Oliver et al. 2020 (PRJNA412370)

General Details

Title Ribosomal coverage with codon resulation in response to RPL12 siRNA treatment vs. no treatment
Organism
Number of Samples 4
Release Date 2017/09/27 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP118987
ENA SRP118987
GEO GSE104329
BioProject PRJNA412370

Publication

Title
Authors Oliver KE,Rauscher R,Mijnders M,Wang W,Wolpert MJ,Maya J,Sabusap CM,Kesterson RA,Kirk KL,Rab A,Braakman I,Hong JS,Hartman JL 4th,Ignatova Z,Sorscher EJ
Journal The Journal of clinical investigation
Publication Date 2019 Dec 2
Abstract Cystic fibrosis (CF) is caused by mutations in the CF transmembrane conductance regulator (CFTR), with approximately 90% of patients harboring at least one copy of the disease-associated variant F508del. We utilized a yeast phenomic system to identify genetic modifiers of F508del-CFTR biogenesis, from which ribosomal protein L12 (RPL12/uL11) emerged as a molecular target. In the present study, we investigated mechanism(s) by which suppression of RPL12 rescues F508del protein synthesis and activity. Using ribosome profiling, we found that rates of translation initiation and elongation were markedly slowed by RPL12 silencing. However, proteolytic stability and patch-clamp assays revealed RPL12 depletion significantly increased F508del-CFTR steady-state expression, interdomain assembly, and baseline open-channel probability. We next evaluated whether Rpl12-corrected F508del-CFTR could be further enhanced with concomitant pharmacologic repair (e.g., using clinically approved modulators lumacaftor and tezacaftor) and demonstrated additivity of these treatments. Rpl12 knockdown also partially restored maturation of specific CFTR variants in addition to F508del, and WT Cftr biogenesis was enhanced in the pancreas, colon, and ileum of Rpl12 haplosufficient mice. Modulation of ribosome velocity therefore represents a robust method for understanding both CF pathogenesis and therapeutic response.
PMC PMC6877332
PMID 31657788
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR6107148 PRJNA412370 Homo sapiens CFBE cells Ribo-Seq Harringtonine
SRR6107149 PRJNA412370 Homo sapiens CFBE cells Ribo-Seq Cycloheximide
SRR6107150 PRJNA412370 Homo sapiens CFBE cells Ribo-Seq Cycloheximide
SRR6107151 PRJNA412370 Homo sapiens CFBE cells Ribo-Seq Cycloheximide
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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