Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis
Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy...
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| Veröffentlicht in: | Cellular and molecular life sciences : CMLS 2022-01, Vol.79 (1), p.66, Article 66 |
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| creator | Zheng, Peiyan Sun, Shixue Wang, Jingxian Cheng, Zhangkai Jason Lei, Kuan Cheok Xue, Mingshan Zhang, Teng Huang, Huimin Zhang, Xiaohua Douglas Sun, Baoqing |
| description | Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells. |
| doi_str_mv | 10.1007/s00018-021-04094-0 |
| format | Article |
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Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.</description><identifier>ISSN: 1420-682X</identifier><identifier>EISSN: 1420-9071</identifier><identifier>DOI: 10.1007/s00018-021-04094-0</identifier><identifier>PMID: 35015148</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Alveoli ; Animals ; Biochemistry ; Biomarkers ; Biomarkers - analysis ; Biomedical and Life Sciences ; Biomedicine ; Bleomycin ; Bleomycin - toxicity ; Butyrophilin ; Butyrophilins - genetics ; Cell Biology ; Cell differentiation ; Cell Differentiation - genetics ; Cell Proliferation - genetics ; Differentiation (biology) ; Disease Models, Animal ; Epithelial cells ; Epithelium ; Extracellular matrix ; Extracellular Matrix - metabolism ; Female ; Fibrosis ; Gene expression ; Gene Expression Profiling ; Genes ; Humans ; Idiopathic Pulmonary Fibrosis - genetics ; Idiopathic Pulmonary Fibrosis - pathology ; Immune system ; Inflammation ; Life Sciences ; Lung diseases ; Male ; Mice ; Mice, Inbred C57BL ; Middle Aged ; Myelin and Lymphocyte-Associated Proteolipid Proteins - genetics ; Original ; Original Article ; Phases ; Proteome - genetics ; Proteomics ; Pulmonary fibrosis ; Repair ; RNA-Seq ; Transcription ; Transcriptome - genetics ; Transcriptomics ; Wound healing ; Wound Healing - genetics</subject><ispartof>Cellular and molecular life sciences : CMLS, 2022-01, Vol.79 (1), p.66, Article 66</ispartof><rights>The Author(s), under exclusive licence to Springer Nature Switzerland AG 2022</rights><rights>2022. The Author(s), under exclusive licence to Springer Nature Switzerland AG.</rights><rights>The Author(s), under exclusive licence to Springer Nature Switzerland AG 2022.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c431t-e8994fb8b080a48c08e3db561daea3512dcf6a1a98e26353aa57739b216b24693</citedby><cites>FETCH-LOGICAL-c431t-e8994fb8b080a48c08e3db561daea3512dcf6a1a98e26353aa57739b216b24693</cites><orcidid>0000-0002-1671-0723</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11075137/pdf/$$EPDF$$P50$$Gpubmedcentral$$H</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC11075137/$$EHTML$$P50$$Gpubmedcentral$$H</linktohtml><link.rule.ids>230,314,723,776,780,881,27901,27902,41464,42533,51294,53766,53768</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35015148$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zheng, Peiyan</creatorcontrib><creatorcontrib>Sun, Shixue</creatorcontrib><creatorcontrib>Wang, Jingxian</creatorcontrib><creatorcontrib>Cheng, Zhangkai Jason</creatorcontrib><creatorcontrib>Lei, Kuan Cheok</creatorcontrib><creatorcontrib>Xue, Mingshan</creatorcontrib><creatorcontrib>Zhang, Teng</creatorcontrib><creatorcontrib>Huang, Huimin</creatorcontrib><creatorcontrib>Zhang, Xiaohua Douglas</creatorcontrib><creatorcontrib>Sun, Baoqing</creatorcontrib><title>Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis</title><title>Cellular and molecular life sciences : CMLS</title><addtitle>Cell. Mol. Life Sci</addtitle><addtitle>Cell Mol Life Sci</addtitle><description>Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.</description><subject>Alveoli</subject><subject>Animals</subject><subject>Biochemistry</subject><subject>Biomarkers</subject><subject>Biomarkers - analysis</subject><subject>Biomedical and Life Sciences</subject><subject>Biomedicine</subject><subject>Bleomycin</subject><subject>Bleomycin - toxicity</subject><subject>Butyrophilin</subject><subject>Butyrophilins - genetics</subject><subject>Cell Biology</subject><subject>Cell differentiation</subject><subject>Cell Differentiation - genetics</subject><subject>Cell Proliferation - genetics</subject><subject>Differentiation (biology)</subject><subject>Disease Models, Animal</subject><subject>Epithelial cells</subject><subject>Epithelium</subject><subject>Extracellular matrix</subject><subject>Extracellular Matrix - metabolism</subject><subject>Female</subject><subject>Fibrosis</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Genes</subject><subject>Humans</subject><subject>Idiopathic Pulmonary Fibrosis - genetics</subject><subject>Idiopathic Pulmonary Fibrosis - pathology</subject><subject>Immune system</subject><subject>Inflammation</subject><subject>Life Sciences</subject><subject>Lung diseases</subject><subject>Male</subject><subject>Mice</subject><subject>Mice, Inbred C57BL</subject><subject>Middle Aged</subject><subject>Myelin and Lymphocyte-Associated Proteolipid Proteins - genetics</subject><subject>Original</subject><subject>Original Article</subject><subject>Phases</subject><subject>Proteome - genetics</subject><subject>Proteomics</subject><subject>Pulmonary fibrosis</subject><subject>Repair</subject><subject>RNA-Seq</subject><subject>Transcription</subject><subject>Transcriptome - 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omics analysis identifies biomarkers of idiopathic pulmonary fibrosis</title><author>Zheng, Peiyan ; Sun, Shixue ; Wang, Jingxian ; Cheng, Zhangkai Jason ; Lei, Kuan Cheok ; Xue, Mingshan ; Zhang, Teng ; Huang, Huimin ; Zhang, Xiaohua Douglas ; Sun, Baoqing</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c431t-e8994fb8b080a48c08e3db561daea3512dcf6a1a98e26353aa57739b216b24693</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Alveoli</topic><topic>Animals</topic><topic>Biochemistry</topic><topic>Biomarkers</topic><topic>Biomarkers - analysis</topic><topic>Biomedical and Life Sciences</topic><topic>Biomedicine</topic><topic>Bleomycin</topic><topic>Bleomycin - toxicity</topic><topic>Butyrophilin</topic><topic>Butyrophilins - genetics</topic><topic>Cell Biology</topic><topic>Cell differentiation</topic><topic>Cell Differentiation - genetics</topic><topic>Cell Proliferation - 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Mol. Life Sci</stitle><addtitle>Cell Mol Life Sci</addtitle><date>2022-01-01</date><risdate>2022</risdate><volume>79</volume><issue>1</issue><spage>66</spage><pages>66-</pages><artnum>66</artnum><issn>1420-682X</issn><eissn>1420-9071</eissn><abstract>Idiopathic pulmonary fibrosis (IPF) is an interstitial lung disease characterized by chronic progressive pulmonary fibrosis and a poor prognosis. Genetic studies, including transcriptomic and proteomics, have provided new insight into revealing mechanisms of IPF. Herein we provided a novel strategy to identify biomarkers by integrative analysis of transcriptomic and proteomic profiles of IPF patients. We examined the landscape of IPF patients' gene expression in the transcription and translation phases and investigated the expression and functions of two new potential biomarkers. Differentially expressed (DE) mRNAs were mainly enriched in pathways associated with immune system activities and inflammatory responses, while DE proteins are related to extracellular matrix production and wound repair. The upregulated genes in both phases are associated with wound repair and cell differentiation, while the downregulated genes in both phases are associated with reduced immune activities and the damage of the alveolar tissues. On this basis, we identified thirteen potential marker genes. Among them, we validated the expression changes of butyrophilin-like 9 (BTNL9) and plasmolipin (PLLP) and investigated their functional pathways in the IPF mechanism. Both genes are downregulated in the tissues of IPF patients and Bleomycin-induced mice, and co-expression analysis indicates that they have a protective effect by inhibiting extracellular matrix production and promoting wound repair in alveolar epithelial cells.</abstract><cop>Cham</cop><pub>Springer International Publishing</pub><pmid>35015148</pmid><doi>10.1007/s00018-021-04094-0</doi><orcidid>https://orcid.org/0000-0002-1671-0723</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Alveoli Animals Biochemistry Biomarkers Biomarkers - analysis Biomedical and Life Sciences Biomedicine Bleomycin Bleomycin - toxicity Butyrophilin Butyrophilins - genetics Cell Biology Cell differentiation Cell Differentiation - genetics Cell Proliferation - genetics Differentiation (biology) Disease Models, Animal Epithelial cells Epithelium Extracellular matrix Extracellular Matrix - metabolism Female Fibrosis Gene expression Gene Expression Profiling Genes Humans Idiopathic Pulmonary Fibrosis - genetics Idiopathic Pulmonary Fibrosis - pathology Immune system Inflammation Life Sciences Lung diseases Male Mice Mice, Inbred C57BL Middle Aged Myelin and Lymphocyte-Associated Proteolipid Proteins - genetics Original Original Article Phases Proteome - genetics Proteomics Pulmonary fibrosis Repair RNA-Seq Transcription Transcriptome - genetics Transcriptomics Wound healing Wound Healing - genetics |
| title | Integrative omics analysis identifies biomarkers of idiopathic pulmonary fibrosis |
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