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Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection
Acute respiratory infection (ARI) with respiratory syncytial virus (RSV) is the most common cause of both hospitalizations and mortality in young infants worldwide. Repeat infections with RSV are common throughout life in both pediatric and elderly populations. Thus far, cotton rats ( Sigmodon hispi...
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| Published in: | Scientific reports 2018-07, Vol.8 (1), p.11318-12, Article 11318 |
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| creator | Rajagopala, Seesandra V. Singh, Harinder Patel, Mira C. Wang, Wei Tan, Yi Shilts, Meghan H. Hartert, Tina V. Boukhvalova, Marina S. Blanco, Jorge C. G. Das, Suman R. |
| description | Acute respiratory infection (ARI) with respiratory syncytial virus (RSV) is the most common cause of both hospitalizations and mortality in young infants worldwide. Repeat infections with RSV are common throughout life in both pediatric and elderly populations. Thus far, cotton rats (
Sigmodon hispidus
) are found to be the best animal model to study RSV infection. However, the lack of a cotton rat reference genome limits genome-wide host gene expression studies. We constructed the first lung tissue
de novo
transcriptome for the cotton rat. Cotton rat lung tissue transcripts were assigned to 12,211 unique UniProt genes, which were then utilized to profile the host immune response after RSV infection. Differential expression analysis showed up-regulation of host genes involved in cellular functions including defense responses to viral infection and immune system processes. A number of transcripts were downregulated during the later stage of infection. A set of transcripts unique to RSV-infected cotton rats was identified. To validate RNA-Seq data of three such transcripts (TR453762, TR529629, and TR5333), their expression was confirmed by quantitative real-time polymerase chain reaction. |
| doi_str_mv | 10.1038/s41598-018-29374-x |
| format | article |
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Sigmodon hispidus
) are found to be the best animal model to study RSV infection. However, the lack of a cotton rat reference genome limits genome-wide host gene expression studies. We constructed the first lung tissue
de novo
transcriptome for the cotton rat. Cotton rat lung tissue transcripts were assigned to 12,211 unique UniProt genes, which were then utilized to profile the host immune response after RSV infection. Differential expression analysis showed up-regulation of host genes involved in cellular functions including defense responses to viral infection and immune system processes. A number of transcripts were downregulated during the later stage of infection. A set of transcripts unique to RSV-infected cotton rats was identified. To validate RNA-Seq data of three such transcripts (TR453762, TR529629, and TR5333), their expression was confirmed by quantitative real-time polymerase chain reaction.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-018-29374-x</identifier><identifier>PMID: 30054492</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>38/39 ; 38/77 ; 45/90 ; 45/91 ; 631/326/596/2097 ; 631/326/596/2553 ; Animal models ; Animals ; Gene expression ; Gene Expression Regulation - immunology ; Gene regulation ; Genome ; Genomes ; Geriatrics ; Host-Parasite Interactions - genetics ; Host-Parasite Interactions - immunology ; Humanities and Social Sciences ; Immune response ; Immune system ; Immunity, Innate - genetics ; Infants ; Infections ; Lung - metabolism ; Lung - virology ; Lungs ; multidisciplinary ; Polymerase chain reaction ; Rats ; Respiratory syncytial virus ; Respiratory Syncytial Virus Infections - genetics ; Respiratory Syncytial Virus Infections - immunology ; Respiratory Syncytial Virus Infections - virology ; Respiratory Syncytial Viruses - immunology ; Respiratory Syncytial Viruses - pathogenicity ; Ribonucleic acid ; RNA ; Rodents ; Science ; Science (multidisciplinary) ; Sigmodon ; Sigmodontinae - genetics ; Sigmodontinae - immunology ; Sigmodontinae - virology ; Transcriptome - genetics ; Viral infections</subject><ispartof>Scientific reports, 2018-07, Vol.8 (1), p.11318-12, Article 11318</ispartof><rights>The Author(s) 2018</rights><rights>2018. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c474t-67b049cca6a8623e0ecf052e36551534634733aff34438a7862272e134200ac53</citedby><cites>FETCH-LOGICAL-c474t-67b049cca6a8623e0ecf052e36551534634733aff34438a7862272e134200ac53</cites><orcidid>0000-0003-2496-9724 ; 0000-0001-7470-1166</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2077457741/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2077457741?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,724,777,781,882,25734,27905,27906,36993,36994,44571,53772,53774,74875</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30054492$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Rajagopala, Seesandra V.</creatorcontrib><creatorcontrib>Singh, Harinder</creatorcontrib><creatorcontrib>Patel, Mira C.</creatorcontrib><creatorcontrib>Wang, Wei</creatorcontrib><creatorcontrib>Tan, Yi</creatorcontrib><creatorcontrib>Shilts, Meghan H.</creatorcontrib><creatorcontrib>Hartert, Tina V.</creatorcontrib><creatorcontrib>Boukhvalova, Marina S.</creatorcontrib><creatorcontrib>Blanco, Jorge C. G.</creatorcontrib><creatorcontrib>Das, Suman R.</creatorcontrib><title>Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Acute respiratory infection (ARI) with respiratory syncytial virus (RSV) is the most common cause of both hospitalizations and mortality in young infants worldwide. Repeat infections with RSV are common throughout life in both pediatric and elderly populations. Thus far, cotton rats (
Sigmodon hispidus
) are found to be the best animal model to study RSV infection. However, the lack of a cotton rat reference genome limits genome-wide host gene expression studies. We constructed the first lung tissue
de novo
transcriptome for the cotton rat. Cotton rat lung tissue transcripts were assigned to 12,211 unique UniProt genes, which were then utilized to profile the host immune response after RSV infection. Differential expression analysis showed up-regulation of host genes involved in cellular functions including defense responses to viral infection and immune system processes. A number of transcripts were downregulated during the later stage of infection. A set of transcripts unique to RSV-infected cotton rats was identified. To validate RNA-Seq data of three such transcripts (TR453762, TR529629, and TR5333), their expression was confirmed by quantitative real-time polymerase chain reaction.</description><subject>38/39</subject><subject>38/77</subject><subject>45/90</subject><subject>45/91</subject><subject>631/326/596/2097</subject><subject>631/326/596/2553</subject><subject>Animal models</subject><subject>Animals</subject><subject>Gene expression</subject><subject>Gene Expression Regulation - immunology</subject><subject>Gene regulation</subject><subject>Genome</subject><subject>Genomes</subject><subject>Geriatrics</subject><subject>Host-Parasite Interactions - genetics</subject><subject>Host-Parasite Interactions - immunology</subject><subject>Humanities and Social Sciences</subject><subject>Immune response</subject><subject>Immune system</subject><subject>Immunity, Innate - genetics</subject><subject>Infants</subject><subject>Infections</subject><subject>Lung - metabolism</subject><subject>Lung - virology</subject><subject>Lungs</subject><subject>multidisciplinary</subject><subject>Polymerase chain reaction</subject><subject>Rats</subject><subject>Respiratory syncytial virus</subject><subject>Respiratory Syncytial Virus Infections - genetics</subject><subject>Respiratory Syncytial Virus Infections - immunology</subject><subject>Respiratory Syncytial Virus Infections - virology</subject><subject>Respiratory Syncytial Viruses - immunology</subject><subject>Respiratory Syncytial Viruses - pathogenicity</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Rodents</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Sigmodon</subject><subject>Sigmodontinae - genetics</subject><subject>Sigmodontinae - immunology</subject><subject>Sigmodontinae - virology</subject><subject>Transcriptome - genetics</subject><subject>Viral infections</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><recordid>eNp9kUtrGzEUhUVpSULqP5BFEGTTzaR6jmY2gWKSNBAoJGm3Qlbv2DIzkiNpQvzvK9eu81hUG110v3t0DwehE0rOKeHN1ySobJuK0KZiLVeiev6AjhgRsmKcsY-v6kM0SWlJypGsFbQ9QIe81EK07AjZacg5eBxNxv3o5zhH45ONbpXDADjCE5g-4UVIGbthGP3mLa2CT4BzwHeldmU2xDW-X3u7zs70-JeLY8LOd2CzC_4z-tQVEZjs7mP08-ryYfq9uv1xfTP9dltZoUSuajUjorXW1KapGQcCtisrA6-lpJKLmgvFuek6LgRvjCoQUwwoF4wQYyU_Rhdb3dU4G-C3BV_M9HoV3WDiWgfj9NuOdws9D0-6JjVvFSkCX3YCMTyOkLIeXLLQ98ZDGJNmRDWyEVLRgp69Q5dhjL7Y21CqMEpsKLalbAwpRej2y1CiNzHqbYy6xKj_xqify9Dpaxv7kX-hFYBvgVRafg7x5e__yP4BN5iqEA</recordid><startdate>20180727</startdate><enddate>20180727</enddate><creator>Rajagopala, Seesandra V.</creator><creator>Singh, Harinder</creator><creator>Patel, Mira C.</creator><creator>Wang, Wei</creator><creator>Tan, Yi</creator><creator>Shilts, Meghan H.</creator><creator>Hartert, Tina V.</creator><creator>Boukhvalova, Marina S.</creator><creator>Blanco, Jorge C. 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G. ; Das, Suman R.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c474t-67b049cca6a8623e0ecf052e36551534634733aff34438a7862272e134200ac53</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2018</creationdate><topic>38/39</topic><topic>38/77</topic><topic>45/90</topic><topic>45/91</topic><topic>631/326/596/2097</topic><topic>631/326/596/2553</topic><topic>Animal models</topic><topic>Animals</topic><topic>Gene expression</topic><topic>Gene Expression Regulation - immunology</topic><topic>Gene regulation</topic><topic>Genome</topic><topic>Genomes</topic><topic>Geriatrics</topic><topic>Host-Parasite Interactions - genetics</topic><topic>Host-Parasite Interactions - immunology</topic><topic>Humanities and Social Sciences</topic><topic>Immune response</topic><topic>Immune system</topic><topic>Immunity, Innate - genetics</topic><topic>Infants</topic><topic>Infections</topic><topic>Lung - metabolism</topic><topic>Lung - virology</topic><topic>Lungs</topic><topic>multidisciplinary</topic><topic>Polymerase chain reaction</topic><topic>Rats</topic><topic>Respiratory syncytial virus</topic><topic>Respiratory Syncytial Virus Infections - genetics</topic><topic>Respiratory Syncytial Virus Infections - immunology</topic><topic>Respiratory Syncytial Virus Infections - virology</topic><topic>Respiratory Syncytial Viruses - immunology</topic><topic>Respiratory Syncytial Viruses - pathogenicity</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>Rodents</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Sigmodon</topic><topic>Sigmodontinae - genetics</topic><topic>Sigmodontinae - immunology</topic><topic>Sigmodontinae - virology</topic><topic>Transcriptome - genetics</topic><topic>Viral infections</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Rajagopala, Seesandra V.</creatorcontrib><creatorcontrib>Singh, Harinder</creatorcontrib><creatorcontrib>Patel, Mira C.</creatorcontrib><creatorcontrib>Wang, Wei</creatorcontrib><creatorcontrib>Tan, Yi</creatorcontrib><creatorcontrib>Shilts, Meghan H.</creatorcontrib><creatorcontrib>Hartert, Tina V.</creatorcontrib><creatorcontrib>Boukhvalova, Marina S.</creatorcontrib><creatorcontrib>Blanco, Jorge C. 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G.</au><au>Das, Suman R.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2018-07-27</date><risdate>2018</risdate><volume>8</volume><issue>1</issue><spage>11318</spage><epage>12</epage><pages>11318-12</pages><artnum>11318</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Acute respiratory infection (ARI) with respiratory syncytial virus (RSV) is the most common cause of both hospitalizations and mortality in young infants worldwide. Repeat infections with RSV are common throughout life in both pediatric and elderly populations. Thus far, cotton rats (
Sigmodon hispidus
) are found to be the best animal model to study RSV infection. However, the lack of a cotton rat reference genome limits genome-wide host gene expression studies. We constructed the first lung tissue
de novo
transcriptome for the cotton rat. Cotton rat lung tissue transcripts were assigned to 12,211 unique UniProt genes, which were then utilized to profile the host immune response after RSV infection. Differential expression analysis showed up-regulation of host genes involved in cellular functions including defense responses to viral infection and immune system processes. A number of transcripts were downregulated during the later stage of infection. A set of transcripts unique to RSV-infected cotton rats was identified. To validate RNA-Seq data of three such transcripts (TR453762, TR529629, and TR5333), their expression was confirmed by quantitative real-time polymerase chain reaction.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>30054492</pmid><doi>10.1038/s41598-018-29374-x</doi><tpages>12</tpages><orcidid>https://orcid.org/0000-0003-2496-9724</orcidid><orcidid>https://orcid.org/0000-0001-7470-1166</orcidid><oa>free_for_read</oa></addata></record> |
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| ispartof | Scientific reports, 2018-07, Vol.8 (1), p.11318-12, Article 11318 |
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| source | Publicly Available Content Database; Full-Text Journals in Chemistry (Open access); PubMed Central; Springer Nature - nature.com Journals - Fully Open Access |
| subjects | 38/39 38/77 45/90 45/91 631/326/596/2097 631/326/596/2553 Animal models Animals Gene expression Gene Expression Regulation - immunology Gene regulation Genome Genomes Geriatrics Host-Parasite Interactions - genetics Host-Parasite Interactions - immunology Humanities and Social Sciences Immune response Immune system Immunity, Innate - genetics Infants Infections Lung - metabolism Lung - virology Lungs multidisciplinary Polymerase chain reaction Rats Respiratory syncytial virus Respiratory Syncytial Virus Infections - genetics Respiratory Syncytial Virus Infections - immunology Respiratory Syncytial Virus Infections - virology Respiratory Syncytial Viruses - immunology Respiratory Syncytial Viruses - pathogenicity Ribonucleic acid RNA Rodents Science Science (multidisciplinary) Sigmodon Sigmodontinae - genetics Sigmodontinae - immunology Sigmodontinae - virology Transcriptome - genetics Viral infections |
| title | Cotton rat lung transcriptome reveals host immune response to Respiratory Syncytial Virus infection |
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