Genomics

Dataset Information

37

Gene expression differences between prion-resistant and prion-susceptible cells


ABSTRACT: Prions consist of aggregates of abnormal conformers of cellular prion protein (PrPC). They propagate by recruiting host-encoded PrPC although the critical interacting proteins and the reasons for the differences in susceptibility of distinct cell lines and populations are unknown. We derived a lineage of cell lines with markedly differing susceptibilities, unexplained by PrPC expression differences, to identify such factors. We examined the transcriptomes of prion-resistant revertants, isolated from highly susceptible cells, and identified a gene expression signature associated with susceptibility. Several of these genes encode proteins with a role in extracellular matrix (ECM) remodelling, a compartment in which disease-related PrP deposits. Loss-of-function of nine of these genes significantly increased susceptibility. Remarkably, inhibition of fibronectin 1 binding to integrin α8 by RGD peptide inhibited metalloproteinases (MMP)-2/9 whilst increasing prion propagation rates. This indicates that prion replication may be controlled by MMPs at the ECM in an integrin-dependent manner. Overall design: For each of the three biological repeats cell clones (samples) were harvested at a subclonfluent state and total RNA isolated using Rneasy (Qiagen) according to the specification of the manufacturer. Retinoic acid treatment of revertant cell clones (R2, R5, R7) increased prion replication by up to fourty-fold. To test differential gene expression under these conditions R7 cells were treated with retinoic acid (0.5 microM) and vehicle for six hours, before isolation of total RNA as described previously (PK 11.1 210307, PK 11.3 210307,PK 13.1 210307,PK 13.2 210307,PK 13.3 210307)

INSTRUMENT(S): [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array

SUBMITTER: Peter Christian Kloehn  

PROVIDER: GSE56275 | GEO | 2014-07-31

SECONDARY ACCESSION(S): PRJNA242814

REPOSITORIES: GEO

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Prions consist of aggregates of abnormal conformers of the cellular prion protein (PrP(C)). They propagate by recruiting host-encoded PrP(C) although the critical interacting proteins and the reasons for the differences in susceptibility of distinct cell lines and populations are unknown. We derived a lineage of cell lines with markedly differing susceptibilities, unexplained by PrP(C) expression differences, to identify such factors. Transcriptome analysis of prion-resistant revertants, isolate  ...[more]

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