bims-micpro 2025-04-06 papers

Mol Cancer. 2025 Apr 02. 24(1): 105

Small open reading frame-encoded microproteins in cancer: identification, biological functions and clinical significance.

Tingting Zhang, Zhang Li, Jiao Li, Yong Peng.

The human genome harbors approximately twenty thousand protein-coding genes, and a significant portion of life science research focuses on elucidating their functions and the underlying mechanisms. Recent studies have revealed that small open reading frame (sORF), originating from non-coding RNAs or the 5' leader sequences of messenger RNAs, can be translated into small peptides called microproteins through cap-dependent or cap-independent mechanisms. These microproteins interact with diverse molecular partners to modulate gene expression at multiple regulatory levels, thereby playing critical roles in various biological processes. Notably, sORF-encoded microproteins exhibit aberrant expression patterns in cancer and are implicated in tumor initiation and progression, expanding our understanding of cancer biology. In this review, we introduce the translational mechanisms and identification methods of microproteins, summarize their dysregulation in cancer and their biological functions in regulating gene expression, and emphasize their roles in driving hallmark events of cancer. Furthermore, we discuss their clinical significance as diagnostic and prognostic biomarkers, as well as therapeutic targets.

DOI: https://doi.org/10.1186/s12943-025-02278-x

Chin J Dent Res. 2025 Mar 31. 28(1): 31-43

Analysis of Differential Translation Profiles of Human Bone Marrow Mesenchymal Stem Cells during Osteogenic Differentiation.

Hua Liu, Zhi Peng Fan, Qiu Bo Yang, Hui Na Liu.

OBJECTIVE: To explore the differential translation profiles and coding products of human jaw bone marrow mesenchymal stem cells (h-JBMMSCs) during osteogenic differentiation.
METHODS: Ribo-seq was used to examine the differential translated genes (DEGs), open reading frames (ORFs) and genes associated with the osteogenic differentiation phase of h-JBMMSCs. Western blotting (WB) was performed to detect the expression of osteocalcin (OCN) and bone sialoprotein (BSP). Alkaline phosphatase (ALP) activity and alizarin red staining (ARS) were used to detect osteogenic differentiation. A lentivirus containing 5'UTR-ORF-GFPmut was designed to transfect h-JBMMSCs, and fluorescence and green fluorescent protein (GFP) expression were analysed. The SNHG1 peptide was synthesised for osteogenic induction and to detect osteogenic markers.
RESULTS: A total of 53,432 ORFs were detected and 199 candidate translation sORFs, including lncRNA SNHG1, were identified after removing the annotated protein-coding genes. In addition, the 5'UTR-ORF-GFPmut showed green fluorescence and expressed GFP. Knockdown of the lncRNA SNHG1 increased the ALP activity of h-JBMMSCs, promoted the expression of OCN and BSP, and enhanced the intensity of ARS and calcium ion content. However, overexpression of lncRNA SNHG1 and the SNHG1 polypeptide inhibited the osteogenic differentiation of h-JBMMSCs.
CONCLUSION: LncRNA SNHG1 inhibited the osteogenic differentiation of h-JBMMSCs. LncRNA SNHG1 can encode a peptide of 19-amino acid and inhibit the osteogenic differentiation of h-JBMMSCs.

Keywords: h-JBMMSCs; lncRNA SNHG1; osteogenic differentiation; peptide; ribosome profiling

DOI: https://doi.org/10.3290/j.cjdr.b6097608

Nat Commun. 2025 Mar 30. 16(1): 3078

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni.

Kathrin Froschauer, Sarah L Svensson, Rick Gelhausen, Elisabetta Fiore, Philipp Kible, Alicia Klaude, Martin Kucklick, Stephan Fuchs, Florian Eggenhofer, Chao Yang, Daniel Falush, Susanne Engelmann, Rolf Backofen, Cynthia M Sharma.

In contrast to transcriptome maps, bacterial small protein (≤50-100 aa) coding landscapes, including overlapping genes, are poorly characterized. However, an emerging number of small proteins have crucial roles in bacterial physiology and virulence. Here, we present a Ribo-seq-based high-resolution translatome map for the major foodborne pathogen Campylobacter jejuni. Besides conventional Ribo-seq, we employed translation initiation site (TIS) profiling to map start codons and also developed a translation termination site (TTS) profiling approach, which revealed stop codons not apparent from the reference genome in virulence loci. Our integrated approach combined with independent validation expanded the small proteome by two-fold, including CioY, a new 34 aa component of the CioAB oxidase. Overall, our study generates a high-resolution annotation of the C. jejuni coding landscape, provided in an interactive browser, and showcases a strategy for applying integrated Ribo-seq to other species to enrich our understanding of small proteomes.

DOI: https://doi.org/10.1038/s41467-025-58329-w

J Virol. 2025 Apr 02. e0196024

Proteogenomic analysis of Cyprinid herpesvirus 2 using high-resolution mass spectrometry.

Chen Xu, Fangxing Yu, Mingyang Xue, Zhenyu Huang, Nan Jiang, Yiqun Li, Yan Meng, Wenzhi Liu, Ya Zheng, Yuding Fan, Yong Zhou.

Cyprinid herpesvirus 2 (CyHV-2) is the main pathogen responsible for the development of herpesviral hematopoietic necrosis disease (HVHND) in crucian carp (Carassius auratus). The CyHV-2 genome encodes approximately 150 genes that are expressed in a well-defined manner during productive infection. However, CyHV-2 open reading frames (ORFs) are primarily derived from sequence and homology analyses, and most lack protein-level evidence to support their properties. In this study, we used high-resolution mass spectrometry followed by proteogenomic mapping to achieve genome re-annotation of CyHV-2. Based on our results, a total of 1,683 MS/MS spectra could be mapped to the CyHV-2 genome through six-frame translation, with 1,665 corresponding to 117 currently annotated protein-coding ORFs. Three of the remaining 18 peptides were mapped to the N-terminal extension region of known ORFs. However, 12 novel CyHV-2 ORFs, designated nORF1-12, were identified and characterized for the first time based on the remaining 15 peptides that could be mapped to previously unannotated regions of the viral genome. And the sequence differences of the novel phosphorylated nORF1, also referred to as ORF25E, in different CyHV-2 strains indicated that the nORF1 is a prospective molecular marker that can monitor the evolution from the Japan (J) to the China (C) genotype of CyHV-2. These findings further validate existing annotations, expand the genomic landscape of CyHV-2, and provide a rich resource for aquatic virology research.IMPORTANCECyHV-2 is a viral pathogen that poses a significant threat to crucian carp farming. CyHV-2 has a large genome with complex sequence features and diverse coding mechanisms, which complicates accurate genome annotation in the absence of protein-level evidence. Here, we employed various protein extraction and separation methods to increase viral protein coverage and performed an integrated proteogenomic analysis to refine the CyHV-2 genome annotation. A total of 129 viral genes were confidently identified, including 117 currently annotated genes and 12 novel genes. For the first time, we present large-scale evidence of peptide presence and levels in the genome of aquatic viruses and confirm the majority of the predicted proteins in CyHV-2. Our findings enhance the understanding of the CyHV-2 genome structure and provide valuable insights for future studies on CyHV-2 biology.

Keywords: Cyprinid herpesvirus 2; gene discovery; mass spectrometry; proteogenomics

DOI: https://doi.org/10.1128/jvi.01960-24