Jorge Ruiz‐Orera

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

Loss of cardiomyocyte eukaryotic elongation factor 1A2 in mice triggers cardiomyopathy due to defective proteostasis

This study shows that loss of eEF1A2 in cardiomyocytes causes cardiomyopathy through proteostasis defects, and mTORC1 inhibition can reverse the condition.

An expanded reference catalog of translated open reading frames for biomedical research

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

LINC01503-MP is a Mitochondrial Microprotein That Promotes Cell Proliferation and Oxidative Metabolism.

This study identifies LINC01503-MP, a mitochondrial microprotein derived from an lncRNA, which promotes cell proliferation and oxidative metabolism in colorectal cancer cells.

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

The paper assesses MS-based identifications of unannotated human microproteins, finding large variation in reported proteins and PSM quality across studies.

Non-canonical ORFs are an important source of tumor-specific antigens in a liver cancer meta-cohort

The paper identifies non-canonical ORFs as a significant source of tumor-specific antigens in liver cancer, showing they can trigger immune responses and are shared among a substantial proportion of patients.

What can Ribo-seq and proteomics tell us about the non-canonical proteome?

This paper discusses the current state of research on non-canonical open reading frames (ORFs) and proposes standards for their investigation and reporting using Ribo-seq and proteomics.

Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart

This study investigates the role of RPL3L in ribosome heterogeneity and mitochondrial activity in cardiomyocytes, finding that its depletion increases ribosome-mitochondria interactions and ATP levels.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes

The paper identifies 27 RBPs that regulate both mRNA abundance and translational efficiency in human hearts, with 21 affecting distinct sets of target genes through differential affinity for target length.

Cap analysis of gene expression (CAGE) sequencing reveals alternative promoter usage in complex disease

The paper uses CAGE sequencing to identify alternative promoter usage in a rat model of hypertension, linking promoter shifts to insulin resistance and blood pressure.

Trans control of cardiac mRNA translation in a protein length-dependent fashion

The paper identifies a trans locus in rats that causes a protein length-dependent shift in translational efficiency, affecting cardiac hypertrophy and sarcomere protein stoichiometry.

Ribosome profiling at isoform level reveals an evolutionary conserved impact of differential splicing on the proteome

The paper introduces ORQAS, a pipeline for quantifying translation of transcript isoforms using ribosome profiling, and finds that differential splicing impacts translation across species.