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Series GSE220967 Query DataSets for GSE220967
Status Public on Jun 07, 2023
Title Alterations of ribosomal RNA pseudouridylation in human breast cancer
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary RNA modifications are key regulatory factors for several biological and pathological processes. They are abundantly represented on ribosomal RNA (rRNA), where they contribute to regulate ribosomal function in mRNA translation. Altered RNA modification pathways have been linked to tumorigenesis as well as to other human diseases. In this study we quantitatively evaluated the site-specific pseudouridylation pattern in rRNA in breast cancer samples exploiting the RBS-Seq technique involving RNA bisulfite treatment coupled with a new NGS approach. We found a wide variability among patients at different sites. The most dysregulated positions in tumors turned out to be hypermodified with respect to a reference RNA. As for 2’O-methylation level of rRNA modification, we detected variable and stable pseudouridine sites, with the most stable sites being the most evolutionary conserved. We also observed that pseudouridylation levels at specific sites are related to some clinical and bio-pathological tumor features and are able to distinguish different patient clusters. This study is the first example of the contribution that newly available high-throughput approaches for site specific pseudouridine detection can provide to the understanding of the intrinsic ribosomal changes occurring in human tumors.
Overall design RBS-seq of 77 bisulfite-treated and untreated breast cancer samples and 5 reference samples
Contributor(s) Dassi E, Montanaro L, Barozzi C
Citation(s) 37260601
Submission date Dec 14, 2022
Last update date Jun 07, 2023
Contact name Erik Dassi
Organization name University of Trento
Department CIBIO
Street address Via Sommarive, 9
City Trento
State/province TN
ZIP/Postal code 38123
Country Italy
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (82)
GSM6833201 10-A
GSM6833202 10-B
GSM6833203 10-NBS
BioProject PRJNA912185

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE220967_scoredPseudouridinePositions.txt.gz 2.7 Mb (ftp)(http) TXT
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