A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation DOI Creative Commons

Jose Manuel Rodríguez,

Miguel Maquedano, Daniel Cerdán-Vélez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have proposed from large-scale RNASeq, ribosome profiling proteomics experiments. Here we carry out an in-depth analysis entire database. We analysed proteins, peptides spectra housed in build PeptideAtlas database to identify regions that are not yet annotated GENCODE reference gene set. find support hundreds missing alternative protein isoforms unannotated upstream translations, evidence cross-contamination other species. There was reliable peptide 34 novel open reading frames (ORFs) PeptideAtlas. almost half belong sets. Most remaining ORFs were conserved beyond human, however, their confirmation restricted cancer cell lines. show this is strong aberrant translation, raising important questions about extent translation how these should be genomes.

Language: Английский

A novel cancer-associated lncRNA, LINC01123, participates in tumor progression, metabolism, immune escape, and resistance DOI Creative Commons
Qiang Liu, He Huang, Shuwen Zhang

et al.

Frontiers in Immunology, Journal Year: 2025, Volume and Issue: 16

Published: April 4, 2025

Long Intergenic Non-Protein Coding RNA 1123 (LINC01123), located on human chromosome 2q13, is a pivotal factor in tumorigenesis, exerting multifaceted oncogenic effects. Its expression strongly correlates with clinicopathological features, patient survival, and disease progression. In vivo vitro experiments further demonstrate that LINC01123 influences diverse cellular processes, including proliferation, apoptosis, viability, migration, invasion, stemness, tumor growth. Notably, it also regulates metabolic reprogramming, immune escape, cell resistance to treatment. regulated by multiple transcription factors participates gene regulation through protein interactions competitive endogenous (ceRNA) networks, thereby modulating cancer-promoting This work systematically elucidates its primary functions molecular mechanisms driving cancer initiation progression, suggesting might serve as novel potential driver biomarker various cancers.

Language: Английский

Citations

0
A deep audit of the PeptideAtlas database uncovers evidence for unannotated coding genes and aberrant translation DOI Creative Commons

Jose Manuel Rodríguez,

Miguel Maquedano, Daniel Cerdán-Vélez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Nov. 15, 2024

The human genome has been the subject of intense scrutiny by experimental and manual curation projects for more than two decades. Novel coding genes have proposed from large-scale RNASeq, ribosome profiling proteomics experiments. Here we carry out an in-depth analysis entire database. We analysed proteins, peptides spectra housed in build PeptideAtlas database to identify regions that are not yet annotated GENCODE reference gene set. find support hundreds missing alternative protein isoforms unannotated upstream translations, evidence cross-contamination other species. There was reliable peptide 34 novel open reading frames (ORFs) PeptideAtlas. almost half belong sets. Most remaining ORFs were conserved beyond human, however, their confirmation restricted cancer cell lines. show this is strong aberrant translation, raising important questions about extent translation how these should be genomes.

Language: Английский

Citations

2