mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice
Purpose The aim of this study is to use RNA sequencing and RT-qPCR to identify the main susceptibility genes linked to the occurrence and development of Hirschsprung disease in the colonic tissues of EDNRB m1yzcm and wild mice. Methods RNA was extracted from colon tissues of 3 mutant homozygous mice...
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| Veröffentlicht in: | Pediatric surgery international 2023-09, Vol.39 (1), p.268-268, Article 268 |
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| creator | Yang, Qiwen Wang, Fuwen Wang, Zhaofei Guo, Jiajun Chang, Tingjin Dalielihan, Baligen Yang, Ge Lei, Chuzhao Dang, Ruihua |
| description | Purpose
The aim of this study is to use RNA sequencing and RT-qPCR to identify the main susceptibility genes linked to the occurrence and development of Hirschsprung disease in the colonic tissues of
EDNRB
m1yzcm
and wild mice.
Methods
RNA was extracted from colon tissues of 3 mutant homozygous mice and 3 wild mice. RNA degradation, contamination concentration, and integrity were then measured. The extracted RNA was then sequenced using the Illumina platform. The obtained sequence data are filtered to ensure data quality and compared to the reference genome for further analysis. DESeq2 was used for gene expression analysis of the raw data. In addition, graphene oxide enrichment analysis and RT-qPCR validation were also performed.
Results
This study identified 8354 differentially expressed genes in
EDNRB
m1yzcm
and wild mouse colon tissues by RNA sequencing, including 4346 upregulated genes and 4005 downregulated genes. Correspondingly, the results of RT-qPCR analysis showed good correlation with the transcriptome data. In addition, GO and KEGG enrichment results suggested that there were 8103 terms and 320 pathways in all DEGs. When
P
|
| doi_str_mv | 10.1007/s00383-023-05544-5 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_cross</sourceid><recordid>TN_cdi_proquest_miscellaneous_2862198042</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>2861985469</sourcerecordid><originalsourceid>FETCH-LOGICAL-c326t-bbc362bfd366f0985fc50fd81bff13bd27368a5d184b50051908ab4b6779e4143</originalsourceid><addsrcrecordid>eNp9kMtO3TAQhq2qFYee9gVYIEts2KT1JXacJUJcKqEiVe3aipNxYnSSHDwJqLu-Bq_Hk2AaKIhFF9bM4vvHMx8he5x94YwVX5ExaWTGRHpK5Xmm3pFdnssiKw2X71_1K_IR8YoxZqQud8hKFrrQohS7xPY_vh9RhOsZhjoMLd3G8SY0gHSAWxoGDG03YWqmkU4d0G01dWMLA2BAOnp6HiLWHW7jPLT3f-6QNgGhQkgJ2ocaPpEPvtogfH6qa_Lr9OTn8Xl2cXn27fjoIqul0FPmXC21cL6RWntWGuVrxXxjuPOeS9eIQmpTqYab3CnGFC-ZqVzudFGUkKc71-RwmZv2T7fgZPuANWw21QDjjFYYLXhpWC4SevAGvRrnOKTtHqkEqVyXiRILVccRMYK32xj6Kv62nNlH_XbRb5N--1e_VSm0_zR6dj00_yLPvhMgFyAZS7Yhvvz9n7EPm9eQ7g</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2861985469</pqid></control><display><type>article</type><title>mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice</title><source>MEDLINE</source><source>SpringerLink_现刊</source><creator>Yang, Qiwen ; Wang, Fuwen ; Wang, Zhaofei ; Guo, Jiajun ; Chang, Tingjin ; Dalielihan, Baligen ; Yang, Ge ; Lei, Chuzhao ; Dang, Ruihua</creator><creatorcontrib>Yang, Qiwen ; Wang, Fuwen ; Wang, Zhaofei ; Guo, Jiajun ; Chang, Tingjin ; Dalielihan, Baligen ; Yang, Ge ; Lei, Chuzhao ; Dang, Ruihua</creatorcontrib><description>Purpose
The aim of this study is to use RNA sequencing and RT-qPCR to identify the main susceptibility genes linked to the occurrence and development of Hirschsprung disease in the colonic tissues of
EDNRB
m1yzcm
and wild mice.
Methods
RNA was extracted from colon tissues of 3 mutant homozygous mice and 3 wild mice. RNA degradation, contamination concentration, and integrity were then measured. The extracted RNA was then sequenced using the Illumina platform. The obtained sequence data are filtered to ensure data quality and compared to the reference genome for further analysis. DESeq2 was used for gene expression analysis of the raw data. In addition, graphene oxide enrichment analysis and RT-qPCR validation were also performed.
Results
This study identified 8354 differentially expressed genes in
EDNRB
m1yzcm
and wild mouse colon tissues by RNA sequencing, including 4346 upregulated genes and 4005 downregulated genes. Correspondingly, the results of RT-qPCR analysis showed good correlation with the transcriptome data. In addition, GO and KEGG enrichment results suggested that there were 8103 terms and 320 pathways in all DEGs. When
P
< 0.05, 1081 GO terms and 320 KEGG pathways reached a significant level. Finally, through the existing studies and the enrichment results of differentially expressed genes, it was determined that axon guidance and the focal adhesion pathway may be closely related to the occurrence of HSCR.
Conclusions
This study analyzed and identified the differential genes in colonic tissues between
EDNRB
m1yzcm
mice and wild mice, which provided new insight for further mining the potential pathogenic genes of Hirschsprung’s disease.</description><identifier>ISSN: 1437-9813</identifier><identifier>ISSN: 0179-0358</identifier><identifier>EISSN: 1437-9813</identifier><identifier>DOI: 10.1007/s00383-023-05544-5</identifier><identifier>PMID: 37676292</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Abdomen ; Animals ; Colon ; Disease ; Gene Expression Profiling ; Genes ; Genomes ; Hirschsprung Disease - genetics ; Medicine ; Medicine & Public Health ; Mice ; MicroRNAs ; Mutation ; Nervous system ; Original Article ; Pathogenesis ; Pediatric Surgery ; Pediatrics ; RNA ; RNA, Messenger ; Surgery</subject><ispartof>Pediatric surgery international, 2023-09, Vol.39 (1), p.268-268, Article 268</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>2023. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c326t-bbc362bfd366f0985fc50fd81bff13bd27368a5d184b50051908ab4b6779e4143</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00383-023-05544-5$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00383-023-05544-5$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/37676292$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Qiwen</creatorcontrib><creatorcontrib>Wang, Fuwen</creatorcontrib><creatorcontrib>Wang, Zhaofei</creatorcontrib><creatorcontrib>Guo, Jiajun</creatorcontrib><creatorcontrib>Chang, Tingjin</creatorcontrib><creatorcontrib>Dalielihan, Baligen</creatorcontrib><creatorcontrib>Yang, Ge</creatorcontrib><creatorcontrib>Lei, Chuzhao</creatorcontrib><creatorcontrib>Dang, Ruihua</creatorcontrib><title>mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice</title><title>Pediatric surgery international</title><addtitle>Pediatr Surg Int</addtitle><addtitle>Pediatr Surg Int</addtitle><description>Purpose
The aim of this study is to use RNA sequencing and RT-qPCR to identify the main susceptibility genes linked to the occurrence and development of Hirschsprung disease in the colonic tissues of
EDNRB
m1yzcm
and wild mice.
Methods
RNA was extracted from colon tissues of 3 mutant homozygous mice and 3 wild mice. RNA degradation, contamination concentration, and integrity were then measured. The extracted RNA was then sequenced using the Illumina platform. The obtained sequence data are filtered to ensure data quality and compared to the reference genome for further analysis. DESeq2 was used for gene expression analysis of the raw data. In addition, graphene oxide enrichment analysis and RT-qPCR validation were also performed.
Results
This study identified 8354 differentially expressed genes in
EDNRB
m1yzcm
and wild mouse colon tissues by RNA sequencing, including 4346 upregulated genes and 4005 downregulated genes. Correspondingly, the results of RT-qPCR analysis showed good correlation with the transcriptome data. In addition, GO and KEGG enrichment results suggested that there were 8103 terms and 320 pathways in all DEGs. When
P
< 0.05, 1081 GO terms and 320 KEGG pathways reached a significant level. Finally, through the existing studies and the enrichment results of differentially expressed genes, it was determined that axon guidance and the focal adhesion pathway may be closely related to the occurrence of HSCR.
Conclusions
This study analyzed and identified the differential genes in colonic tissues between
EDNRB
m1yzcm
mice and wild mice, which provided new insight for further mining the potential pathogenic genes of Hirschsprung’s disease.</description><subject>Abdomen</subject><subject>Animals</subject><subject>Colon</subject><subject>Disease</subject><subject>Gene Expression Profiling</subject><subject>Genes</subject><subject>Genomes</subject><subject>Hirschsprung Disease - genetics</subject><subject>Medicine</subject><subject>Medicine & Public Health</subject><subject>Mice</subject><subject>MicroRNAs</subject><subject>Mutation</subject><subject>Nervous system</subject><subject>Original Article</subject><subject>Pathogenesis</subject><subject>Pediatric Surgery</subject><subject>Pediatrics</subject><subject>RNA</subject><subject>RNA, Messenger</subject><subject>Surgery</subject><issn>1437-9813</issn><issn>0179-0358</issn><issn>1437-9813</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><recordid>eNp9kMtO3TAQhq2qFYee9gVYIEts2KT1JXacJUJcKqEiVe3aipNxYnSSHDwJqLu-Bq_Hk2AaKIhFF9bM4vvHMx8he5x94YwVX5ExaWTGRHpK5Xmm3pFdnssiKw2X71_1K_IR8YoxZqQud8hKFrrQohS7xPY_vh9RhOsZhjoMLd3G8SY0gHSAWxoGDG03YWqmkU4d0G01dWMLA2BAOnp6HiLWHW7jPLT3f-6QNgGhQkgJ2ocaPpEPvtogfH6qa_Lr9OTn8Xl2cXn27fjoIqul0FPmXC21cL6RWntWGuVrxXxjuPOeS9eIQmpTqYab3CnGFC-ZqVzudFGUkKc71-RwmZv2T7fgZPuANWw21QDjjFYYLXhpWC4SevAGvRrnOKTtHqkEqVyXiRILVccRMYK32xj6Kv62nNlH_XbRb5N--1e_VSm0_zR6dj00_yLPvhMgFyAZS7Yhvvz9n7EPm9eQ7g</recordid><startdate>20230907</startdate><enddate>20230907</enddate><creator>Yang, Qiwen</creator><creator>Wang, Fuwen</creator><creator>Wang, Zhaofei</creator><creator>Guo, Jiajun</creator><creator>Chang, Tingjin</creator><creator>Dalielihan, Baligen</creator><creator>Yang, Ge</creator><creator>Lei, Chuzhao</creator><creator>Dang, Ruihua</creator><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</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>3V.</scope><scope>7RV</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>CCPQU</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>K9-</scope><scope>K9.</scope><scope>KB0</scope><scope>M0R</scope><scope>M0S</scope><scope>M1P</scope><scope>NAPCQ</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>7X8</scope></search><sort><creationdate>20230907</creationdate><title>mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice</title><author>Yang, Qiwen ; Wang, Fuwen ; Wang, Zhaofei ; Guo, Jiajun ; Chang, Tingjin ; Dalielihan, Baligen ; Yang, Ge ; Lei, Chuzhao ; Dang, Ruihua</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c326t-bbc362bfd366f0985fc50fd81bff13bd27368a5d184b50051908ab4b6779e4143</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Abdomen</topic><topic>Animals</topic><topic>Colon</topic><topic>Disease</topic><topic>Gene Expression Profiling</topic><topic>Genes</topic><topic>Genomes</topic><topic>Hirschsprung Disease - genetics</topic><topic>Medicine</topic><topic>Medicine & Public Health</topic><topic>Mice</topic><topic>MicroRNAs</topic><topic>Mutation</topic><topic>Nervous system</topic><topic>Original Article</topic><topic>Pathogenesis</topic><topic>Pediatric Surgery</topic><topic>Pediatrics</topic><topic>RNA</topic><topic>RNA, Messenger</topic><topic>Surgery</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yang, Qiwen</creatorcontrib><creatorcontrib>Wang, Fuwen</creatorcontrib><creatorcontrib>Wang, Zhaofei</creatorcontrib><creatorcontrib>Guo, Jiajun</creatorcontrib><creatorcontrib>Chang, Tingjin</creatorcontrib><creatorcontrib>Dalielihan, Baligen</creatorcontrib><creatorcontrib>Yang, Ge</creatorcontrib><creatorcontrib>Lei, Chuzhao</creatorcontrib><creatorcontrib>Dang, Ruihua</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>ProQuest Nursing & Allied Health Database</collection><collection>Health Medical collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>ProQuest One Community College</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>Consumer Health Database (Alumni Edition)</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Nursing & Allied Health Database (Alumni Edition)</collection><collection>ProQuest Consumer Health Database</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>PML(ProQuest Medical Library)</collection><collection>Nursing & Allied Health Premium</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><jtitle>Pediatric surgery international</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yang, Qiwen</au><au>Wang, Fuwen</au><au>Wang, Zhaofei</au><au>Guo, Jiajun</au><au>Chang, Tingjin</au><au>Dalielihan, Baligen</au><au>Yang, Ge</au><au>Lei, Chuzhao</au><au>Dang, Ruihua</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice</atitle><jtitle>Pediatric surgery international</jtitle><stitle>Pediatr Surg Int</stitle><addtitle>Pediatr Surg Int</addtitle><date>2023-09-07</date><risdate>2023</risdate><volume>39</volume><issue>1</issue><spage>268</spage><epage>268</epage><pages>268-268</pages><artnum>268</artnum><issn>1437-9813</issn><issn>0179-0358</issn><eissn>1437-9813</eissn><abstract>Purpose
The aim of this study is to use RNA sequencing and RT-qPCR to identify the main susceptibility genes linked to the occurrence and development of Hirschsprung disease in the colonic tissues of
EDNRB
m1yzcm
and wild mice.
Methods
RNA was extracted from colon tissues of 3 mutant homozygous mice and 3 wild mice. RNA degradation, contamination concentration, and integrity were then measured. The extracted RNA was then sequenced using the Illumina platform. The obtained sequence data are filtered to ensure data quality and compared to the reference genome for further analysis. DESeq2 was used for gene expression analysis of the raw data. In addition, graphene oxide enrichment analysis and RT-qPCR validation were also performed.
Results
This study identified 8354 differentially expressed genes in
EDNRB
m1yzcm
and wild mouse colon tissues by RNA sequencing, including 4346 upregulated genes and 4005 downregulated genes. Correspondingly, the results of RT-qPCR analysis showed good correlation with the transcriptome data. In addition, GO and KEGG enrichment results suggested that there were 8103 terms and 320 pathways in all DEGs. When
P
< 0.05, 1081 GO terms and 320 KEGG pathways reached a significant level. Finally, through the existing studies and the enrichment results of differentially expressed genes, it was determined that axon guidance and the focal adhesion pathway may be closely related to the occurrence of HSCR.
Conclusions
This study analyzed and identified the differential genes in colonic tissues between
EDNRB
m1yzcm
mice and wild mice, which provided new insight for further mining the potential pathogenic genes of Hirschsprung’s disease.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><pmid>37676292</pmid><doi>10.1007/s00383-023-05544-5</doi><tpages>1</tpages></addata></record> |
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| identifier | ISSN: 1437-9813 |
| ispartof | Pediatric surgery international, 2023-09, Vol.39 (1), p.268-268, Article 268 |
| issn | 1437-9813 0179-0358 1437-9813 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2862198042 |
| source | MEDLINE; SpringerLink_现刊 |
| subjects | Abdomen Animals Colon Disease Gene Expression Profiling Genes Genomes Hirschsprung Disease - genetics Medicine Medicine & Public Health Mice MicroRNAs Mutation Nervous system Original Article Pathogenesis Pediatric Surgery Pediatrics RNA RNA, Messenger Surgery |
| title | mRNA sequencing provides new insights into the pathogenesis of Hirschsprung’s disease in mice |
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