A candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic research
Abstract Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plaus...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2018-06-01
|
| Series: | Respiratory Research |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12931-018-0795-y |
| _version_ | 1811196106567057408 |
|---|---|
| author | Sangeetha Vishweswaraiah Leema George Natarajan Purushothaman Koustav Ganguly |
| author_facet | Sangeetha Vishweswaraiah Leema George Natarajan Purushothaman Koustav Ganguly |
| author_sort | Sangeetha Vishweswaraiah |
| collection | DOAJ |
| description | Abstract Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set. Methods Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets. Results Significant association (p < 0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected. Conclusion Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research. |
| first_indexed | 2024-04-12T00:53:11Z |
| format | Article |
| id | doaj.art-0d1cfce5c75d4084a4644c1eb046cfc6 |
| institution | Directory Open Access Journal |
| issn | 1465-993X |
| language | English |
| last_indexed | 2024-04-12T00:53:11Z |
| publishDate | 2018-06-01 |
| publisher | BMC |
| record_format | Article |
| series | Respiratory Research |
| spelling | doaj.art-0d1cfce5c75d4084a4644c1eb046cfc62022-12-22T03:54:40ZengBMCRespiratory Research1465-993X2018-06-0119111110.1186/s12931-018-0795-yA candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic researchSangeetha Vishweswaraiah0Leema George1Natarajan Purushothaman2Koustav Ganguly3SRM Research Institute, SRM UniversitySRM Research Institute, SRM UniversityDepartment of Genetic Engineering, School of Bioengineering, Faculty of Engineering and Technology, SRM UniversitySRM Research Institute, SRM UniversityAbstract Background Early life impairments leading to lower lung function by adulthood are considered as risk factors for chronic obstructive pulmonary disease (COPD). Recently, we compared the lung transcriptomic profile between two mouse strains with extreme total lung capacities to identify plausible pulmonary function determining genes using microarray analysis (GSE80078). Advancement of high-throughput techniques like deep sequencing (eg. RNA-seq) and microarray have resulted in an explosion of genomic data in the online public repositories which however remains under-exploited. Strategic curation of publicly available genomic data with a mouse-human translational approach can effectively implement “3R- Tenet” by reducing screening experiments with animals and performing mechanistic studies using physiologically relevant in vitro model systems. Therefore, we sought to analyze the association of functional variations within human orthologs of mouse lung function candidate genes in a publicly available COPD lung RNA-seq data-set. Methods Association of missense single nucleotide polymorphisms, insertions, deletions, and splice junction variants were analyzed for susceptibility to COPD using RNA-seq data of a Korean population (GSE57148). Expression of the associated genes were studied using the Gene Paint (mouse embryo) and Human Protein Atlas (normal adult human lung) databases. The genes were also assessed for replication of the associations and expression in COPD−/mouse cigarette smoke exposed lung tissues using other datasets. Results Significant association (p < 0.05) of variations in 20 genes to higher COPD susceptibility have been detected within the investigated cohort. Association of HJURP, MCRS1 and TLR8 are novel in relation to COPD. The associated ADAM19 and KIT loci have been reported earlier. The remaining 15 genes have also been previously associated to COPD. Differential transcript expression levels of the associated genes in COPD- and/ or mouse emphysematous lung tissues have been detected. Conclusion Our findings suggest strategic mouse-human datamining approaches can identify novel COPD candidate genes using existing datasets in the online repositories. The candidates can be further evaluated for mechanistic role through in vitro studies using appropriate primary cells/cell lines. Functional studies can be limited to transgenic animal models of only well supported candidate genes. This approach will lead to a significant reduction of animal experimentation in respiratory research.http://link.springer.com/article/10.1186/s12931-018-0795-y3RAlternate modelsCOPDAsthmaLungGene |
| spellingShingle | Sangeetha Vishweswaraiah Leema George Natarajan Purushothaman Koustav Ganguly A candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic research Respiratory Research 3R Alternate models COPD Asthma Lung Gene |
| title | A candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic research |
| title_full | A candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic research |
| title_fullStr | A candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic research |
| title_full_unstemmed | A candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic research |
| title_short | A candidate gene identification strategy utilizing mouse to human big-data mining: “3R-tenet” in COPD genetic research |
| title_sort | candidate gene identification strategy utilizing mouse to human big data mining 3r tenet in copd genetic research |
| topic | 3R Alternate models COPD Asthma Lung Gene |
| url | http://link.springer.com/article/10.1186/s12931-018-0795-y |
| work_keys_str_mv | AT sangeethavishweswaraiah acandidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch AT leemageorge acandidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch AT natarajanpurushothaman acandidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch AT koustavganguly acandidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch AT sangeethavishweswaraiah candidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch AT leemageorge candidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch AT natarajanpurushothaman candidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch AT koustavganguly candidategeneidentificationstrategyutilizingmousetohumanbigdatamining3rtenetincopdgeneticresearch |