastName": "Almeida" }, { "creatorType": "author", "firstName": "Israel", "lastName": "Salguero" }, { "creatorType": "author", "firstName": "Amy", "lastName": "Sherborne" }, { "creatorType": "author", "firstName": "Daniel", "lastName": "Chubb" }, { "creatorType": "author", "firstName": "Luis G.", "lastName": "Carvajal-Carmona" }, { "creatorType": "author", "firstName": "Yusanne", "lastName": "Ma" }, { "creatorType": "author", "firstName": "Kulvinder", "lastName": "Kaur" }, { "creatorType": "author", "firstName": "Sara", "lastName": "Dobbins" }, { "creatorType": "author", "firstName": "Ella", "lastName": "Barclay" }, { "creatorType": "author", "firstName": "Maggie", "lastName": "Gorman" }, { "creatorType": "author", "firstName": "Lynn", "lastName": "Martin" }, { "creatorType": "author", "firstName": "Michal B.", "lastName": "Kovac" }, { "creatorType": "author", "firstName": "Sean", "lastName": "Humphray" }, { "creatorType": "author", "firstName": "Anneke", "lastName": "Lucassen" }, { "creatorType": "author", "firstName": "Christopher C.", "lastName": "Holmes" }, { "creatorType": "author", "firstName": "David", "lastName": "Bentley" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Donnelly" }, { "creatorType": "author", "firstName": "Jenny", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "Christos", "lastName": "Petridis" }, { "creatorType": "author", "firstName": "Rebecca", "lastName": "Roylance" }, { "creatorType": "author", "firstName": "Elinor J.", "lastName": "Sawyer" }, { "creatorType": "author", "firstName": "David J.", "lastName": "Kerr" }, { "creatorType": "author", "firstName": "Susan", "lastName": "Clark" }, { "creatorType": "author", "firstName": "Jonathan", "lastName": "Grimes" }, { "creatorType": "author", "firstName": "Stephen E.", "lastName": "Kearsey" }, { "creatorType": "author", "firstName": "Huw J. W.", "lastName": "Thomas" }, { "creatorType": "author", "firstName": "Gilean", "lastName": "McVean" }, { "creatorType": "author", "firstName": "Richard S.", "lastName": "Houlston" }, { "creatorType": "author", "firstName": "Ian", "lastName": "Tomlinson" } ], "abstractNote": "Many individuals with multiple or large colorectal adenomas or early-onset colorectal cancer (CRC) have no detectable germline mutations in the known cancer predisposition genes. Using whole-genome sequencing, supplemented by linkage and association analysis, we identified specific heterozygous POLE or POLD1 germline variants in several multiple-adenoma and/or CRC cases but in no controls. The variants associated with susceptibility, POLE p.Leu424Val and POLD1 p.Ser478Asn, have high penetrance, and POLD1 mutation was also associated with endometrial cancer predisposition. The mutations map to equivalent sites in the proofreading (exonuclease) domain of DNA polymerases E and 8 and are predicted to cause a defect in the correction of mispaired bases inserted during DNA replication. In agreement with this prediction, the tumors from mutation carriers were microsatellite stable but tended to acquire base substitution mutations, as confirmed by yeast functional assays. Further analysis of published data showed that the recently described group of hypermutant, microsatellite-stable CRCs is likely to be caused by somatic POLE mutations affecting the exonuclease domain.", "publicationTitle": "Nature Genetics", "publisher": "", "place": "", "date": "FEB 2013", "volume": "45", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "136-144", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nature Genet.", "DOI": "10.1038/ng.2503", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1061-4036", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000314333000008", "tags": [ { "tag": "cancer susceptibility", "type": 1 }, { "tag": "cell-lines", "type": 1 }, { "tag": "colon-cancer", "type": 1 }, { "tag": "dna-polymerase-delta", "type": 1 }, { "tag": "excision-repair", "type": 1 }, { "tag": "mice", "type": 1 }, { "tag": "mismatch repair", "type": 1 }, { "tag": "mutator", "type": 1 }, { "tag": "replication", "type": 1 }, { "tag": "yeast", "type": 1 } ], "collections": [ "P5BTA2PX" ], "relations": {}, "dateAdded": "2013-03-12T10:48:22Z", "dateModified": "2013-03-12T10:48:22Z" } }, { "key": "GVM2AW4H", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/GVM2AW4H", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/GVM2AW4H", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Farkash-Amar et al.", "parsedDate": "2012-11-07", "numChildren": 1 }, "data": { "key": "GVM2AW4H", "version": 7693, "itemType": "journalArticle", "title": "Dynamic Proteomics of Human Protein Level and Localization across the Cell Cycle", "creators": [ { "creatorType": "author", "firstName": "Shlomit", "lastName": "Farkash-Amar" }, { "creatorType": "author", "firstName": "Eran", "lastName": "Eden" }, { "creatorType": "author", "firstName": "Ariel", "lastName": "Cohen" }, { "creatorType": "author", "firstName": "Naama", "lastName": "Geva-Zatorsky" }, { "creatorType": "author", "firstName": "Lydia", "lastName": "Cohen" }, { "creatorType": "author", "firstName": "Ron", "lastName": "Milo" }, { "creatorType": "author", "firstName": "Alex", "lastName": "Sigal" }, { "creatorType": "author", "firstName": "Tamar", "lastName": "Danon" }, { "creatorType": "author", "firstName": "Uri", "lastName": "Alon" } ], "abstractNote": "Regulation of proteins across the cell cycle is a basic process in cell biology. It has been difficult to study this globally in human cells due to lack of methods to accurately follow protein levels and localizations over time. Estimates based on global mRNA measurements suggest that only a few percent of human genes have cell-cycle dependent mRNA levels. Here, we used dynamic proteomics to study the cell-cycle dependence of proteins. We used 495 clones of a human cell line, each with a different protein tagged fluorescently at its endogenous locus. Protein level and localization was quantified in individual cells over 24h of growth using time-lapse microscopy. Instead of standard chemical or mechanical methods for cell synchronization, we employed in-silico synchronization to place protein levels and localization on a time axis between two cell divisions. This non-perturbative synchronization approach, together with the high accuracy of the measurements, allowed a sensitive assay of cell-cycle dependence. We further developed a computational approach that uses texture features to evaluate changes in protein localizations. We find that 40% of the proteins showed cell cycle dependence, of which 11% showed changes in protein level and 35% in localization. This suggests that a broader range of cell-cycle dependent proteins exists in human cells than was previously appreciated. Most of the cell-cycle dependent proteins exhibit changes in cellular localization. Such changes can be a useful tool in the regulation of the cell-cycle being fast and efficient.", "publicationTitle": "Plos One", "publisher": "", "place": "", "date": "NOV 7 2012", "volume": "7", "issue": "11", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "PLoS One", "DOI": "10.1371/journal.pone.0048722", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1932-6203", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000311935800110", "tags": [ { "tag": "cancer-cells", "type": 1 }, { "tag": "classification", "type": 1 }, { "tag": "cytokinesis", "type": 1 }, { "tag": "dna-replication", "type": 1 }, { "tag": "genes", "type": 1 }, { "tag": "genome", "type": 1 }, { "tag": "identification", "type": 1 }, { "tag": "living human-cells", "type": 1 }, { "tag": "wide transcriptional analysis", "type": 1 }, { "tag": "yeast", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "JGDP9FPC", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/JGDP9FPC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/JGDP9FPC", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/28561/items/GVM2AW4H", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "JGDP9FPC", "version": 7692, "parentItem": "GVM2AW4H", "itemType": "note", "note": "

Free PMC Article

", "tags": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "RM5R4TI2", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/RM5R4TI2", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/RM5R4TI2", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Sironi et al.", "parsedDate": "2011-05", "numChildren": 0 }, "data": { "key": "RM5R4TI2", "version": 7692, "itemType": "journalArticle", "title": "Automatic Quantification of Microtubule Dynamics Enables RNAi-screening of New Mitotic Spindle Regulators", "creators": [ { "creatorType": "author", "firstName": "Lucia", "lastName": "Sironi" }, { "creatorType": "author", "firstName": "Jerome", "lastName": "Solon" }, { "creatorType": "author", "firstName": "Christian", "lastName": "Conrad" }, { "creatorType": "author", "firstName": "Thomas U.", "lastName": "Mayer" }, { "creatorType": "author", "firstName": "Damian", "lastName": "Brunner" }, { "creatorType": "author", "firstName": "Jan", "lastName": "Ellenberg" } ], "abstractNote": "The genetic integrity of every organism depends on the faithful partitioning of its genome between two daughter cells in mitosis. In all eukaryotes, chromosome segregation requires the assembly of the mitotic spindle, a bipolar array of dynamic microtubules. Perturbations in microtubule dynamics affect spindle assembly and maintenance and ultimately result in aberrant cell divisions. To identify new regulators of microtubule dynamics within the hundreds of mitotic hits, reported in RNAi screens performed in C. elegans, Drosophila and mammalian tissue culture cells [Sonnichsen et al., 2005; Goshima et al., 2007; Neumann et al., 2010], we established a fast and quantitative assay to measure microtubule dynamics in living cells. Here we present a fully automated workflow from RNAi transfection, via image acquisition and data processing, to the quantitative characterization of microtubule behaviour. Candidate genes are knocked down by solid-phase reverse transfection with siRNA oligos in HeLa cells stably expressing EB3-EGFP, a microtubule plus end marker. Mitotic cells are selected using an automatic classifier [Conrad et al., 2011] and imaged on a spinning disk confocal microscope at high temporal and spatial resolution. The time-lapse movies are analysed using a multiple particle tracking software, developed in-house, that automatically detects microtubule plus ends, tracks microtubule growth events over consecutive frames and calculates growth speeds, lengths and lifetimes of the tracked microtubules. The entire assay provides a powerful tool to analyse the effect of essential mitotic genes on microtubule dynamics in living cells and to dissect their contribution in spindle assembly and maintenance. (C) 2011 Wiley-Liss, Inc.", "publicationTitle": "Cytoskeleton", "publisher": "", "place": "", "date": "MAY 2011", "volume": "68", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "266-278", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cytoskeleton", "DOI": "10.1002/cm.20510", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1949-3584", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000291052800002", "tags": [ { "tag": "RNAi screening", "type": 1 }, { "tag": "binding protein eb1", "type": 1 }, { "tag": "cell-proliferation", "type": 1 }, { "tag": "eb3", "type": 1 }, { "tag": "growth", "type": 1 }, { "tag": "in-vitro", "type": 1 }, { "tag": "instability", "type": 1 }, { "tag": "microscopy", "type": 1 }, { "tag": "microtubule dynamics", "type": 1 }, { "tag": "mitosis", "type": 1 }, { "tag": "multiple particle tracking", "type": 1 }, { "tag": "plus ends", "type": 1 }, { "tag": "pole organization", "type": 1 }, { "tag": "quantitative microscopy", "type": 1 }, { "tag": "reverse transfection", "type": 1 }, { "tag": "xmap215", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "W2QI6JH5", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/W2QI6JH5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/W2QI6JH5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Wurzenberger and Gerlich", "parsedDate": "2011-08", "numChildren": 0 }, "data": { "key": "W2QI6JH5", "version": 7692, "itemType": "journalArticle", "title": "Phosphatases: providing safe passage through mitotic exit", "creators": [ { "creatorType": "author", "firstName": "Claudia", "lastName": "Wurzenberger" }, { "creatorType": "author", "firstName": "Daniel W.", "lastName": "Gerlich" } ], "abstractNote": "The mitosis-to-interphase transition involves dramatic cellular reorganization from a state that supports chromosome segregation to a state that complies with all functions of an interphase cell. This process, termed mitotic exit, depends on the removal of mitotic phosphorylations from a broad range of substrates. Mitotic exit regulation involves inactivation of mitotic kinases and activation of counteracting protein phosphatases. The key mitotic exit phosphatase in budding yeast, Cdc14, is now well understood. By contrast, in animal cells, it is now emerging that mitotic exit relies on distinct regulatory networks, including the protein phosphatases PP1 and PP2A.", "publicationTitle": "Nature Reviews Molecular Cell Biology", "publisher": "", "place": "", "date": "AUG 2011", "volume": "12", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "469-482", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Rev. Mol. Cell Biol.", "DOI": "10.1038/nrm3149", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1471-0072", "archive": "", "archiveLocation": "", "shortTitle": "Phosphatases", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000292998800010", "tags": [ { "tag": "anaphase-promoting complex/cyclosome", "type": 1 }, { "tag": "aurora-b kinase", "type": 1 }, { "tag": "budding yeast", "type": 1 }, { "tag": "cell-cycle progression", "type": 1 }, { "tag": "chromosomal passenger complex", "type": 1 }, { "tag": "human cdc14a phosphatase", "type": 1 }, { "tag": "protein phosphatase", "type": 1 }, { "tag": "saccharomyces-cerevisiae", "type": 1 }, { "tag": "spindle-assembly checkpoint", "type": 1 }, { "tag": "xenopus egg extracts", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "BTZXHGRV", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/BTZXHGRV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/BTZXHGRV", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Guizetti and Gerlich", "parsedDate": "2012-03", "numChildren": 0 }, "data": { "key": "BTZXHGRV", "version": 7692, "itemType": "journalArticle", "title": "ESCRT-III polymers in membrane neck constriction", "creators": [ { "creatorType": "author", "firstName": "Julien", "lastName": "Guizetti" }, { "creatorType": "author", "firstName": "Daniel W.", "lastName": "Gerlich" } ], "abstractNote": "The endosomal sorting complex required for transport (ESCRT)-III machinery contributes to membrane deformation and scission in cytokinesis, intraluminal vesicle formation, autophagy and virus budding. Recombinant ESCRT-III subunits polymerize in vitro into filaments, tubes, sheets or rings, and ESCRT-III-dependent filaments have been observed in cells at virus bud necks and at the cytokinetic abscission site. These observations have inspired speculation about how ESCRT-III could mediate constriction and fission of membrane necks. Based on the polymer structures observed in vitro and in vivo, we discuss models for ESCRT-III function and outline how emerging technologies could be used to test these models.", "publicationTitle": "Trends in Cell Biology", "publisher": "", "place": "", "date": "MAR 2012", "volume": "22", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "133-140", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Trends Cell Biol.", "DOI": "10.1016/j.tcb.2011.11.007", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0962-8924", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000302447300002", "tags": [ { "tag": "cell-division", "type": 1 }, { "tag": "complex", "type": 1 }, { "tag": "cytokinesis", "type": 1 }, { "tag": "filaments", "type": 1 }, { "tag": "helical structures", "type": 1 }, { "tag": "machinery", "type": 1 }, { "tag": "plasma-membrane", "type": 1 }, { "tag": "proteins", "type": 1 }, { "tag": "structural basis", "type": 1 }, { "tag": "vesicle formation", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "RRSEXNAQ", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/RRSEXNAQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/RRSEXNAQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Zhong et al.", "parsedDate": "2012-07", "numChildren": 0 }, "data": { "key": "RRSEXNAQ", "version": 7692, "itemType": "journalArticle", "title": "Unsupervised modeling of cell morphology dynamics for time-lapse microscopy", "creators": [ { "creatorType": "author", "firstName": "Qing", "lastName": "Zhong" }, { "creatorType": "author", "firstName": "Alberto Giovanni", "lastName": "Busetto" }, { "creatorType": "author", "firstName": "Juan P.", "lastName": "Fededa" }, { "creatorType": "author", "firstName": "Joachim M.", "lastName": "Buhmann" }, { "creatorType": "author", "firstName": "Daniel W.", "lastName": "Gerlich" } ], "abstractNote": "Analysis of cellular phenotypes in large imaging data sets conventionally involves supervised statistical methods, which require user-annotated training data. This paper introduces an unsupervised learning method, based on temporally constrained combinatorial clustering, for automatic prediction of cell morphology classes in time-resolved images. We applied the unsupervised method to diverse fluorescent markers and screening data and validated accurate classification of human cell phenotypes, demonstrating fully objective data labeling in image-based systems biology.", "publicationTitle": "Nature Methods", "publisher": "", "place": "", "date": "JUL 2012", "volume": "9", "issue": "7", "section": "", "partNumber": "", "partTitle": "", "pages": "711-U267", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Methods", "DOI": "10.1038/NMETH.2046", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1548-7091", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000305942200025", "tags": [ { "tag": "automated microscopy", "type": 1 }, { "tag": "binding", "type": 1 }, { "tag": "genes", "type": 1 }, { "tag": "lines", "type": 1 }, { "tag": "systems", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "BUC9IEB3", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/BUC9IEB3", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/BUC9IEB3", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Wurzenberger et al.", "parsedDate": "2012-07-23", "numChildren": 1 }, "data": { "key": "BUC9IEB3", "version": 7692, "itemType": "journalArticle", "title": "Sds22 and Repo-Man stabilize chromosome segregation by counteracting Aurora B on anaphase kinetochores", "creators": [ { "creatorType": "author", "firstName": "Claudia", "lastName": "Wurzenberger" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Held" }, { "creatorType": "author", "firstName": "Michael A.", "lastName": "Lampson" }, { "creatorType": "author", "firstName": "Ina", "lastName": "Poser" }, { "creatorType": "author", "firstName": "Anthony A.", "lastName": "Hyman" }, { "creatorType": "author", "firstName": "Daniel W.", "lastName": "Gerlich" } ], "abstractNote": "During mitotic spindle assembly, Aurora B kinase is part of an error correction mechanism that detaches microtubules from kinetochores that are under low mechanical tension. During anaphase, however, kinetochore-microtubule attachments must be maintained despite a drop of tension after removal of sister chromatid cohesion. Consistent with this requirement, Aurora B relocates away from chromosomes to the central spindle at the metaphase-anaphase transition. By ribonucleic acid interference screening using a phosphorylation biosensor, we identified two PP1-targeting subunits, Sds22 and Repo-Man, which counteracted Aurora B-dependent phosphorylation of the outer kinetochore component Dsn1 during anaphase. Sds22 or Repo-Man depletion induced transient pauses during poleward chromosome movement and a high incidence of chromosome missegregation. Thus, our study identifies PP1-targeting subunits that regulate the microtubule-kinetochore interface during anaphase for faithful chromosome segregation.", "publicationTitle": "Journal of Cell Biology", "publisher": "", "place": "", "date": "JUL 23 2012", "volume": "198", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "173-183", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Cell Biol.", "DOI": "10.1083/jcb.201112112", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0021-9525", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000306686100006", "tags": [ { "tag": "cell-division", "type": 1 }, { "tag": "cytokinesis", "type": 1 }, { "tag": "histone h3", "type": 1 }, { "tag": "incenp", "type": 1 }, { "tag": "kinase", "type": 1 }, { "tag": "mitosis", "type": 1 }, { "tag": "mitotic exit", "type": 1 }, { "tag": "phosphorylation", "type": 1 }, { "tag": "protein phosphatase 1", "type": 1 }, { "tag": "spindle-assembly checkpoint", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "TDC2HIUZ", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/TDC2HIUZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/TDC2HIUZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Mall et al.", "parsedDate": "2012-09-17", "numChildren": 0 }, "data": { "key": "TDC2HIUZ", "version": 7692, "itemType": "journalArticle", "title": "Mitotic lamin disassembly is triggered by lipid-mediated signaling", "creators": [ { "creatorType": "author", "firstName": "Moritz", "lastName": "Mall" }, { "creatorType": "author", "firstName": "Thomas", "lastName": "Walter" }, { "creatorType": "author", "firstName": "Matyas", "lastName": "Gorjanacz" }, { "creatorType": "author", "firstName": "Iain F.", "lastName": "Davidson" }, { "creatorType": "author", "firstName": "Thi Bach Nga", "lastName": "Ly-Hartig" }, { "creatorType": "author", "firstName": "Jan", "lastName": "Ellenberg" }, { "creatorType": "author", "firstName": "Iain W.", "lastName": "Mattaj" } ], "abstractNote": "Disassembly of the nuclear lamina is a key step during open mitosis in higher eukaryotes. The activity of several kinases, including CDK1 (cyclin-dependent kinase 1) and protein kinase C (PKC), has been shown to trigger mitotic lamin disassembly, yet their precise contributions are unclear. In this study, we develop a quantitative imaging assay to study mitotic lamin B1 disassembly in living cells. We find that CDK1 and PKC act in concert to mediate phosphorylation-dependent lamin B1 disassembly during mitosis. Using ribonucleic acid interference (RNAi), we showed that diacylglycerol (DAG)-dependent PKCs triggered rate-limiting steps of lamin disassembly. RNAi-mediated depletion or chemical inhibition of lipins, enzymes that produce DAG, delayed lamin disassembly to a similar extent as does PKC inhibition/depletion. Furthermore, the delay of lamin B1 disassembly after lipin depletion could be rescued by the addition of DAG. These findings suggest that lipins activate a PKC-dependent pathway during mitotic lamin disassembly and provide evidence for a lipid-mediated mitotic signaling event.", "publicationTitle": "Journal of Cell Biology", "publisher": "", "place": "", "date": "SEP 17 2012", "volume": "198", "issue": "6", "section": "", "partNumber": "", "partTitle": "", "pages": "981-990", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "J. Cell Biol.", "DOI": "10.1083/jcb.201205103", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "0021-9525", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000309004300005", "tags": [ { "tag": "cdc2 kinase", "type": 1 }, { "tag": "cell-cycle", "type": 1 }, { "tag": "g(2)/m phase-transition", "type": 1 }, { "tag": "identification", "type": 1 }, { "tag": "mammalian-cells", "type": 1 }, { "tag": "nuclear-envelope breakdown", "type": 1 }, { "tag": "phosphatidate phosphatase", "type": 1 }, { "tag": "phosphorylation sites", "type": 1 }, { "tag": "protein-kinase-c", "type": 1 }, { "tag": "rnai screen", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "IUQHIQRV", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/IUQHIQRV", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/IUQHIQRV", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/28561/items/PMXDT4Z5", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "IUQHIQRV", "version": 7692, "parentItem": "PMXDT4Z5", "itemType": "note", "note": "

Free PMC Article

", "tags": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "D8VIXGD4", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/D8VIXGD4", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/D8VIXGD4", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/28561/items/BUC9IEB3", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "D8VIXGD4", "version": 7692, "parentItem": "BUC9IEB3", "itemType": "note", "note": "

Free PMC Article

", "tags": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "PMXDT4Z5", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/PMXDT4Z5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/PMXDT4Z5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Conrad et al.", "parsedDate": "2011-03", "numChildren": 1 }, "data": { "key": "PMXDT4Z5", "version": 7692, "itemType": "journalArticle", "title": "Micropilot: automation of fluorescence microscopy-based imaging for systems biology", "creators": [ { "creatorType": "author", "firstName": "Christian", "lastName": "Conrad" }, { "creatorType": "author", "firstName": "Annelie", "lastName": "Wuensche" }, { "creatorType": "author", "firstName": "Tze Heng", "lastName": "Tan" }, { "creatorType": "author", "firstName": "Jutta", "lastName": "Bulkescher" }, { "creatorType": "author", "firstName": "Frank", "lastName": "Sieckmann" }, { "creatorType": "author", "firstName": "Fatima", "lastName": "Verissimo" }, { "creatorType": "author", "firstName": "Arthur", "lastName": "Edelstein" }, { "creatorType": "author", "firstName": "Thomas", "lastName": "Walter" }, { "creatorType": "author", "firstName": "Urban", "lastName": "Liebel" }, { "creatorType": "author", "firstName": "Rainer", "lastName": "Pepperkok" }, { "creatorType": "author", "firstName": "Jan", "lastName": "Ellenberg" } ], "abstractNote": "Quantitative microscopy relies on imaging of large cell numbers but is often hampered by time-consuming manual selection of specific cells. The 'Micropilot' software automatically detects cells of interest and launches complex imaging experiments including three-dimensional multicolor time-lapse or fluorescence recovery after photobleaching in live cells. In three independent experimental setups this allowed us to statistically analyze biological processes in detail and is thus a powerful tool for systems biology.", "publicationTitle": "Nature Methods", "publisher": "", "place": "", "date": "MAR 2011", "volume": "8", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "246-U89", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Methods", "DOI": "10.1038/NMETH.1558", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1548-7091", "archive": "", "archiveLocation": "", "shortTitle": "Micropilot", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000287734800017", "tags": [ { "tag": "cellular phenotypes", "type": 1 }, { "tag": "dynamics", "type": 1 }, { "tag": "heterochromatin", "type": 1 }, { "tag": "human-cells", "type": 1 }, { "tag": "identification", "type": 1 }, { "tag": "selection", "type": 1 }, { "tag": "sites", "type": 1 }, { "tag": "support vector machines", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "G7PDAGMC", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/G7PDAGMC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/G7PDAGMC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Fededa and Gerlich", "parsedDate": "2012-05", "numChildren": 0 }, "data": { "key": "G7PDAGMC", "version": 7692, "itemType": "journalArticle", "title": "Molecular control of animal cell cytokinesis", "creators": [ { "creatorType": "author", "firstName": "Juan Pablo", "lastName": "Fededa" }, { "creatorType": "author", "firstName": "Daniel W.", "lastName": "Gerlich" } ], "abstractNote": "Cytokinesis is the process by which mitotic cells physically split in two following chromosome segregation. Dividing animal cells first ingress a cytokinetic furrow and then separate the plasma membrane by abscission. The general cytological events and several conserved molecular factors involved in cytokinesis have been known for many years. However, recent progress in microscopy, chemical genetics, biochemical reconstitution and biophysical methodology has tremendously increased our understanding of the underlying molecular mechanisms. We discuss how recent insights have led to refined models of the distinct steps of animal cell cytokinesis, including anaphase spindle reorganization, division plane specification, actomyosin ring assembly and contraction, and abscission. We highlight how molecular signalling pathways coordinate the individual events to ensure faithful partitioning of the genome to emerging daughter cells.", "publicationTitle": "Nature Cell Biology", "publisher": "", "place": "", "date": "MAY 2012", "volume": "14", "issue": "5", "section": "", "partNumber": "", "partTitle": "", "pages": "440-447", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Nat. Cell Biol.", "DOI": "10.1038/ncb2482", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1465-7392", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000303598300002", "tags": [ { "tag": "actomyosin contractile ring", "type": 1 }, { "tag": "aurora-b", "type": 1 }, { "tag": "central spindle", "type": 1 }, { "tag": "chromosomal passenger complex", "type": 1 }, { "tag": "cleavage furrow formation", "type": 1 }, { "tag": "escrt-iii", "type": 1 }, { "tag": "mediated abscission checkpoint", "type": 1 }, { "tag": "mitotic spindle", "type": 1 }, { "tag": "myosin-ii", "type": 1 }, { "tag": "polo-like kinase-1", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "BSQQS8UB", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/BSQQS8UB", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/BSQQS8UB", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Hoehndorf et al.", "parsedDate": "2012-07-01", "numChildren": 0 }, "data": { "key": "BSQQS8UB", "version": 7692, "itemType": "journalArticle", "title": "Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology", "creators": [ { "creatorType": "author", "firstName": "Robert", "lastName": "Hoehndorf" }, { "creatorType": "author", "firstName": "Midori A.", "lastName": "Harris" }, { "creatorType": "author", "firstName": "Heinrich", "lastName": "Herre" }, { "creatorType": "author", "firstName": "Gabriella", "lastName": "Rustici" }, { "creatorType": "author", "firstName": "Georgios V.", "lastName": "Gkoutos" } ], "abstractNote": "Motivation: The systematic observation of phenotypes has become a crucial tool of functional genomics, and several large international projects are currently underway to identify and characterize the phenotypes that are associated with genotypes in several species. To integrate phenotype descriptions within and across species, phenotype ontologies have been developed. Applying ontologies to unify phenotype descriptions in the domain of physiology has been a particular challenge due to the high complexity of the underlying domain. Results: In this study, we present the outline of a theory and its implementation for an ontology of physiology-related phenotypes. We provide a formal description of process attributes and relate them to the attributes of their temporal parts and participants. We apply our theory to create the Cellular Phenotype Ontology (CPO). The CPO is an ontology of morphological and physiological phenotypic characteristics of cells, cell components and cellular processes. Its prime application is to provide terms and uniform definition patterns for the annotation of cellular phenotypes. The CPO can be used for the annotation of observed abnormalities in domains, such as systems microscopy, in which cellular abnormalities are observed and for which no phenotype ontology has been created.", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "JUL 1 2012", "volume": "28", "issue": "13", "section": "", "partNumber": "", "partTitle": "", "pages": "1783-1789", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Bioinformatics", "DOI": "10.1093/bioinformatics/bts250", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1367-4803", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000305825600016", "tags": [ { "tag": "biology", "type": 1 }, { "tag": "genome", "type": 1 }, { "tag": "microscopy", "type": 1 }, { "tag": "obo", "type": 1 }, { "tag": "owl", "type": 1 }, { "tag": "tool", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "SRE28BFZ", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/SRE28BFZ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/SRE28BFZ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "van der Waal et al.", "parsedDate": "2012-09", "numChildren": 0 }, "data": { "key": "SRE28BFZ", "version": 7692, "itemType": "journalArticle", "title": "Mps1 promotes rapid centromere accumulation of Aurora B", "creators": [ { "creatorType": "author", "firstName": "Maike S.", "lastName": "van der Waal" }, { "creatorType": "author", "firstName": "Adrian T.", "lastName": "Saurin" }, { "creatorType": "author", "firstName": "Martijn J. M.", "lastName": "Vromans" }, { "creatorType": "author", "firstName": "Mathijs", "lastName": "Vleugel" }, { "creatorType": "author", "firstName": "Claudia", "lastName": "Wurzenberger" }, { "creatorType": "author", "firstName": "Daniel W.", "lastName": "Gerlich" }, { "creatorType": "author", "firstName": "Rene H.", "lastName": "Medema" }, { "creatorType": "author", "firstName": "Geert J. P. L.", "lastName": "Kops" }, { "creatorType": "author", "firstName": "Susanne M. A.", "lastName": "Lens" } ], "abstractNote": "Aurora B localization to mitotic centromeres, which is required for proper chromosome alignment during mitosis, relies on Haspin-dependent histone H3 phosphorylation and on Bub1-dependent histone H2A phosphorylation-which interacts with Borealin through a Shugoshin (Sgo) intermediate. We demonstrate that Mps1 stimulates the latter recruitment axis. Mps1 activity enhances H2A-T120ph and is critical for Sgo1 recruitment to centromeres, thereby promoting Aurora B centromere recruitment in early mitosis. Importantly, chromosome biorientation defects caused by Mps1 inhibition are improved by restoring Aurora B centromere recruitment. As Mps1 kinetochore localization reciprocally depends on Aurora B, we propose that this Aurora B-Mps1 recruitment circuitry cooperates with the Aurora B-Haspin feedback loop to ensure rapid centromere accumulation of Aurora B at the onset of mitosis.", "publicationTitle": "Embo Reports", "publisher": "", "place": "", "date": "SEP 2012", "volume": "13", "issue": "9", "section": "", "partNumber": "", "partTitle": "", "pages": "847-854", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "EMBO Rep.", "DOI": "10.1038/embor.2012.93", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1469-221X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000308564600019", "tags": [ { "tag": "Aurora B", "type": 1 }, { "tag": "Mps1", "type": 1 }, { "tag": "activation", "type": 1 }, { "tag": "alignment", "type": 1 }, { "tag": "anaphase", "type": 1 }, { "tag": "biorientation", "type": 1 }, { "tag": "centromere", "type": 1 }, { "tag": "chromosome biorientation", "type": 1 }, { "tag": "kinase", "type": 1 }, { "tag": "kinetochores", "type": 1 }, { "tag": "mitosis", "type": 1 }, { "tag": "orientation", "type": 1 }, { "tag": "phosphorylation gradient", "type": 1 }, { "tag": "spindle assembly checkpoint", "type": 1 } ], "collections": [], "relations": {}, "dateAdded": "2013-03-12T10:47:59Z", "dateModified": "2013-03-12T10:47:59Z" } }, { "key": "DWPK869P", "version": 7693, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/DWPK869P", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/DWPK869P", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Navas et al.", "parsedDate": "2012-09-11", "numChildren": 0 }, "data": { "key": "DWPK869P", "version": 7693, "itemType": "journalArticle", "title": "EGF Receptor Signaling Is Essential for K-Ras Oncogene-Driven Pancreatic Ductal Adenocarcinoma", "creators": [ { "creatorType": "author", "firstName": "Carolina", "lastName": "Navas" }, { "creatorType": "author", "firstName": "Isabel", "lastName": "Hernandez-Porras" }, { "creatorType": "author", "firstName": "Alberto J.", "lastName": "Schuhmacher" }, { "creatorType": "author", "firstName": "Maria", "lastName": "Sibilia" }, { "creatorType": "author", "firstName": "Carmen", "lastName": "Guerra" }, { "creatorType": "author", "firstName": "Mariano", "lastName": "Barbacid" } ], "abstractNote": "Clinical evidence indicates that mutation/activation of EGF receptors (EGFRs) is mutually exclusive with the presence of K-RAS oncogenes in lung and colon tumors. We have validated these observations using genetically engineered mouse models. However, development of pancreatic ductal adenocarcinomas driven by K-Ras oncogenes are totally dependent on EGFR signaling. Similar results were obtained using human pancreatic tumor cell lines. EGFRs were also essential even in the context of pancreatic injury and absence of p16Ink4a/p19Arf. Only loss of p53 made pancreatic tumors independent of EGFR signaling. Additional inhibition of PI3K and STAT3 effectively prevented proliferation of explants derived from these p53-defective pancreatic tumors. These findings may provide the bases for more rational approaches to treat pancreatic tumors in the clinic.", "publicationTitle": "Cancer Cell", "publisher": "", "place": "", "date": "SEP 11 2012", "volume": "22", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "318-330", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cancer Cell", "DOI": "10.1016/j.ccr.2012.08.001", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "1535-6108", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000308735400008", "tags": [ { "tag": "Survival", "type": 1 }, { "tag": "cancer", "type": 1 }, { "tag": "carcinoma", "type": 1 }, { "tag": "gemcitabine", "type": 1 }, { "tag": "growth-factor receptor", "type": 1 }, { "tag": "inhibitor", "type": 1 }, { "tag": "intraepithelial neoplasia", "type": 1 }, { "tag": "mouse model", "type": 1 }, { "tag": "mutations", "type": 1 }, { "tag": "progression", "type": 1 } ], "collections": [ "THN2E49S" ], "relations": {}, "dateAdded": "2013-03-11T13:33:35Z", "dateModified": "2013-03-11T13:33:35Z" } }, { "key": "WVPHDHFC", "version": 7692, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/WVPHDHFC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/WVPHDHFC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "creatorSummary": "Jaspers et al.", "parsedDate": "2013-01", "numChildren": 0 }, "data": { "key": "WVPHDHFC", "version": 7692, "itemType": "journalArticle", "title": "Loss of 53BP1 Causes PARP Inhibitor Resistance in Brca1-Mutated Mouse Mammary Tumors", "creators": [ { "creatorType": "author", "firstName": "Janneke E.", "lastName": "Jaspers" }, { "creatorType": "author", "firstName": "Ariena", "lastName": "Kersbergen" }, { "creatorType": "author", "firstName": "Ute", "lastName": "Boon" }, { "creatorType": "author", "firstName": "Wendy", "lastName": "Sol" }, { "creatorType": "author", "firstName": "Liesbeth", "lastName": "van Deemter" }, { "creatorType": "author", "firstName": "Serge A.", "lastName": "Zander" }, { "creatorType": "author", "firstName": "Rinske", "lastName": "Drost" }, { "creatorType": "author", "firstName": "Ellen", "lastName": "Wientjens" }, { "creatorType": "author", "firstName": "Jiuping", "lastName": "Ji" }, { "creatorType": "author", "firstName": "Amal", "lastName": "Aly" }, { "creatorType": "author", "firstName": "James H.", "lastName": "Doroshow" }, { "creatorType": "author", "firstName": "Aaron", "lastName": "Cranston" }, { "creatorType": "author", "firstName": "Niall M. B.", "lastName": "Martin" }, { "creatorType": "author", "firstName": "Alan", "lastName": "Lau" }, { "creatorType": "author", "firstName": "Mark J.", "lastName": "O'Connor" }, { "creatorType": "author", "firstName": "Shridar", "lastName": "Ganesan" }, { "creatorType": "author", "firstName": "Piet", "lastName": "Borst" }, { "creatorType": "author", "firstName": "Jos", "lastName": "Jonkers" }, { "creatorType": "author", "firstName": "Sven", "lastName": "Rottenberg" } ], "abstractNote": "Inhibition of PARP is a promising therapeutic strategy for homologous recombination-deficient tumors, such as BRCA1-associated cancers. We previously reported that BRCA1-deficient mouse mammary tumors may acquire resistance to the clinical PARP inhibitor (PARPi) olaparib through activation of the P-glycoprotein drug efflux transporter. Here, we show that tumorspecific genetic inactivation of P-glycoprotein increases the long-term response of BRCA1-deficient mouse mammary tumors to olaparib, but these tumors eventually developed PARPi resistance. In a fraction of cases, this resistance is caused by partial restoration of homologous recombination due to somatic loss of 53BP1. Importantly, PARPi resistance was minimized by long-term treatment with the novel PARP inhibitor AZD2461, which is a poor P-glycoprotein substrate. Together, our data suggest that restoration of homologous recombination is an important mechanism for PARPi resistance in BRCA1-deficient mammary tumors and that the risk of relapse of BRCA1-deficient tumors can be effectively minimized by using optimized PARP inhibitors.", "publicationTitle": "Cancer Discovery", "publisher": "", "place": "", "date": "JAN 2013", "volume": "3", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "68-81", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "Cancer Discov.", "DOI": "10.1158/2159-8290.CD-12-0049", "citationKey": "", "url": "", "accessDate": "", "PMID": "", "PMCID": "", "ISSN": "2159-8274", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "English", "libraryCatalog": "ISI Web of Knowledge", "callNumber": "", "rights": "", "extra": "WOS:000313642900025", "tags": [ { "tag": "brca1", "type": 1 }, { "tag": "brca2-deficient tumors", "type": 1 }, { "tag": "cell-cycle", "type": 1 }, { "tag": "chemotherapy resistance", "type": 1 }, { "tag": "dna-end resection", "type": 1 }, { "tag": "homologous recombination", "type": 1 }, { "tag": "ovarian carcinomas", "type": 1 }, { "tag": "poly(adp-ribose) polymerase", "type": 1 }, { "tag": "sensitivity", "type": 1 }, { "tag": "strand-break repair", "type": 1 } ], "collections": [ "THN2E49S" ], "relations": {}, "dateAdded": "2013-03-11T13:33:35Z", "dateModified": "2013-03-11T13:33:35Z" } }, { "key": "3QG93R5G", "version": 7690, "library": { "type": "group", "id": 28561, "name": "OpenAIRE - FP7", "links": { "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/28561/items/3QG93R5G", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/openaire_-_fp7/items/3QG93R5G", "type": "text/html" }, "up": { "href": "https://api.zotero.org/groups/28561/items/676XMUWF", "type": "application/json" } }, "meta": { "createdByUser": { "id": 1331492, "username": "publications.ki.se", "name": "", "links": { "alternate": { "href": "https://www.zotero.org/publications.ki.se", "type": "text/html" } } }, "numChildren": 0 }, "data": { "key": "3QG93R5G", "version": 7690, "parentItem": "676XMUWF", "itemType": "note", "note": "

Free PMC Article

", "tags": [], "relations": {}, "dateAdded": "2013-03-11T13:33:35Z", "dateModified": "2013-03-11T13:33:35Z" } } ]