Identification and characterization of a 19q12 amplicon in esophageal adenocarcinomas reveals Cyclin E as the best candidate gene for this amplicon
Genomic DNA amplification in tumors is frequently associated with an increased gene copy number of oncogenes or other cancer-related genes. We have used a two-dimensional whole-genome scanning technique to identify gene amplification events in esophageal adenocarcinomas. A multicopy genomic fragment...
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| Veröffentlicht in: | Cancer research (Chicago, Ill.) Ill.), 2000-12, Vol.60 (24), p.7021-7027 |
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| creator | LIN LIN PRESCOTT, Michael S ZHOUQIN ZHU PUJA SINGH CHUN, Sang Y KUICK, Rork D HANASH, Samir M ORRINGER, Mark B GLOVER, Thomas W BEER, David G |
| description | Genomic DNA amplification in tumors is frequently associated with an increased gene copy number of oncogenes or other cancer-related genes. We have used a two-dimensional whole-genome scanning technique to identify gene amplification events in esophageal adenocarcinomas. A multicopy genomic fragment from a tumor two-dimensional gel was cloned, and genomic amplification encompassing this fragment was confirmed by Southern blot analysis. The corresponding DNA sequence was matched by BLAST to a BAC contig, which allowed the use of electronic-PCR to localize this amplicon to 19q12. Sequence tagged site-amplification mapping, an approach recently implemented in our laboratory (Lin, L. et al., Cancer Res., 60: 1341-1347,2000), was used to characterize the amplicon. Genomic DNA from 65 esophageal and 11 gastric cardia adenocarcinomas were investigated for 19q12 amplification using quantitative PCR at 11 sequence tagged site markers neighboring the cloned fragment. The amplicon was narrowed from >8 cM to a minimal critical region spanning |
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We have used a two-dimensional whole-genome scanning technique to identify gene amplification events in esophageal adenocarcinomas. A multicopy genomic fragment from a tumor two-dimensional gel was cloned, and genomic amplification encompassing this fragment was confirmed by Southern blot analysis. The corresponding DNA sequence was matched by BLAST to a BAC contig, which allowed the use of electronic-PCR to localize this amplicon to 19q12. Sequence tagged site-amplification mapping, an approach recently implemented in our laboratory (Lin, L. et al., Cancer Res., 60: 1341-1347,2000), was used to characterize the amplicon. Genomic DNA from 65 esophageal and 11 gastric cardia adenocarcinomas were investigated for 19q12 amplification using quantitative PCR at 11 sequence tagged site markers neighboring the cloned fragment. The amplicon was narrowed from >8 cM to a minimal critical region spanning <0.8 cM, between D19S919 and D19S882. This region includes the cyclin E gene. Fourteen expressed sequence tags (ESTs) covering the minimal region were then assayed for potential gene overexpression using quantitative reverse transcription-PCR. Seven of the selected ESTs were found to be both amplified and overexpressed. Among these seven ESTs, cyclin E showed the highest frequency of gene amplification and overexpression in the tumors examined, which allowed us to finalize the core-amplified region to <300 kb. These results indicate that cyclin E is the likely target gene selected by the amplification event at 19q12. The fact that cyclin E overexpression was found only in the amplified tumors examined indicates that gene amplification underlies the cyclin E gene overexpression. Our study represents the first extensive analysis of the 19q12 amplicon, and is the first to physically map the core-amplified domain to a region of <300 kb that includes cyclin E. Amplification of 19q12 was found neither in the 28 esophageal squamous cancers nor in the 39 lung adenocarcinomas examined but was observed in 13.8% of esophageal and 9.1% of gastric cardia adenocarcinomas.</description><identifier>ISSN: 0008-5472</identifier><identifier>EISSN: 1538-7445</identifier><identifier>PMID: 11156406</identifier><identifier>CODEN: CNREA8</identifier><language>eng</language><publisher>Philadelphia, PA: American Association for Cancer Research</publisher><subject>Adenocarcinoma - genetics ; Biological and medical sciences ; Blotting, Southern ; Carcinoma, Squamous Cell - genetics ; Carcinoma, Squamous Cell - pathology ; chromosome 19 ; Chromosome Mapping ; Chromosomes, Human, Pair 19 ; Cloning, Molecular ; Contig Mapping ; Cyclin E - biosynthesis ; Cyclin E - genetics ; Electrophoresis, Gel, Two-Dimensional ; Esophageal Neoplasms - genetics ; Esophageal Neoplasms - metabolism ; Esophageal Neoplasms - pathology ; Esophagus ; Esophagus - metabolism ; Esophagus - pathology ; Expressed Sequence Tags ; Gastroenterology. Liver. Pancreas. Abdomen ; Humans ; Lung Neoplasms - genetics ; Medical sciences ; Models, Genetic ; Polymerase Chain Reaction ; Reverse Transcriptase Polymerase Chain Reaction ; Stomach Neoplasms - genetics ; Stomach Neoplasms - pathology ; Tumors</subject><ispartof>Cancer research (Chicago, Ill.), 2000-12, Vol.60 (24), p.7021-7027</ispartof><rights>2001 INIST-CNRS</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>314,780,784</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=849702$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/11156406$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>LIN LIN</creatorcontrib><creatorcontrib>PRESCOTT, Michael S</creatorcontrib><creatorcontrib>ZHOUQIN ZHU</creatorcontrib><creatorcontrib>PUJA SINGH</creatorcontrib><creatorcontrib>CHUN, Sang Y</creatorcontrib><creatorcontrib>KUICK, Rork D</creatorcontrib><creatorcontrib>HANASH, Samir M</creatorcontrib><creatorcontrib>ORRINGER, Mark B</creatorcontrib><creatorcontrib>GLOVER, Thomas W</creatorcontrib><creatorcontrib>BEER, David G</creatorcontrib><title>Identification and characterization of a 19q12 amplicon in esophageal adenocarcinomas reveals Cyclin E as the best candidate gene for this amplicon</title><title>Cancer research (Chicago, Ill.)</title><addtitle>Cancer Res</addtitle><description>Genomic DNA amplification in tumors is frequently associated with an increased gene copy number of oncogenes or other cancer-related genes. We have used a two-dimensional whole-genome scanning technique to identify gene amplification events in esophageal adenocarcinomas. A multicopy genomic fragment from a tumor two-dimensional gel was cloned, and genomic amplification encompassing this fragment was confirmed by Southern blot analysis. The corresponding DNA sequence was matched by BLAST to a BAC contig, which allowed the use of electronic-PCR to localize this amplicon to 19q12. Sequence tagged site-amplification mapping, an approach recently implemented in our laboratory (Lin, L. et al., Cancer Res., 60: 1341-1347,2000), was used to characterize the amplicon. Genomic DNA from 65 esophageal and 11 gastric cardia adenocarcinomas were investigated for 19q12 amplification using quantitative PCR at 11 sequence tagged site markers neighboring the cloned fragment. The amplicon was narrowed from >8 cM to a minimal critical region spanning <0.8 cM, between D19S919 and D19S882. This region includes the cyclin E gene. Fourteen expressed sequence tags (ESTs) covering the minimal region were then assayed for potential gene overexpression using quantitative reverse transcription-PCR. Seven of the selected ESTs were found to be both amplified and overexpressed. Among these seven ESTs, cyclin E showed the highest frequency of gene amplification and overexpression in the tumors examined, which allowed us to finalize the core-amplified region to <300 kb. These results indicate that cyclin E is the likely target gene selected by the amplification event at 19q12. The fact that cyclin E overexpression was found only in the amplified tumors examined indicates that gene amplification underlies the cyclin E gene overexpression. Our study represents the first extensive analysis of the 19q12 amplicon, and is the first to physically map the core-amplified domain to a region of <300 kb that includes cyclin E. Amplification of 19q12 was found neither in the 28 esophageal squamous cancers nor in the 39 lung adenocarcinomas examined but was observed in 13.8% of esophageal and 9.1% of gastric cardia adenocarcinomas.</description><subject>Adenocarcinoma - genetics</subject><subject>Biological and medical sciences</subject><subject>Blotting, Southern</subject><subject>Carcinoma, Squamous Cell - genetics</subject><subject>Carcinoma, Squamous Cell - pathology</subject><subject>chromosome 19</subject><subject>Chromosome Mapping</subject><subject>Chromosomes, Human, Pair 19</subject><subject>Cloning, Molecular</subject><subject>Contig Mapping</subject><subject>Cyclin E - biosynthesis</subject><subject>Cyclin E - genetics</subject><subject>Electrophoresis, Gel, Two-Dimensional</subject><subject>Esophageal Neoplasms - genetics</subject><subject>Esophageal Neoplasms - metabolism</subject><subject>Esophageal Neoplasms - pathology</subject><subject>Esophagus</subject><subject>Esophagus - metabolism</subject><subject>Esophagus - pathology</subject><subject>Expressed Sequence Tags</subject><subject>Gastroenterology. Liver. Pancreas. Abdomen</subject><subject>Humans</subject><subject>Lung Neoplasms - genetics</subject><subject>Medical sciences</subject><subject>Models, Genetic</subject><subject>Polymerase Chain Reaction</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>Stomach Neoplasms - genetics</subject><subject>Stomach Neoplasms - pathology</subject><subject>Tumors</subject><issn>0008-5472</issn><issn>1538-7445</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2000</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkE1Lw0AQhoMotlb_giwI3gL7kc3HUUrVQsGLnsNkd7ZZSTbpbirUv-EfdqG1Vy8zzDvPvDPMRTJnUpRpkWXyMplTSstUZgWfJTchfMZSMiqvkxljTOYZzefJz1qjm6yxCiY7OAJOE9WCBzWht99HcTAECKt2jBPox86qqFlHMAxjC1uEjkB0GRR4Zd3QQyAev6IcyPKgukiuSNSmFkmDYSIqLrEaJiRbdEjM4GPPhrP3bXJl4jDenfIi-XhevS9f083by3r5tElbQemUloqWXOclbyqkFCs0VHEuC8MVz1lZKW1Q6FxziNFkUmKJBhkKZTQ0RopF8nj0Hf2w28fL6t4GhV0HDod9qAsuRcGL_0FWVExIxiJ4fwL3TY-6Hr3twR_qv39H4OEEQFDQGQ9O2XDmyqwqKBe_vOiMGQ</recordid><startdate>20001215</startdate><enddate>20001215</enddate><creator>LIN LIN</creator><creator>PRESCOTT, Michael S</creator><creator>ZHOUQIN ZHU</creator><creator>PUJA SINGH</creator><creator>CHUN, Sang Y</creator><creator>KUICK, Rork D</creator><creator>HANASH, Samir M</creator><creator>ORRINGER, Mark B</creator><creator>GLOVER, Thomas W</creator><creator>BEER, David G</creator><general>American Association for Cancer Research</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>8FD</scope><scope>FR3</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20001215</creationdate><title>Identification and characterization of a 19q12 amplicon in esophageal adenocarcinomas reveals Cyclin E as the best candidate gene for this amplicon</title><author>LIN LIN ; PRESCOTT, Michael S ; ZHOUQIN ZHU ; PUJA SINGH ; CHUN, Sang Y ; KUICK, Rork D ; HANASH, Samir M ; ORRINGER, Mark B ; GLOVER, Thomas W ; BEER, David G</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-h300t-8c082d682b9e00e9ef0c2257f2c26189cdfe3d6d2a3d6f455e8efe1e3cfdabf53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2000</creationdate><topic>Adenocarcinoma - genetics</topic><topic>Biological and medical sciences</topic><topic>Blotting, Southern</topic><topic>Carcinoma, Squamous Cell - genetics</topic><topic>Carcinoma, Squamous Cell - pathology</topic><topic>chromosome 19</topic><topic>Chromosome Mapping</topic><topic>Chromosomes, Human, Pair 19</topic><topic>Cloning, Molecular</topic><topic>Contig Mapping</topic><topic>Cyclin E - biosynthesis</topic><topic>Cyclin E - genetics</topic><topic>Electrophoresis, Gel, Two-Dimensional</topic><topic>Esophageal Neoplasms - genetics</topic><topic>Esophageal Neoplasms - metabolism</topic><topic>Esophageal Neoplasms - pathology</topic><topic>Esophagus</topic><topic>Esophagus - metabolism</topic><topic>Esophagus - pathology</topic><topic>Expressed Sequence Tags</topic><topic>Gastroenterology. Liver. Pancreas. Abdomen</topic><topic>Humans</topic><topic>Lung Neoplasms - genetics</topic><topic>Medical sciences</topic><topic>Models, Genetic</topic><topic>Polymerase Chain Reaction</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>Stomach Neoplasms - genetics</topic><topic>Stomach Neoplasms - pathology</topic><topic>Tumors</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>LIN LIN</creatorcontrib><creatorcontrib>PRESCOTT, Michael S</creatorcontrib><creatorcontrib>ZHOUQIN ZHU</creatorcontrib><creatorcontrib>PUJA SINGH</creatorcontrib><creatorcontrib>CHUN, Sang Y</creatorcontrib><creatorcontrib>KUICK, Rork D</creatorcontrib><creatorcontrib>HANASH, Samir M</creatorcontrib><creatorcontrib>ORRINGER, Mark B</creatorcontrib><creatorcontrib>GLOVER, Thomas W</creatorcontrib><creatorcontrib>BEER, David G</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Cancer research (Chicago, Ill.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>LIN LIN</au><au>PRESCOTT, Michael S</au><au>ZHOUQIN ZHU</au><au>PUJA SINGH</au><au>CHUN, Sang Y</au><au>KUICK, Rork D</au><au>HANASH, Samir M</au><au>ORRINGER, Mark B</au><au>GLOVER, Thomas W</au><au>BEER, David G</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification and characterization of a 19q12 amplicon in esophageal adenocarcinomas reveals Cyclin E as the best candidate gene for this amplicon</atitle><jtitle>Cancer research (Chicago, Ill.)</jtitle><addtitle>Cancer Res</addtitle><date>2000-12-15</date><risdate>2000</risdate><volume>60</volume><issue>24</issue><spage>7021</spage><epage>7027</epage><pages>7021-7027</pages><issn>0008-5472</issn><eissn>1538-7445</eissn><coden>CNREA8</coden><abstract>Genomic DNA amplification in tumors is frequently associated with an increased gene copy number of oncogenes or other cancer-related genes. We have used a two-dimensional whole-genome scanning technique to identify gene amplification events in esophageal adenocarcinomas. A multicopy genomic fragment from a tumor two-dimensional gel was cloned, and genomic amplification encompassing this fragment was confirmed by Southern blot analysis. The corresponding DNA sequence was matched by BLAST to a BAC contig, which allowed the use of electronic-PCR to localize this amplicon to 19q12. Sequence tagged site-amplification mapping, an approach recently implemented in our laboratory (Lin, L. et al., Cancer Res., 60: 1341-1347,2000), was used to characterize the amplicon. Genomic DNA from 65 esophageal and 11 gastric cardia adenocarcinomas were investigated for 19q12 amplification using quantitative PCR at 11 sequence tagged site markers neighboring the cloned fragment. The amplicon was narrowed from >8 cM to a minimal critical region spanning <0.8 cM, between D19S919 and D19S882. This region includes the cyclin E gene. Fourteen expressed sequence tags (ESTs) covering the minimal region were then assayed for potential gene overexpression using quantitative reverse transcription-PCR. Seven of the selected ESTs were found to be both amplified and overexpressed. Among these seven ESTs, cyclin E showed the highest frequency of gene amplification and overexpression in the tumors examined, which allowed us to finalize the core-amplified region to <300 kb. These results indicate that cyclin E is the likely target gene selected by the amplification event at 19q12. The fact that cyclin E overexpression was found only in the amplified tumors examined indicates that gene amplification underlies the cyclin E gene overexpression. Our study represents the first extensive analysis of the 19q12 amplicon, and is the first to physically map the core-amplified domain to a region of <300 kb that includes cyclin E. Amplification of 19q12 was found neither in the 28 esophageal squamous cancers nor in the 39 lung adenocarcinomas examined but was observed in 13.8% of esophageal and 9.1% of gastric cardia adenocarcinomas.</abstract><cop>Philadelphia, PA</cop><pub>American Association for Cancer Research</pub><pmid>11156406</pmid><tpages>7</tpages></addata></record> |
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| subjects | Adenocarcinoma - genetics Biological and medical sciences Blotting, Southern Carcinoma, Squamous Cell - genetics Carcinoma, Squamous Cell - pathology chromosome 19 Chromosome Mapping Chromosomes, Human, Pair 19 Cloning, Molecular Contig Mapping Cyclin E - biosynthesis Cyclin E - genetics Electrophoresis, Gel, Two-Dimensional Esophageal Neoplasms - genetics Esophageal Neoplasms - metabolism Esophageal Neoplasms - pathology Esophagus Esophagus - metabolism Esophagus - pathology Expressed Sequence Tags Gastroenterology. Liver. Pancreas. Abdomen Humans Lung Neoplasms - genetics Medical sciences Models, Genetic Polymerase Chain Reaction Reverse Transcriptase Polymerase Chain Reaction Stomach Neoplasms - genetics Stomach Neoplasms - pathology Tumors |
| title | Identification and characterization of a 19q12 amplicon in esophageal adenocarcinomas reveals Cyclin E as the best candidate gene for this amplicon |
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