Core transcriptional regulatory circuits in prion diseases

Taek Kyun Kim, Inyoul Lee, Ji Hoon Cho, Brenda Canine, Andrew Keller, Nathan D. Price, Daehee Hwang, George Carlson, Leroy Hood

Research output: Contribution to journalArticlepeer-review

Abstract

Complex diseases involve dynamic perturbations of pathophysiological processes during disease progression. Transcriptional programs underlying such perturbations are unknown in many diseases. Here, we present core transcriptional regulatory circuits underlying early and late perturbations in prion disease. We first identified cellular processes perturbed early and late using time-course gene expression data from three prion-infected mouse strains. We then built a transcriptional regulatory network (TRN) describing regulation of early and late processes. We found over-represented feed-forward loops (FFLs) comprising transcription factor (TF) pairs and target genes in the TRN. Using gene expression data of brain cell types, we further selected active FFLs where TF pairs and target genes were expressed in the same cell type and showed correlated temporal expression changes in the brain. We finally determined core transcriptional regulatory circuits by combining these active FFLs. These circuits provide insights into transcriptional programs for early and late pathophysiological processes in prion disease.

Original languageEnglish (US)
Article number10
JournalMolecular Brain
Volume13
Issue number1
DOIs
StatePublished - Jan 20 2020
Externally publishedYes

Keywords

  • Brain cell type
  • Feed-forward loops
  • Gene expression
  • Murine PrP-prion disease
  • Transcriptional regulatory circuits

ASJC Scopus subject areas

  • Molecular Biology
  • Cellular and Molecular Neuroscience

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