Publications

BibTex format

@unpublished{Bernabeu-Herrero:2021:10.1101/2021.12.05.471269,
author = {Bernabeu-Herrero, M and Patel, D and Bielowka, A and Srikaran, S and Guerrero, PC and Govani, F and Mollet, I and Noseda, M and Aldred, M and Shovlin, C},
doi = {10.1101/2021.12.05.471269},
publisher = {BioRxiv},
title = {Heterozygous transcriptional and nonsense decay signatures in blood outgrowth endothelial cells from patients with hereditary haemorrhagic telangiectasia},
url = {http://dx.doi.org/10.1101/2021.12.05.471269},
year = {2021}
}

Download

RIS format (EndNote, RefMan)

TY  - UNPB
AB  - In order to identify cellular phenotypes resulting from nonsense (gain of stop/premature termination codon) variants, we devised a framework of analytic methods that minimised confounder contributions, and applied to blood outgrowth endothelial cells (BOECs) derived from controls and patients with heterozygous nonsense variants in ACVRL1 , ENG or SMAD4 causing hereditary haemorrhagic telangiectasia (HHT). Following validation of 48 pre-selected genes by single cell qRT-PCR, discovery RNASeq ranked HHT-differential alignments of 16,807 Ensembl transcripts. Consistent gene ontology (GO) processes enriched compared to randomly-selected gene lists included bone morphogenetic protein, transforming growth factor-β and angiogenesis GO processes already implicated in HHT, further validating methodologies. Additional terms/genes including for endoplasmic reticulum stress could be attributed to a generic process of inefficient nonsense mediated decay (NMD). NMD efficiency ranged from 78-92% (mean 87%) in different BOEC cultures, with misprocessed mutant protein production confirmed by pulse chase experiments. Genes in HHT-specific and generic nonsense decay (ND) lists displayed differing expression profiles in normal endothelial cells exposed to an additional stress of exogenous 10μmol/L iron which acutely upregulates multiple mRNAs: Despite differing donors and endothelial cell types, >50% of iron-induced variability could be explained by the magnitude of transcript downregulation in HHT BOECs with less efficient NMD. The Genotype Tissue Expression (GTEx) Project indicated ND list genes were usually most highly expressed in non-endothelial tissues. However, across 5 major tissues, although 18/486 nonsense and frameshift variants in highly expressed genes were captured in GTEx, none were sufficiently prevalent to obtain genome-wide significant p values for expression quantitative trait loci (GnomAD allele frequencies <0.0005). In conclusion, RNASeq analytics of
AU  - Bernabeu-Herrero,M
AU  - Patel,D
AU  - Bielowka,A
AU  - Srikaran,S
AU  - Guerrero,PC
AU  - Govani,F
AU  - Mollet,I
AU  - Noseda,M
AU  - Aldred,M
AU  - Shovlin,C
DO  - 10.1101/2021.12.05.471269
PB  - BioRxiv
PY  - 2021///
TI  - Heterozygous transcriptional and nonsense decay signatures in blood outgrowth endothelial cells from patients with hereditary haemorrhagic telangiectasia
UR  - http://dx.doi.org/10.1101/2021.12.05.471269
UR  - http://hdl.handle.net/10044/1/93610
ER  -

Download

Claire L. Shovlin PhD FRCP

Contact

Location

Summary

Citation

BibTex format

RIS format (EndNote, RefMan)