Transcriptomic landscape of lncRNAs in inflammatory bowel disease

Research output: Contribution to journalJournal articlepeer-review

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Transcriptomic landscape of lncRNAs in inflammatory bowel disease. / Mirza, Aashiq Hussain; Bang-Berthelsen, Claus Heiner; Seemann, Ernst Stefan; Pan, Xiaoyong; Frederiksen, Klaus S; Vilien, Mogens; Gorodkin, Jan; Pociot, Flemming.

In: Genome Medicine, Vol. 7, 39, 2015.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Mirza, AH, Bang-Berthelsen, CH, Seemann, ES, Pan, X, Frederiksen, KS, Vilien, M, Gorodkin, J & Pociot, F 2015, 'Transcriptomic landscape of lncRNAs in inflammatory bowel disease', Genome Medicine, vol. 7, 39. https://doi.org/10.1186/s13073-015-0162-2

APA

Mirza, A. H., Bang-Berthelsen, C. H., Seemann, E. S., Pan, X., Frederiksen, K. S., Vilien, M., Gorodkin, J., & Pociot, F. (2015). Transcriptomic landscape of lncRNAs in inflammatory bowel disease. Genome Medicine, 7, [39]. https://doi.org/10.1186/s13073-015-0162-2

Vancouver

Mirza AH, Bang-Berthelsen CH, Seemann ES, Pan X, Frederiksen KS, Vilien M et al. Transcriptomic landscape of lncRNAs in inflammatory bowel disease. Genome Medicine. 2015;7. 39. https://doi.org/10.1186/s13073-015-0162-2

Author

Mirza, Aashiq Hussain ; Bang-Berthelsen, Claus Heiner ; Seemann, Ernst Stefan ; Pan, Xiaoyong ; Frederiksen, Klaus S ; Vilien, Mogens ; Gorodkin, Jan ; Pociot, Flemming. / Transcriptomic landscape of lncRNAs in inflammatory bowel disease. In: Genome Medicine. 2015 ; Vol. 7.

Bibtex

@article{753e54ccd33b4a8fbddd0e73c82c7953,
title = "Transcriptomic landscape of lncRNAs in inflammatory bowel disease",
abstract = "BACKGROUND: Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn's disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD.METHODS: In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in 96 colon pinch biopsies (inflamed and non-inflamed) extracted from multiple colonic locations from 45 patients (CD = 13, UC = 20, controls = 12) using an expression microarray platform.RESULTS: In our study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC compared to the healthy controls. In cases of inflamed CD and UC, we identified 438 and 745 differentially expressed lncRNAs, respectively, while in cases of the non-inflamed CD and UC, we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (P-value <0.001, Pearson's Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed their involvement in the immune response, pro-inflammatory cytokine activity and MHC protein complex.CONCLUSIONS: The lncRNA expression profiling in both inflamed and non-inflamed CD and UC successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggest their potential as biomarkers in IBD.",
author = "Mirza, {Aashiq Hussain} and Bang-Berthelsen, {Claus Heiner} and Seemann, {Ernst Stefan} and Xiaoyong Pan and Frederiksen, {Klaus S} and Mogens Vilien and Jan Gorodkin and Flemming Pociot",
year = "2015",
doi = "10.1186/s13073-015-0162-2",
language = "English",
volume = "7",
journal = "Genome Medicine",
issn = "1756-994X",
publisher = "BioMed Central Ltd.",

}

RIS

TY - JOUR

T1 - Transcriptomic landscape of lncRNAs in inflammatory bowel disease

AU - Mirza, Aashiq Hussain

AU - Bang-Berthelsen, Claus Heiner

AU - Seemann, Ernst Stefan

AU - Pan, Xiaoyong

AU - Frederiksen, Klaus S

AU - Vilien, Mogens

AU - Gorodkin, Jan

AU - Pociot, Flemming

PY - 2015

Y1 - 2015

N2 - BACKGROUND: Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn's disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD.METHODS: In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in 96 colon pinch biopsies (inflamed and non-inflamed) extracted from multiple colonic locations from 45 patients (CD = 13, UC = 20, controls = 12) using an expression microarray platform.RESULTS: In our study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC compared to the healthy controls. In cases of inflamed CD and UC, we identified 438 and 745 differentially expressed lncRNAs, respectively, while in cases of the non-inflamed CD and UC, we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (P-value <0.001, Pearson's Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed their involvement in the immune response, pro-inflammatory cytokine activity and MHC protein complex.CONCLUSIONS: The lncRNA expression profiling in both inflamed and non-inflamed CD and UC successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggest their potential as biomarkers in IBD.

AB - BACKGROUND: Inflammatory bowel disease (IBD) is a complex multi-factorial inflammatory disease with Crohn's disease (CD) and ulcerative colitis (UC) being the two most common forms. A number of transcriptional profiling studies have provided compelling evidence that describe the role of protein-coding genes and microRNAs in modulating the immune responses in IBD.METHODS: In the present study, we performed a genome-wide transcriptome profiling of lncRNAs and protein-coding genes in 96 colon pinch biopsies (inflamed and non-inflamed) extracted from multiple colonic locations from 45 patients (CD = 13, UC = 20, controls = 12) using an expression microarray platform.RESULTS: In our study, we identified widespread dysregulation of lncRNAs and protein-coding genes in both inflamed and non-inflamed CD and UC compared to the healthy controls. In cases of inflamed CD and UC, we identified 438 and 745 differentially expressed lncRNAs, respectively, while in cases of the non-inflamed CD and UC, we identified 12 and 19 differentially expressed lncRNAs, respectively. We also observed significant enrichment (P-value <0.001, Pearson's Chi-squared test) for 96 differentially expressed lncRNAs and 154 protein-coding genes within the IBD susceptibility loci. Furthermore, we found strong positive expression correlations for the intersecting and cis-neighboring differentially expressed IBD loci-associated lncRNA-protein-coding gene pairs. The functional annotation analysis of differentially expressed genes revealed their involvement in the immune response, pro-inflammatory cytokine activity and MHC protein complex.CONCLUSIONS: The lncRNA expression profiling in both inflamed and non-inflamed CD and UC successfully stratified IBD patients from the healthy controls. Taken together, the identified lncRNA transcriptional signature along with clinically relevant parameters suggest their potential as biomarkers in IBD.

U2 - 10.1186/s13073-015-0162-2

DO - 10.1186/s13073-015-0162-2

M3 - Journal article

C2 - 25991924

VL - 7

JO - Genome Medicine

JF - Genome Medicine

SN - 1756-994X

M1 - 39

ER -

ID: 138723146