Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure
1 National Research Center for Environment and Health (GSF), Institute for Inhalation Biology, Neuherberg, Germany 2 Center for Environmental Genetics, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio 3 Department of Environmental and Occupational Health, University of...
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| Veröffentlicht in: | Physiological genomics 2007-11, Vol.31 (3), p.410-421 |
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| creator | Ganguly, Koustav Stoeger, Tobias Wesselkamper, Scott C Reinhard, Claudia Sartor, Maureen A Medvedovic, Mario Tomlinson, Craig R Bolle, Ines Mason, John M Leikauf, George D Schulz, Holger |
| description | 1 National Research Center for Environment and Health (GSF), Institute for Inhalation Biology, Neuherberg, Germany
2 Center for Environmental Genetics, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio
3 Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
Impaired development and reduced lung capacity are risk factors of asthma and chronic obstructive pulmonary disease. Previously, our genomewide linkage analysis of C3H/HeJ (C3H) and JF1/Msf (JF1) mouse strains identified quantitative trait loci (QTLs) associated with the complex traits of dead space volume (V D ), total lung capacity (TLC), lung compliance (C L ), and diffusing capacity for CO (D CO ). We assessed positional candidate genes by comparing C3H with JF1 lung transcript levels by microarray and by comparing C3H, BALB/cByJ, C57BL/6J, A/J, PWD/PhJ, and JF1 strains, using exon sequencing to predict protein structure. Microarray identified >900 transcripts differing in C3H and JF1 lungs related to lung development, function, and remodeling. Of these, three genes localized to QTLs associated with differences in lung function. C3H and JF1 strains differed in transcript and protein levels of superoxide dismutase 3, extracellular [SOD3; mouse chromosome (mCh) 5: V D ] and transcript of trefoil factor 2 (TFF2; mCh 17: TLC and D CO ), and ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2; mCh 15: TLC and C L ). Nucleotide sequencing of Sod3 , Tff2 , and previously identified Relaxin 1 ( Rln1 ; mCh 19: C L ) uncovered polymorphisms that could lead to nonsynonymous amino acid changes and altered predicted protein structure. Gene-targeted Sod3 –/– mice had increased conducting airway volume (V D /TLC) compared with strain-matched control Sod3 +/+ mice, consistent with the QTL on mCh 5. Two novel genes ( Tff2 and Enpp2 ) have been identified and two suspected genes ( Sod3 and Rln1 ) have been supported as determinants of lung function in mice. Findings with gene-targeted mice suggest that SOD3 is a contributing factor defining the complex trait of conducting airway volume.
complex trait; chronic obstructive pulmonary disease; asthma; Sod3 |
| doi_str_mv | 10.1152/physiolgenomics.00260.2006 |
| format | Article |
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2 Center for Environmental Genetics, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio
3 Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
Impaired development and reduced lung capacity are risk factors of asthma and chronic obstructive pulmonary disease. Previously, our genomewide linkage analysis of C3H/HeJ (C3H) and JF1/Msf (JF1) mouse strains identified quantitative trait loci (QTLs) associated with the complex traits of dead space volume (V D ), total lung capacity (TLC), lung compliance (C L ), and diffusing capacity for CO (D CO ). We assessed positional candidate genes by comparing C3H with JF1 lung transcript levels by microarray and by comparing C3H, BALB/cByJ, C57BL/6J, A/J, PWD/PhJ, and JF1 strains, using exon sequencing to predict protein structure. Microarray identified >900 transcripts differing in C3H and JF1 lungs related to lung development, function, and remodeling. Of these, three genes localized to QTLs associated with differences in lung function. C3H and JF1 strains differed in transcript and protein levels of superoxide dismutase 3, extracellular [SOD3; mouse chromosome (mCh) 5: V D ] and transcript of trefoil factor 2 (TFF2; mCh 17: TLC and D CO ), and ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2; mCh 15: TLC and C L ). Nucleotide sequencing of Sod3 , Tff2 , and previously identified Relaxin 1 ( Rln1 ; mCh 19: C L ) uncovered polymorphisms that could lead to nonsynonymous amino acid changes and altered predicted protein structure. Gene-targeted Sod3 –/– mice had increased conducting airway volume (V D /TLC) compared with strain-matched control Sod3 +/+ mice, consistent with the QTL on mCh 5. Two novel genes ( Tff2 and Enpp2 ) have been identified and two suspected genes ( Sod3 and Rln1 ) have been supported as determinants of lung function in mice. Findings with gene-targeted mice suggest that SOD3 is a contributing factor defining the complex trait of conducting airway volume.
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2 Center for Environmental Genetics, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio
3 Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
Impaired development and reduced lung capacity are risk factors of asthma and chronic obstructive pulmonary disease. Previously, our genomewide linkage analysis of C3H/HeJ (C3H) and JF1/Msf (JF1) mouse strains identified quantitative trait loci (QTLs) associated with the complex traits of dead space volume (V D ), total lung capacity (TLC), lung compliance (C L ), and diffusing capacity for CO (D CO ). We assessed positional candidate genes by comparing C3H with JF1 lung transcript levels by microarray and by comparing C3H, BALB/cByJ, C57BL/6J, A/J, PWD/PhJ, and JF1 strains, using exon sequencing to predict protein structure. Microarray identified >900 transcripts differing in C3H and JF1 lungs related to lung development, function, and remodeling. Of these, three genes localized to QTLs associated with differences in lung function. C3H and JF1 strains differed in transcript and protein levels of superoxide dismutase 3, extracellular [SOD3; mouse chromosome (mCh) 5: V D ] and transcript of trefoil factor 2 (TFF2; mCh 17: TLC and D CO ), and ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2; mCh 15: TLC and C L ). Nucleotide sequencing of Sod3 , Tff2 , and previously identified Relaxin 1 ( Rln1 ; mCh 19: C L ) uncovered polymorphisms that could lead to nonsynonymous amino acid changes and altered predicted protein structure. Gene-targeted Sod3 –/– mice had increased conducting airway volume (V D /TLC) compared with strain-matched control Sod3 +/+ mice, consistent with the QTL on mCh 5. Two novel genes ( Tff2 and Enpp2 ) have been identified and two suspected genes ( Sod3 and Rln1 ) have been supported as determinants of lung function in mice. Findings with gene-targeted mice suggest that SOD3 is a contributing factor defining the complex trait of conducting airway volume.
complex trait; chronic obstructive pulmonary disease; asthma; Sod3</description><subject>Animals</subject><subject>Female</subject><subject>Gene Expression Profiling</subject><subject>Male</subject><subject>Mice</subject><subject>Mice, Inbred Strains</subject><subject>Mice, Knockout</subject><subject>Polymorphism, Genetic</subject><subject>Quantitative Trait Loci</subject><subject>Respiratory Function Tests</subject><subject>RNA, Messenger - genetics</subject><subject>Species Specificity</subject><subject>Superoxide Dismutase - genetics</subject><issn>1094-8341</issn><issn>1531-2267</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp1kEFr3DAQhUVpSdI0f6GYHHrzViPLsp1LCUvSFgK9pGchy-NdFVlyJZlm_3202Q2BhAqEZsT73kiPkEugK4CafZ23u2i83aDzk9FxRSkTdMUoFe_IGdQVlIyJ5n2uacfLtuJwSj7G-IdS4E1bn5BTaFrKBWVnxK6VG8ygEhbZD2OhvUvBW2vcppgXO3mnwq4YF6eT8a4wrsgz8apIQbmog5lTMQc_micge-UOB6MT7iufMAMxhUWnJeAn8mFUNuLF8Twnv29v7tc_yrtf33-ur-9KzaFJpaoFcKoEwy4v3jA2QpOvsBY4CNRdN7Q9tqznvGfNqLGqeuCd7jBvldtz8uXgm1_wd8GY5GSiRmuVQ79EKdoaqKCQhVcHoQ4-xoCjnIOZ8oclULnPWr7KWj5lLfdZZ_jzccrSTzi8oMdws6A6CLZms_1nAj67-c3ujXEFspIcaKa-_Z-6Xay9x4f0Gn-m5TyM1SMBZq5V</recordid><startdate>20071114</startdate><enddate>20071114</enddate><creator>Ganguly, Koustav</creator><creator>Stoeger, Tobias</creator><creator>Wesselkamper, Scott C</creator><creator>Reinhard, Claudia</creator><creator>Sartor, Maureen A</creator><creator>Medvedovic, Mario</creator><creator>Tomlinson, Craig R</creator><creator>Bolle, Ines</creator><creator>Mason, John M</creator><creator>Leikauf, George D</creator><creator>Schulz, Holger</creator><general>Am Physiological Soc</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20071114</creationdate><title>Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure</title><author>Ganguly, Koustav ; Stoeger, Tobias ; Wesselkamper, Scott C ; Reinhard, Claudia ; Sartor, Maureen A ; Medvedovic, Mario ; Tomlinson, Craig R ; Bolle, Ines ; Mason, John M ; Leikauf, George D ; Schulz, Holger</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c417t-a56140a62e99994722f17614e56ed6ec99d8be82b44b27fce33b149c9e9c9ace3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>Animals</topic><topic>Female</topic><topic>Gene Expression Profiling</topic><topic>Male</topic><topic>Mice</topic><topic>Mice, Inbred Strains</topic><topic>Mice, Knockout</topic><topic>Polymorphism, Genetic</topic><topic>Quantitative Trait Loci</topic><topic>Respiratory Function Tests</topic><topic>RNA, Messenger - genetics</topic><topic>Species Specificity</topic><topic>Superoxide Dismutase - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ganguly, Koustav</creatorcontrib><creatorcontrib>Stoeger, Tobias</creatorcontrib><creatorcontrib>Wesselkamper, Scott C</creatorcontrib><creatorcontrib>Reinhard, Claudia</creatorcontrib><creatorcontrib>Sartor, Maureen A</creatorcontrib><creatorcontrib>Medvedovic, Mario</creatorcontrib><creatorcontrib>Tomlinson, Craig R</creatorcontrib><creatorcontrib>Bolle, Ines</creatorcontrib><creatorcontrib>Mason, John M</creatorcontrib><creatorcontrib>Leikauf, George D</creatorcontrib><creatorcontrib>Schulz, Holger</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Physiological genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ganguly, Koustav</au><au>Stoeger, Tobias</au><au>Wesselkamper, Scott C</au><au>Reinhard, Claudia</au><au>Sartor, Maureen A</au><au>Medvedovic, Mario</au><au>Tomlinson, Craig R</au><au>Bolle, Ines</au><au>Mason, John M</au><au>Leikauf, George D</au><au>Schulz, Holger</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure</atitle><jtitle>Physiological genomics</jtitle><addtitle>Physiol Genomics</addtitle><date>2007-11-14</date><risdate>2007</risdate><volume>31</volume><issue>3</issue><spage>410</spage><epage>421</epage><pages>410-421</pages><issn>1094-8341</issn><eissn>1531-2267</eissn><abstract>1 National Research Center for Environment and Health (GSF), Institute for Inhalation Biology, Neuherberg, Germany
2 Center for Environmental Genetics, Department of Environmental Health, University of Cincinnati, Cincinnati, Ohio
3 Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, Pennsylvania
Impaired development and reduced lung capacity are risk factors of asthma and chronic obstructive pulmonary disease. Previously, our genomewide linkage analysis of C3H/HeJ (C3H) and JF1/Msf (JF1) mouse strains identified quantitative trait loci (QTLs) associated with the complex traits of dead space volume (V D ), total lung capacity (TLC), lung compliance (C L ), and diffusing capacity for CO (D CO ). We assessed positional candidate genes by comparing C3H with JF1 lung transcript levels by microarray and by comparing C3H, BALB/cByJ, C57BL/6J, A/J, PWD/PhJ, and JF1 strains, using exon sequencing to predict protein structure. Microarray identified >900 transcripts differing in C3H and JF1 lungs related to lung development, function, and remodeling. Of these, three genes localized to QTLs associated with differences in lung function. C3H and JF1 strains differed in transcript and protein levels of superoxide dismutase 3, extracellular [SOD3; mouse chromosome (mCh) 5: V D ] and transcript of trefoil factor 2 (TFF2; mCh 17: TLC and D CO ), and ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2; mCh 15: TLC and C L ). Nucleotide sequencing of Sod3 , Tff2 , and previously identified Relaxin 1 ( Rln1 ; mCh 19: C L ) uncovered polymorphisms that could lead to nonsynonymous amino acid changes and altered predicted protein structure. Gene-targeted Sod3 –/– mice had increased conducting airway volume (V D /TLC) compared with strain-matched control Sod3 +/+ mice, consistent with the QTL on mCh 5. Two novel genes ( Tff2 and Enpp2 ) have been identified and two suspected genes ( Sod3 and Rln1 ) have been supported as determinants of lung function in mice. Findings with gene-targeted mice suggest that SOD3 is a contributing factor defining the complex trait of conducting airway volume.
complex trait; chronic obstructive pulmonary disease; asthma; Sod3</abstract><cop>United States</cop><pub>Am Physiological Soc</pub><pmid>17804602</pmid><doi>10.1152/physiolgenomics.00260.2006</doi><tpages>12</tpages></addata></record> |
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| ispartof | Physiological genomics, 2007-11, Vol.31 (3), p.410-421 |
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| source | MEDLINE; American Physiological Society; EZB-FREE-00999 freely available EZB journals |
| subjects | Animals Female Gene Expression Profiling Male Mice Mice, Inbred Strains Mice, Knockout Polymorphism, Genetic Quantitative Trait Loci Respiratory Function Tests RNA, Messenger - genetics Species Specificity Superoxide Dismutase - genetics |
| title | Candidate genes controlling pulmonary function in mice: transcript profiling and predicted protein structure |
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