Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis

Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hy...
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Autor*in:	Ghosh, Auyon J. [verfasserIn] Hobbs, Brian D. Yun, Jeong H. Saferali, Aabida Moll, Matthew Xu, Zhonghui Chase, Robert P. Morrow, Jarrett Ziniti, John Sciurba, Frank Barwick, Lucas Limper, Andrew H. Flaherty, Kevin Criner, Gerard Brown, Kevin K. Wise, Robert Martinez, Fernando J. McGoldrick, Daniel Cho, Michael H. DeMeo, Dawn L. Silverman, Edwin K. Castaldi, Peter J. Hersh, Craig P.

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2022

Schlagwörter:	COPD IPF RNA sequencing

Anmerkung:	© The Author(s) 2022

Übergeordnetes Werk:	Enthalten in: Respiratory research - London : BioMed Central, 2001, 23(2022), 1 vom: 21. Apr.
Übergeordnetes Werk:	volume:23 ; year:2022 ; number:1 ; day:21 ; month:04

Links:	Volltext

DOI / URN:	10.1186/s12931-022-02013-w

Katalog-ID:	SPR050657720

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520			\|a Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF.
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700	1		\|a Xu, Zhonghui \|4 aut
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allfields	10.1186/s12931-022-02013-w doi (DE-627)SPR050657720 (SPR)s12931-022-02013-w-e DE-627 ger DE-627 rakwb eng Ghosh, Auyon J. verfasserin aut Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. COPD (dpeaa)DE-He213 IPF (dpeaa)DE-He213 RNA sequencing (dpeaa)DE-He213 Hobbs, Brian D. aut Yun, Jeong H. aut Saferali, Aabida aut Moll, Matthew aut Xu, Zhonghui aut Chase, Robert P. aut Morrow, Jarrett aut Ziniti, John aut Sciurba, Frank aut Barwick, Lucas aut Limper, Andrew H. aut Flaherty, Kevin aut Criner, Gerard aut Brown, Kevin K. aut Wise, Robert aut Martinez, Fernando J. aut McGoldrick, Daniel aut Cho, Michael H. aut DeMeo, Dawn L. aut Silverman, Edwin K. aut Castaldi, Peter J. aut Hersh, Craig P. (orcid)0000-0002-1342-4334 aut Enthalten in Respiratory research London : BioMed Central, 2001 23(2022), 1 vom: 21. Apr. (DE-627)326646485 (DE-600)2041675-1 1465-993X nnns volume:23 year:2022 number:1 day:21 month:04 https://dx.doi.org/10.1186/s12931-022-02013-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 21 04
spelling	10.1186/s12931-022-02013-w doi (DE-627)SPR050657720 (SPR)s12931-022-02013-w-e DE-627 ger DE-627 rakwb eng Ghosh, Auyon J. verfasserin aut Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. COPD (dpeaa)DE-He213 IPF (dpeaa)DE-He213 RNA sequencing (dpeaa)DE-He213 Hobbs, Brian D. aut Yun, Jeong H. aut Saferali, Aabida aut Moll, Matthew aut Xu, Zhonghui aut Chase, Robert P. aut Morrow, Jarrett aut Ziniti, John aut Sciurba, Frank aut Barwick, Lucas aut Limper, Andrew H. aut Flaherty, Kevin aut Criner, Gerard aut Brown, Kevin K. aut Wise, Robert aut Martinez, Fernando J. aut McGoldrick, Daniel aut Cho, Michael H. aut DeMeo, Dawn L. aut Silverman, Edwin K. aut Castaldi, Peter J. aut Hersh, Craig P. (orcid)0000-0002-1342-4334 aut Enthalten in Respiratory research London : BioMed Central, 2001 23(2022), 1 vom: 21. Apr. (DE-627)326646485 (DE-600)2041675-1 1465-993X nnns volume:23 year:2022 number:1 day:21 month:04 https://dx.doi.org/10.1186/s12931-022-02013-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 21 04
allfields_unstemmed	10.1186/s12931-022-02013-w doi (DE-627)SPR050657720 (SPR)s12931-022-02013-w-e DE-627 ger DE-627 rakwb eng Ghosh, Auyon J. verfasserin aut Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. COPD (dpeaa)DE-He213 IPF (dpeaa)DE-He213 RNA sequencing (dpeaa)DE-He213 Hobbs, Brian D. aut Yun, Jeong H. aut Saferali, Aabida aut Moll, Matthew aut Xu, Zhonghui aut Chase, Robert P. aut Morrow, Jarrett aut Ziniti, John aut Sciurba, Frank aut Barwick, Lucas aut Limper, Andrew H. aut Flaherty, Kevin aut Criner, Gerard aut Brown, Kevin K. aut Wise, Robert aut Martinez, Fernando J. aut McGoldrick, Daniel aut Cho, Michael H. aut DeMeo, Dawn L. aut Silverman, Edwin K. aut Castaldi, Peter J. aut Hersh, Craig P. (orcid)0000-0002-1342-4334 aut Enthalten in Respiratory research London : BioMed Central, 2001 23(2022), 1 vom: 21. Apr. (DE-627)326646485 (DE-600)2041675-1 1465-993X nnns volume:23 year:2022 number:1 day:21 month:04 https://dx.doi.org/10.1186/s12931-022-02013-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 21 04
allfieldsGer	10.1186/s12931-022-02013-w doi (DE-627)SPR050657720 (SPR)s12931-022-02013-w-e DE-627 ger DE-627 rakwb eng Ghosh, Auyon J. verfasserin aut Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. COPD (dpeaa)DE-He213 IPF (dpeaa)DE-He213 RNA sequencing (dpeaa)DE-He213 Hobbs, Brian D. aut Yun, Jeong H. aut Saferali, Aabida aut Moll, Matthew aut Xu, Zhonghui aut Chase, Robert P. aut Morrow, Jarrett aut Ziniti, John aut Sciurba, Frank aut Barwick, Lucas aut Limper, Andrew H. aut Flaherty, Kevin aut Criner, Gerard aut Brown, Kevin K. aut Wise, Robert aut Martinez, Fernando J. aut McGoldrick, Daniel aut Cho, Michael H. aut DeMeo, Dawn L. aut Silverman, Edwin K. aut Castaldi, Peter J. aut Hersh, Craig P. (orcid)0000-0002-1342-4334 aut Enthalten in Respiratory research London : BioMed Central, 2001 23(2022), 1 vom: 21. Apr. (DE-627)326646485 (DE-600)2041675-1 1465-993X nnns volume:23 year:2022 number:1 day:21 month:04 https://dx.doi.org/10.1186/s12931-022-02013-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 21 04
allfieldsSound	10.1186/s12931-022-02013-w doi (DE-627)SPR050657720 (SPR)s12931-022-02013-w-e DE-627 ger DE-627 rakwb eng Ghosh, Auyon J. verfasserin aut Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis 2022 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © The Author(s) 2022 Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. COPD (dpeaa)DE-He213 IPF (dpeaa)DE-He213 RNA sequencing (dpeaa)DE-He213 Hobbs, Brian D. aut Yun, Jeong H. aut Saferali, Aabida aut Moll, Matthew aut Xu, Zhonghui aut Chase, Robert P. aut Morrow, Jarrett aut Ziniti, John aut Sciurba, Frank aut Barwick, Lucas aut Limper, Andrew H. aut Flaherty, Kevin aut Criner, Gerard aut Brown, Kevin K. aut Wise, Robert aut Martinez, Fernando J. aut McGoldrick, Daniel aut Cho, Michael H. aut DeMeo, Dawn L. aut Silverman, Edwin K. aut Castaldi, Peter J. aut Hersh, Craig P. (orcid)0000-0002-1342-4334 aut Enthalten in Respiratory research London : BioMed Central, 2001 23(2022), 1 vom: 21. Apr. (DE-627)326646485 (DE-600)2041675-1 1465-993X nnns volume:23 year:2022 number:1 day:21 month:04 https://dx.doi.org/10.1186/s12931-022-02013-w kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_702 GBV_ILN_2001 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2006 GBV_ILN_2008 GBV_ILN_2009 GBV_ILN_2010 GBV_ILN_2011 GBV_ILN_2014 GBV_ILN_2015 GBV_ILN_2020 GBV_ILN_2021 GBV_ILN_2025 GBV_ILN_2031 GBV_ILN_2038 GBV_ILN_2044 GBV_ILN_2048 GBV_ILN_2050 GBV_ILN_2055 GBV_ILN_2056 GBV_ILN_2057 GBV_ILN_2061 GBV_ILN_2111 GBV_ILN_2113 GBV_ILN_2153 GBV_ILN_2190 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 23 2022 1 21 04
language	English
source	Enthalten in Respiratory research 23(2022), 1 vom: 21. Apr. volume:23 year:2022 number:1 day:21 month:04
sourceStr	Enthalten in Respiratory research 23(2022), 1 vom: 21. Apr. volume:23 year:2022 number:1 day:21 month:04
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	COPD IPF RNA sequencing
isfreeaccess_bool	true
container_title	Respiratory research
authorswithroles_txt_mv	Ghosh, Auyon J. @@aut@@ Hobbs, Brian D. @@aut@@ Yun, Jeong H. @@aut@@ Saferali, Aabida @@aut@@ Moll, Matthew @@aut@@ Xu, Zhonghui @@aut@@ Chase, Robert P. @@aut@@ Morrow, Jarrett @@aut@@ Ziniti, John @@aut@@ Sciurba, Frank @@aut@@ Barwick, Lucas @@aut@@ Limper, Andrew H. @@aut@@ Flaherty, Kevin @@aut@@ Criner, Gerard @@aut@@ Brown, Kevin K. @@aut@@ Wise, Robert @@aut@@ Martinez, Fernando J. @@aut@@ McGoldrick, Daniel @@aut@@ Cho, Michael H. @@aut@@ DeMeo, Dawn L. @@aut@@ Silverman, Edwin K. @@aut@@ Castaldi, Peter J. @@aut@@ Hersh, Craig P. @@aut@@
publishDateDaySort_date	2022-04-21T00:00:00Z
hierarchy_top_id	326646485
id	SPR050657720
language_de	englisch
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Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. 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author	Ghosh, Auyon J.
spellingShingle	Ghosh, Auyon J. misc COPD misc IPF misc RNA sequencing Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
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topic_title	Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis COPD (dpeaa)DE-He213 IPF (dpeaa)DE-He213 RNA sequencing (dpeaa)DE-He213
topic	misc COPD misc IPF misc RNA sequencing
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title	Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
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title_full	Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
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author_browse	Ghosh, Auyon J. Hobbs, Brian D. Yun, Jeong H. Saferali, Aabida Moll, Matthew Xu, Zhonghui Chase, Robert P. Morrow, Jarrett Ziniti, John Sciurba, Frank Barwick, Lucas Limper, Andrew H. Flaherty, Kevin Criner, Gerard Brown, Kevin K. Wise, Robert Martinez, Fernando J. McGoldrick, Daniel Cho, Michael H. DeMeo, Dawn L. Silverman, Edwin K. Castaldi, Peter J. Hersh, Craig P.
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title_sort	lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
title_auth	Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
abstract	Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. © The Author(s) 2022
abstractGer	Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. © The Author(s) 2022
abstract_unstemmed	Background Chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF) are characterized by shared exposures and clinical features, but distinct genetic and pathologic features exist. These features have not been well-studied using large-scale gene expression datasets. We hypothesized that there are divergent gene, pathway, and cellular signatures between COPD and IPF. Methods We performed RNA-sequencing on lung tissues from individuals with IPF (n = 231) and COPD (n = 377) compared to control (n = 267), defined as individuals with normal spirometry. We grouped the overlapping differential expression gene sets based on direction of expression and examined the resultant sets for genes of interest, pathway enrichment, and cell composition. Using gene set variation analysis, we validated the overlap group gene sets in independent COPD and IPF data sets. Results We found 5010 genes differentially expressed between COPD and control, and 11,454 genes differentially expressed between IPF and control (1% false discovery rate). 3846 genes overlapped between IPF and COPD. Several pathways were enriched for genes upregulated in COPD and downregulated in IPF; however, no pathways were enriched for genes downregulated in COPD and upregulated in IPF. There were many myeloid cell genes with increased expression in COPD but decreased in IPF. We found that the genes upregulated in COPD but downregulated in IPF were associated with lower lung function in the independent validation cohorts. Conclusions We identified a divergent gene expression signature between COPD and IPF, with increased expression in COPD and decreased in IPF. This signature is associated with worse lung function in both COPD and IPF. © The Author(s) 2022
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title_short	Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis
url	https://dx.doi.org/10.1186/s12931-022-02013-w
remote_bool	true
author2	Hobbs, Brian D. Yun, Jeong H. Saferali, Aabida Moll, Matthew Xu, Zhonghui Chase, Robert P. Morrow, Jarrett Ziniti, John Sciurba, Frank Barwick, Lucas Limper, Andrew H. Flaherty, Kevin Criner, Gerard Brown, Kevin K. Wise, Robert Martinez, Fernando J. McGoldrick, Daniel Cho, Michael H. DeMeo, Dawn L. Silverman, Edwin K. Castaldi, Peter J. Hersh, Craig P.
author2Str	Hobbs, Brian D. Yun, Jeong H. Saferali, Aabida Moll, Matthew Xu, Zhonghui Chase, Robert P. Morrow, Jarrett Ziniti, John Sciurba, Frank Barwick, Lucas Limper, Andrew H. Flaherty, Kevin Criner, Gerard Brown, Kevin K. Wise, Robert Martinez, Fernando J. McGoldrick, Daniel Cho, Michael H. DeMeo, Dawn L. Silverman, Edwin K. Castaldi, Peter J. Hersh, Craig P.
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Lung tissue shows divergent gene expression between chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis

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