bims-micpro 2023-01-29 papers

bims-micpro

Biomed News

on Discovery and characterization of microproteins

Issue of 2023–01–29
six papers selected by
Thomas Farid Martínez, University of California, Irvine

sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs.
Interaction of DWORF with SERCA and PLB as determined by EPR spectroscopy.
Dwarf Open Reading Frame (DWORF) Gene Therapy Ameliorated Duchenne Muscular Dystrophy Cardiomyopathy in Aged mdx Mice.
Shiny transcriptional junk: lncRNA-derived peptides in cancers and immune responses.
A novel polypeptide encoded by the circular RNA ZKSCAN1 suppresses HCC via degradation of mTOR.
Long Noncoding RNA U90926 Is Induced in Activated Macrophages, Is Protective in Endotoxic Shock, and Encodes a Novel Secreted Protein.

Interdiscip Sci. 2023 Jan 27.

sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs.

Ziwei Chen, Jun Meng, Siyuan Zhao, Chao Yin, Yushi Luan.

  Long non-coding RNAs (lncRNAs) are important regulators of biological processes. It has recently been shown that some lncRNAs include small open reading frames (sORFs) that can encode small peptides of no more than 100 amino acids. However, existing methods are commonly applied to human and animal datasets and still suffer from low feature representation capability. Thus, accurate and credible prediction of sORFs with coding ability in plant lncRNAs is imperative. This paper proposes a new method termed sORFPred, in which we design a model named MCSEN by combining multi-scale convolution and Squeeze-and-Excitation Networks to fully mine distinct information embedded in sORFs, integrate and optimize multiple sequence-based and physicochemical feature descriptors, and built a two-layer prediction classifier based on Bayesian optimization algorithm and Extra Trees. sORFPred has been evaluated on sORFs datasets of three species and experimentally validated sORFs dataset. Results indicate that sORFPred outperforms existing methods and achieves 97.28% accuracy, 97.06% precision, 97.52% recall, and 97.29% F1-score on Arabidopsis thaliana, which shows a significant improvement in prediction performance compared to various conventional shallow machine learning and deep learning models.

Keywords:  Comprehensive features; Ensemble learning; LncRNAs; Small peptides; sORFs

DOI:  https://doi.org/10.1007/s12539-023-00552-4
Biochem Biophys Res Commun. 2023 Jan 14. pii: S0006-291X(23)00072-4. [Epub ahead of print]645 97-102

Interaction of DWORF with SERCA and PLB as determined by EPR spectroscopy.

Mark D Rustad, Osha Roopnarine, Razvan L Cornea, David D Thomas.

  Insufficient sarco/endoplasmic reticulum calcium ATPase (SERCA) activity significantly contributes to heart failure, which is a leading cause of death worldwide. A characteristic pathology of cardiac disease is the slow and incomplete Ca2+ removal from the myocyte cytoplasm in diastole, which is primarily driven by SERCA, the integral transmembrane Ca2+ pump. Phospholamban (PLB) allosterically inhibits SERCA by reducing its apparent Ca2+ affinity. Recently, the 34-codon novel dwarf open reading frame (DWORF) micropeptide has been identified as a muscle-specific SERCA effector, capable of reversing the inhibitory effects of PLB and independently activating SERCA in the absence of PLB. However, the structural basis for these functions has not yet been determined in a system of defined molecular components. We have used electron paramagnetic resonance (EPR) spectroscopy to investigate the protein-protein interactions of DWORF, co-reconstituted in proteoliposomes with SERCA and spin-labeled PLB. We analyzed the change of PLB rotational mobility in response to varying DWORF concentration, to quantify competitive binding of DWORF and PLB. We determined that DWORF competes with PLB for binding to SERCA at low [Ca2+], although the measured affinity of DWORF for SERCA is an order of magnitude weaker than that of PLB for SERCA, indicating cooperativity. The sensitivity of EPR to structural dynamics, using stereospecifically attached spin labels, allows us to obtain new information needed to refine the molecular model for regulation of SERCA activity, as needed for development of novel therapeutic remedies against cardiac pathologies.

Keywords:  DWORF; EPR; Membrane protein dynamics; Phospholamban; SERCA; Spin label

DOI:  https://doi.org/10.1016/j.bbrc.2023.01.041
J Am Heart Assoc. 2023 Jan 25. e027480

Dwarf Open Reading Frame (DWORF) Gene Therapy Ameliorated Duchenne Muscular Dystrophy Cardiomyopathy in Aged mdx Mice.

Emily D Morales, Yongping Yue, Thais B Watkins, Jin Han, Xiufang Pan, Aaron M Gibson, Bryan Hu, Omar Brito-Estrada, Gang Yao, Catherine A Makarewich, Gopal J Babu, Dongsheng Duan.

  Background Cardiomyopathy is a leading health threat in Duchenne muscular dystrophy (DMD). Cytosolic calcium upregulation is implicated in DMD cardiomyopathy. Calcium is primarily removed from the cytosol by the sarcoendoplasmic reticulum calcium ATPase (SERCA). SERCA activity is reduced in DMD. Improving SERCA function may treat DMD cardiomyopathy. Dwarf open reading frame (DWORF) is a recently discovered positive regulator for SERCA, hence, a potential therapeutic target. Methods and Results To study DWORF's involvement in DMD cardiomyopathy, we quantified DWORF expression in the heart of wild-type mice and the mdx model of DMD. To test DWORF gene therapy, we engineered and characterized an adeno-associated virus serotype 9-DWORF vector. To determine if this vector can mitigate DMD cardiomyopathy, we delivered it to 6-week-old mdx mice (6×1012 vector genome particles/mouse) via the tail vein. Exercise capacity, heart histology, and cardiac function were examined at 18 months of age. We found DWORF expression was significantly reduced at the transcript and protein levels in mdx mice. Adeno-associated virus serotype 9-DWORF vector significantly enhanced SERCA activity. Systemic adeno-associated virus serotype 9-DWORF therapy reduced myocardial fibrosis and improved treadmill running, electrocardiography, and heart hemodynamics. Conclusions Our data suggest that DWORF deficiency contributes to SERCA dysfunction in mdx mice and that DWORF gene therapy holds promise to treat DMD cardiomyopathy.

Keywords:  AAV; DMD; DWORF; Duchenne muscular dystrophy; SERCA2a; adeno‐associated virus; cardiomyopathy

DOI:  https://doi.org/10.1161/JAHA.122.027480
Life Sci. 2023 Jan 24. pii: S0024-3205(23)00068-1. [Epub ahead of print] 121434

Shiny transcriptional junk: lncRNA-derived peptides in cancers and immune responses.

Yanli Zhang, Xiaocong Wang, Cong Hu, Huanfa Yi.

  By interacting with DNA, RNA, and proteins, long noncoding RNAs (lncRNAs) have been linked to several pathological states. LncRNA-derived peptides, as a novel modality of action of lncRNAs, have recently become a research hotspot. An increasing body of evidence has demonstrated the important role of these peptides in carcinogenesis and cancer progression and immune response. This review first describes lncRNA-derived peptides, the regulators that control their translation, and the roles of these peptides in multiple biological processes and disease states including cancers. In the following section, we comprehensively analyzed the significant role lncRNA-derived peptide played in the immune response. This review provides fresh perspectives on the biological role of lncRNAs and their relationship with diseases, particularly with cancers and the immune response, providing a theoretical basis for these lncRNA-derived peptides as therapeutic and diagnostic targets in cancers and inflammatory diseases.

Keywords:  Alternative splicing; Immune response; Inflammatory diseases; Long noncoding RNA; Peptides

DOI:  https://doi.org/10.1016/j.lfs.2023.121434
Mol Cancer. 2023 Jan 23. 22(1): 16

A novel polypeptide encoded by the circular RNA ZKSCAN1 suppresses HCC via degradation of mTOR.

Runjie Song, Shuoqian Ma, Jiajia Xu, Xin Ren, Peilan Guo, Huijiao Liu, Peng Li, Fan Yin, Mei Liu, Qiang Wang, Lei Yu, Jiali Liu, Binwei Duan, Nafis A Rahman, Sławomir Wołczyński, Guangming Li, Xiangdong Li.

   BACKGROUND: hsa_circ_0001727 (circZKSCAN1) has been reported to be a tumor-associated circRNA by sponging microRNAs. Intriguingly, we found that circZKSCAN1 encoded a secretory peptide (circZKSaa) in the liver. The present study aims to elucidate the potential role and molecular mechanism of circZKSaa in the regulation of hepatocellular carcinoma (HCC) progression.
METHODS: The circRNA profiling datasets (RNA-seq data GSE143233 and GSE140202) were reanalyzed and circZKSCAN1 was selected for further study. Mass spectrometry, polysome fractionation assay, dual-luciferase reporter, and a series of experiments showed that circZKSCAN1 encodes circZKSaa. Cell proliferation, apoptosis, and tumorigenesis in nude mice were examined to investigate the functions of circZKSaa. Mechanistically, the relationship between the circZKSaa and mTOR in HCC was verified by immunoprecipitation analyses, mass spectrometry, and immunofluorescence staining analyses.
RESULTS: Receiver operating characteristic (ROC) analysis demonstrated that the secretory peptide circZKSaa encoded by circZKSCAN1 might be the potential biomarker for HCC tissues. Through a series of experiments, we found that circZKSaa inhibited HCC progression and sensitize HCC cells to sorafenib. Mechanistically, we found that the sponge function of circZKSCAN1 to microRNA is weak in HCC, while overexpression of circZKSaa promoted the interaction of FBXW7 with the mammalian target of rapamycin (mTOR) to promote the ubiquitination of mTOR, thereby inhibiting the PI3K/AKT/mTOR pathway. Furthermore, we found that the high expression of cicZKSCAN1 in sorafenib-treated HCC cells was regulated by QKI-5.
CONCLUSIONS: These results reveal that a novel circZKSCAN1-encoded peptide acts as a tumor suppressor on PI3K/AKT/mTOR pathway, and sensitizes HCC cells to sorafenib via ubiquitination of mTOR. These findings demonstrated that circZKSaa has the potential to serve as a therapeutic target and biomarker for HCC treatment.

Keywords:  Biomarker; HCC; Sorafenib; circZKSaa; mTOR

DOI:  https://doi.org/10.1186/s12943-023-01719-9
J Immunol. 2023 Jan 27. pii: ji2200215. [Epub ahead of print]

Long Noncoding RNA U90926 Is Induced in Activated Macrophages, Is Protective in Endotoxic Shock, and Encodes a Novel Secreted Protein.

Bristy Sabikunnahar, Sydney Caldwell, Stella Varnum, Tyler Hogan, Alexei Cooper, Karolyn G Lahue, Joseph J Bivona, Phoebe M Cousens, Menelaos Symeonides, Bryan A Ballif, Matthew E Poynter, Dimitry N Krementsov.

Thousands of long noncoding RNAs are encoded in mammalian genomes, yet most remain uncharacterized. In this study, we functionally characterized a mouse long noncoding RNA named U90926. Analysis of U90926 RNA levels revealed minimal expression across multiple tissues at steady state. However, the expression of this gene was highly induced in macrophages and dendritic cells by TLR activation, in a p38 MAPK- and MyD88-dependent manner. To study the function of U90926, we generated U90926-deficient (U9-KO) mice. Surprisingly, we found minimal effects of U90926 deficiency in cultured macrophages. Given the lack of macrophage-intrinsic effect, we investigated the subcellular localization of U90926 transcript and its protein-coding potential. We found that U90926 RNA localizes to the cytosol, associates with ribosomes, and contains an open reading frame that encodes a novel glycosylated protein (termed U9-ORF), which is secreted from the cell. An in vivo model of endotoxic shock revealed that, in comparison with wild type mice, U9-KO mice exhibited increased sickness responses and mortality. Mechanistically, serum levels of IL-6 were elevated in U9-KO mice, and IL-6 neutralization improved endotoxemia outcomes in U9-KO mice. Taken together, these results suggest that U90926 expression is protective during endotoxic shock, potentially mediated by the paracrine and/or endocrine actions of the novel U9-ORF protein secreted by activated myeloid cells.

DOI: https://doi.org/10.4049/jimmunol.2200215