A Bayesian gene network reveals insight into the JAK-STAT pathway in systemic lupus erythematosus

Yupeng Li, Richard E. Higgs, Robert W. Hoffman, Ernst R. Dow, Xiong Liu, Michelle Petri, Daniel J. Wallace, Thomas Dörner, Brian J. Eastwood, Bradley B. Miller, Yushi Liu

Research output: Contribution to journalArticle

Abstract

Systemic lupus erythematosus (SLE) is a chronic, remitting, and relapsing, inflammatory disease involving multiple organs, which exhibits abnormalities of both the innate and adaptive immune responses. A limited number of transcriptomic studies have characterized the gene pathways involved in SLE in an attempt to identify the key pathogenic drivers of the disease. In order to further advance our understanding of the pathogenesis of SLE, we used a novel Bayesian network algorithm to hybridize knowledge- and data-driven methods, and then applied the algorithm to build an SLE gene network using transcriptomic data from 1,760 SLE patients’ RNA from the two tabalumab Phase III trials (ILLUMINATE-I & -II), the largest SLE RNA dataset to date. Further, based on the gene network, we carried out hub- and key driver-gene analyses for gene prioritization. Our analyses identified that the JAK-STAT pathway genes, including JAK2, STAT1, and STAT2, played essential roles in SLE pathogenesis, and reaffirmed the recent discovery of pathogenic relevance of JAK-STAT signaling in SLE. Additionally, we showed that other genes, such as IRF1, IRF7, PDIA4, FAM72C, TNFSF10, DHX58, SIGLEC1, and PML, may be also important in SLE and serve as potential therapeutic targets for SLE. In summary, using a hybridized network construction approach, we systematically investigated gene-gene interactions based on their transcriptomic profiles, prioritized genes based on their importance in the network structure, and revealed new insights into SLE activity.

Original languageEnglish (US)
Article numbere0225651
JournalPloS one
Volume14
Issue number12
DOIs
StatePublished - Jan 1 2019

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lupus erythematosus
Gene Regulatory Networks
Systemic Lupus Erythematosus
Genes
transcriptomics
genes
gene regulatory networks
pathogenesis
RNA
gene interaction
Bayesian networks
prioritization
Adaptive Immunity
Innate Immunity

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

A Bayesian gene network reveals insight into the JAK-STAT pathway in systemic lupus erythematosus. / Li, Yupeng; Higgs, Richard E.; Hoffman, Robert W.; Dow, Ernst R.; Liu, Xiong; Petri, Michelle; Wallace, Daniel J.; Dörner, Thomas; Eastwood, Brian J.; Miller, Bradley B.; Liu, Yushi.

In: PloS one, Vol. 14, No. 12, e0225651, 01.01.2019.

Research output: Contribution to journalArticle

Li, Y, Higgs, RE, Hoffman, RW, Dow, ER, Liu, X, Petri, M, Wallace, DJ, Dörner, T, Eastwood, BJ, Miller, BB & Liu, Y 2019, 'A Bayesian gene network reveals insight into the JAK-STAT pathway in systemic lupus erythematosus', PloS one, vol. 14, no. 12, e0225651. https://doi.org/10.1371/journal.pone.0225651
Li, Yupeng ; Higgs, Richard E. ; Hoffman, Robert W. ; Dow, Ernst R. ; Liu, Xiong ; Petri, Michelle ; Wallace, Daniel J. ; Dörner, Thomas ; Eastwood, Brian J. ; Miller, Bradley B. ; Liu, Yushi. / A Bayesian gene network reveals insight into the JAK-STAT pathway in systemic lupus erythematosus. In: PloS one. 2019 ; Vol. 14, No. 12.
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