bims-micpro 2024-11-10 papers

BMC Genomics. 2024 Nov 05. 25(1): 1034

Microprotein-encoding RNA regulation in cells treated with pro-inflammatory and pro-fibrotic stimuli.

Victor J Pai, Calvin J Lau, Almudena Garcia-Ruiz, Cynthia Donaldson, Joan M Vaughan, Brendan Miller, Eduardo V De Souza, Antonio M Pinto, Jolene Diedrich, Narender R Gavva, Shan Yu, Christopher DeBoever, Shane R Horman, Alan Saghatelian.

BACKGROUND: Recent analysis of the human proteome via proteogenomics and ribosome profiling of the transcriptome revealed the existence of thousands of previously unannotated microprotein-coding small open reading frames (smORFs). Most functional microproteins were chosen for characterization because of their evolutionary conservation. However, one example of a non-conserved immunomodulatory microprotein in mice suggests that strict sequence conservation misses some intriguing microproteins.
RESULTS: We examine the ability of gene regulation to identify human microproteins with potential roles in inflammation or fibrosis of the intestine. To do this, we collected ribosome profiling data of intestinal cell lines and peripheral blood mononuclear cells and used gene expression of microprotein-encoding transcripts to identify strongly regulated microproteins, including several examples of microproteins that are only conserved with primates.
CONCLUSION: This approach reveals a number of new microproteins worthy of additional functional characterization and provides a dataset that can be queried in different ways to find additional gut microproteins of interest.

Keywords: Fibrosis; Inflammation; Microproteins; Ribosome profiling; Small open reading frames (smORFs)

DOI: https://doi.org/10.1186/s12864-024-10948-1

J Mol Biol. 2024 Oct 30. pii: S0022-2836(24)00480-7. [Epub ahead of print] 168850

Translation complex profile sequencing allows discrimination of leaky scanning and reinitiation in upstream open reading frame-controlled translation.

Dmitri E Andreev, Jack A S Tierney, Pavel V Baranov.

Upstream open reading frames (uORFs) are a class of translated regions (translons) in mRNA 5' leaders. uORFs are believed to be pervasive regulators of the translation of mammalian mRNAs. Some uORFs are highly repressive but others have little or no impact on downstream mRNA translation either due to inefficient recognition of their start codon(s) or/and due to efficient reinitiation after uORF translation. While experiments with uORF reporter constructs proved to be instrumental in the investigation of uORF-mediated mechanisms of translation control, they can have serious limitations as manipulations with uORF sequences can yield various artefacts. Here we propose a general approach for using translation complex profiling (TCP-seq) data for exploring uORF regulatory characteristics. Using several examples, we show how TCP-seq could be used to estimate both repressiveness and modes of action of individual uORFs. We demonstrate how this approach could be used to assess the mechanisms of uORF-mediated translation control in the mRNA of several human genes, including EIF5, IFRD1, MDM2, MIEF1, PPP1R15B, TAF7, and UCP2.

Keywords: Leaky scanning; Reinitiation; Ribo-seq; TCP-seq; uORF

DOI: https://doi.org/10.1016/j.jmb.2024.168850

Commun Med (Lond). 2024 Nov 01. 4(1): 224

Iroquois homeobox 4 (IRX4) derived micropeptide promotes prostate cancer progression and chemoresistance through Wnt signalling dysregulation.

Achala Fernando, Chamikara Liyanage, Srilakshmi Srinivasan, Janaththani Panchadsaram, Joseph A Rothnagel, Judith Clements, Jyotsna Batra.

BACKGROUND: Prostate cancer (PCa) is a commonly diagnosed cancer. Genome-wide association studies have implicated Iroquois homeobox 4 (IRX4) in PCa susceptibility, yet its functional roles remain unclear. We discovered a 78-amino acid micropeptide (miPEP, IRX4_PEP1), encoded from the alternative start site within the IRX4 gene. The miPEPs, encoded through short open reading frames (sORFs) have emerged as regulators of diverse biological processes. However, the significance of miPEPs in prostate tumorigenesis and therapy response remains unexplored to date. Here, we demonstrated the unique role of IRX4_PEP1 in PCa.
METHODS: The role of IRX4_PEP1 was evaluated in PCa in vitro via functional assays and comprehensive pathway analysis. The interacting partners of IRX4_PEP1 were identified using an immunoprecipitation assay, and the impact of IRX4_PEP1 on PCa stem cells was assessed through a stem cell enrichment assay. Additionally, the expression of IRX4_PEP1 was evaluated in PCa patient samples for its potential diagnostic and prognostic significance.
RESULTS: Here we show IRX4_PEP1 promotes PCa cell proliferation, migration, and invasion by interacting with heterogeneous nuclear ribonucleoprotein K (HNRPK). Notably, IRX4_PEP1 dysregulates Wnt signalling by interacting with Catenin beta 1 (β catenin; CTNB1), elevating PCa stemness markers, and fostering docetaxel resistance. Clinically, IRX4_PEP1 expression is elevated in PCa tissues and correlates positively with disease aggressiveness. CTNNB1, HNRNPK levels, and ssGSEA enrichment score of WNT/CTNB1 signalling correlate positively with IRX4_PEP1 in PCa tissues.
CONCLUSIONS: These findings highlight IRX4_PEP1 role in PCa stemness and chemoresistance, suggesting it as a therapeutic target and potential diagnostic marker.

DOI: https://doi.org/10.1038/s43856-024-00613-9

J Proteome Res. 2024 Nov 01.

Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.

Valeriia Vasylieva, Ihor Arefiev, Francis Bourassa, Félix-Antoine Trifiro, Marie A Brunet.

Throughout the past decade, technological advances in genomics and transcriptomics have revealed pervasive translation throughout mammalian genomes. These putative proteins are usually excluded from proteomics analyses, as they are absent from common protein repositories. A sizable portion of these noncanonical proteins is translated from pseudogenes. Pseudogenes are commonly termed defective copies of coding genes unable to produce proteins. Here, we suggest that proteomics can help in their annotation. First, we define important terms and review specific examples underlining the caveats in pseudogene annotation and their coding potential. Then, we will discuss the challenges inherent to pseudogenes that have thus far rendered complex their confidence in omics data. Finally, we identify recent developments in experimental procedures, instrumentation, and computational methods in proteomics that put the field in a unique position to solve the pseudogene annotation conundrum.

Keywords: mass spectrometry; microprotein; noncanonical ORF; proteomics; pseudogene; pseudogenic protein; small ORF

DOI: https://doi.org/10.1021/acs.jproteome.4c00116