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Ren Y, Liao H, Yan J, Lu H, Mao X, Wang C, Li YF, Liu Y, Chen C, Chen L, Wang X, Zhou KY, Liu HM, Liu Y, Hua YM, Yu L, Xue Z. Capture of RNA-binding proteins across mouse tissues using HARD-AP. Nat Commun 2024; 15:8421. [PMID: 39341811 DOI: 10.1038/s41467-024-52765-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 09/20/2024] [Indexed: 10/01/2024] Open
Abstract
RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly associated RNA regulatory complexes from cultured cells and fresh tissues. We successfully use HARD-AP to establish a comprehensive atlas of RBPs across mouse primary organs. We then systematically map RNA-binding sites of these RBPs using machine learning-based modeling. Notably, the modeling reveals that the LIM domain as an RNA-binding domain in many RBPs. We validate the LIM-domain-only protein Csrp1 as a tissue-dependent RNA binding protein. Taken together, HARD-AP is a powerful approach that can be used to identify RBPomes from any type of sample, allowing comprehensive and physiologically relevant networks of RNA-protein interactions.
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Affiliation(s)
- Yijia Ren
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Hongyu Liao
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jun Yan
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Hongyu Lu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiaowei Mao
- Sichuan Provincial Key Laboratory for Human Disease Gene Study and the Center for Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, 610072, China
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, China
- Shimmer Center, Tianfu Jiangxi Laboratory, Chengdu, Sichuan, 641419, China
| | - Chuan Wang
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi-Fei Li
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yu Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chong Chen
- Department of Urology, Institute of Urology, State Key Laboratory of Biotherapy and Cancer Center, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Xiangfeng Wang
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100094, China
| | - Kai-Yu Zhou
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Han-Min Liu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Yi-Min Hua
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Lin Yu
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Zhihong Xue
- Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, Department of Pediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, 610041, China.
- Development and Related Diseases of Women and Children Key Laboratory of Sichuan Province, Chengdu, Sichuan, 610041, China.
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Gallardo-Dodd CJ, Kutter C. The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer. Hum Genomics 2024; 18:109. [PMID: 39334294 PMCID: PMC11437681 DOI: 10.1186/s40246-024-00678-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 09/22/2024] [Indexed: 09/30/2024] Open
Abstract
Biological systems encompass intricate networks governed by RNA-protein interactions that play pivotal roles in cellular functions. RNA and proteins constituting 1.1% and 18% of the mammalian cell weight, respectively, orchestrate vital processes from genome organization to translation. To date, disentangling the functional fraction of the human genome has presented a major challenge, particularly for noncoding regions, yet recent discoveries have started to unveil a host of regulatory functions for noncoding RNAs (ncRNAs). While ncRNAs exist at different sizes, structures, degrees of evolutionary conservation and abundances within the cell, they partake in diverse roles either alone or in combination. However, certain ncRNA subtypes, including those that have been described or remain to be discovered, are poorly characterized given their heterogeneous nature. RNA activity is in most cases coordinated through interactions with RNA-binding proteins (RBPs). Extensive efforts are being made to accurately reconstruct RNA-RBP regulatory networks, which have provided unprecedented insight into cellular physiology and human disease. In this review, we provide a comprehensive view of RNAs and RBPs, focusing on how their interactions generate functional signals in living cells, particularly in the context of post-transcriptional regulatory processes and cancer.
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Affiliation(s)
- Carlos J Gallardo-Dodd
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden
| | - Claudia Kutter
- Department of Microbiology, Tumor, and Cell Biology, Science for Life Laboratory, Karolinska Institute, Solna, Sweden.
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3
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Van Goubergen J, Peřina M, Handle F, Morales E, Kremer A, Schmidt O, Kristiansen G, Cronauer MV, Santer FR. Targeting the CLK2/SRSF9 splicing axis in prostate cancer leads to decreased ARV7 expression. Mol Oncol 2024. [PMID: 39258426 DOI: 10.1002/1878-0261.13728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 07/31/2024] [Accepted: 08/23/2024] [Indexed: 09/12/2024] Open
Abstract
In advanced prostate cancer (PC), in particular after acquisition of resistance to androgen receptor (AR) signaling inhibitors (ARSI), upregulation of AR splice variants compromises endocrine therapy efficiency. Androgen receptor splice variant-7 (ARV7) is clinically the most relevant and has a distinct 3' untranslated region (3'UTR) compared to the AR full-length variant, suggesting a unique post-transcriptional regulation. Here, we set out to evaluate the applicability of the ARV7 3'UTR as a therapy target. A common single nucleotide polymorphism, rs5918762, was found to affect the splicing rate and thus the expression of ARV7 in cellular models and patient specimens. Serine/arginine-rich splicing factor 9 (SRSF9) was found to bind to and increase the inclusion of the cryptic exon 3 of ARV7 during the splicing process in the alternative C allele of rs5918762. The dual specificity protein kinase CLK2 interferes with the activity of SRSF9 by regulating its expression. Inhibition of the Cdc2-like kinase (CLK) family by the small molecules cirtuvivint or lorecivivint results in the decreased expression of ARV7. Both inhibitors show potent anti-proliferative effects in enzalutamide-treated or -naive PC models. Thus, targeting aberrant alternative splicing at the 3'UTR of ARV7 by disturbing the CLK2/SRSF9 axis might be a valuable therapeutic approach in late stage, ARSI-resistant PC.
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Affiliation(s)
- Jasper Van Goubergen
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
| | - Miroslav Peřina
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
- Department of Experimental Biology, Faculty of Science, Palacký University Olomouc, Czech Republic
| | - Florian Handle
- Institute of Pathology, Neuropathology & Molecular Pathology, Medical University of Innsbruck, Austria
| | - Elisa Morales
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
| | - Anika Kremer
- Institute of Pathology, University Hospital Bonn, Germany
| | - Oliver Schmidt
- Institute of Cell Biology, Biocenter, Medical University of Innsbruck, Austria
| | | | | | - Frédéric R Santer
- Division of Experimental Urology, Department of Urology, Medical University of Innsbruck, Austria
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4
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Qi Z, Xue S, Chen J, Zhao W, Johnson K, Wen X, Richard JLC, Zhong S. Genome-Wide Mapping of RNA-Protein Associations via Sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.04.611288. [PMID: 39282297 PMCID: PMC11398515 DOI: 10.1101/2024.09.04.611288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
RNA-protein interactions are crucial for regulating gene expression and cellular functions, with their dysregulation potentially impacting disease progression. Systematically mapping these interactions is resource-intensive due to the vast number of potential RNA and protein interactions. Here, we introduce PRIM-seq ( P rotein- R NA Interaction M apping by sequencing), a method for the concurrent de novo identification of RNA-binding proteins (RBPs) and the elucidation of their associated RNAs. PRIM-seq works by converting each RNA-protein pair into a unique chimeric DNA sequence, which is then decoded through DNA sequencing. Applied to two human cell types, PRIM-seq generated a comprehensive human RNA-protein association network (HuRPA), consisting of more than 350,000 RNA-proteins pairs involving approximately 7,000 RNAs and 11,000 proteins. The data revealed an enrichment of previously reported RBPs and RNA-protein interactions within HuRPA. We also identified LINC00339 as a protein-associating non-coding RNA and PHGDH as an RNA-associating protein. Notably, PHGDH interacts with BECN1 and ATF4 mRNAs, suppressing their protein expression and consequently inhibiting autophagy, apoptosis, and neurite outgrowth while promoting cell proliferation. PRIM-seq offers a powerful tool for discovering RBPs and RNA-protein associations, contributing to more comprehensive functional genome annotations.
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Cogan JA, Benova N, Kuklinkova R, Boyne JR, Anene CA. Meta-analysis of RNA interaction profiles of RNA-binding protein using the RBPInper tool. BIOINFORMATICS ADVANCES 2024; 4:vbae127. [PMID: 39233897 PMCID: PMC11374027 DOI: 10.1093/bioadv/vbae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/29/2024] [Accepted: 08/22/2024] [Indexed: 09/06/2024]
Abstract
Motivation Recent RNA-centric experimental methods have significantly expanded our knowledge of proteins with known RNA-binding functions. However, the complete regulatory network and pathways for many of these RNA-binding proteins (RBPs) in different cellular contexts remain unknown. Although critical to understanding the role of RBPs in health and disease, experimentally mapping the RBP-RNA interactomes in every single context is an impossible task due the cost and manpower required. Additionally, identifying relevant RNAs bound by RBPs is challenging due to their diverse binding modes and function. Results To address these challenges, we developed RBP interaction mapper RBPInper an integrative framework that discovers global RBP interactome using statistical data fusion. Experiments on splicing factor proline and glutamine rich (SFPQ) datasets revealed cogent global SFPQ interactome. Several biological processes associated with this interactome were previously linked with SFPQ function. Furthermore, we conducted tests using independent dataset to assess the transferability of the SFPQ interactome to another context. The results demonstrated robust utility in generating interactomes that transfers to unseen cellular context. Overall, RBPInper is a fast and user-friendly method that enables a systems-level understanding of RBP functions by integrating multiple molecular datasets. The tool is designed with a focus on simplicity, minimal dependencies, and straightforward input requirements. This intentional design aims to empower everyday biologists, making it easy for them to incorporate the tool into their research. Availability and implementation The source code, documentation, and installation instructions as well as results for use case are freely available at https://github.com/AneneLab/RBPInper. A user can easily compile similar datasets for a target RBP.
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Affiliation(s)
- Joseph A Cogan
- School of Biological Sciences, University of Huddersfield, Huddersfield, HD1 3DH, United Kingdom
- School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom
| | - Natalia Benova
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, Leeds, LS1 3HE, United Kingdom
| | - Rene Kuklinkova
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, Leeds, LS1 3HE, United Kingdom
| | - James R Boyne
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, Leeds, LS1 3HE, United Kingdom
| | - Chinedu A Anene
- Centre for Biomedical Science Research, School of Health, Leeds Beckett University, Leeds, LS1 3HE, United Kingdom
- Centre for Cancer Genomics and Computation Biology, Barts Cancer Institute, Queen Mary University of London, London, E1 4NS, United Kingdom
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6
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Wang Y, Shu M, Wang T, He T, Yuan J, Yang Y. Comprehensive characterization of somatic mutations associated with chimeric RNAs in human cancers. Int J Cancer 2024; 155:683-696. [PMID: 38613405 DOI: 10.1002/ijc.34955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/14/2024] [Accepted: 03/19/2024] [Indexed: 04/14/2024]
Abstract
Chimeric RNAs, which can arise from gene recombination at the DNA level or non-canonical splicing events at the RNA level, have been identified as important roles in human tumors. Dysregulated gene expression caused by somatic mutations and altered splicing patterns of oncogenes or tumor suppressor genes can contribute to the development of tumors. Therefore, investigating the formation mechanism of chimeric RNAs via somatic mutations is critical for understanding tumor pathogenesis. This project is the first to propose studying the association between somatic single nucleotide variants and chimeric RNAs, identifying around 2900 somatic SNVs affecting chimeric RNAs in pan-cancer level. The somatic SNVs on chimeric RNAs were commonly observed in various types of tumor tissues, providing a valuable resource for future study. Additionally, these SNVs show distinct tumor specificity, and those with high frequency had a significant impact on the survival time of patients with tumors. Further research revealed that somatic SNVs associated with chimeric RNA (chiR-SNVs) were typically found within 10 nt of the junction site of chimeric RNAs and had a particularly significant effect on chimeric RNAs from different chromosomes. The enrichment analysis revealed that chiR-SNVs were significantly overrepresented in oncogenes and genes related to RNA binding proteins involved in RNA splicing, which could imply that chiR-SNVs may disrupt the process of RNA splicing and induce the occurrence of chimeric RNAs. This study sheds light on the potential molecular interaction mechanism between somatic SNVs and chimeric RNAs, which opens up a new avenue for researching disease pathway and tumorigenesis development.
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Affiliation(s)
- Yuting Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Meng Shu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Tianqiang Wang
- Neurosurgery Department II Ward, Yidu Central Hospital of Weifang, Shandong, China
| | - Tongxin He
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jiapei Yuan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Yang Yang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory of Inflammatory Biology, Tianjin Geriatrics Institute, Tianjin Medical University General Hospital, Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Department of Family Planning, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Geriatrics, Tianjin Medical University General Hospital, Tianjin Medical University, Tianjin, China
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Fierro-Monti I. RBPs: an RNA editor's choice. Front Mol Biosci 2024; 11:1454241. [PMID: 39165644 PMCID: PMC11333368 DOI: 10.3389/fmolb.2024.1454241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/25/2024] [Indexed: 08/22/2024] Open
Abstract
RNA-binding proteins (RBPs) play a key role in gene expression and post-transcriptional RNA regulation. As integral components of ribonucleoprotein complexes, RBPs are susceptible to genomic and RNA Editing derived amino acid substitutions, impacting functional interactions. This article explores the prevalent RNA Editing of RBPs, unravelling the complex interplay between RBPs and RNA Editing events. Emphasis is placed on their influence on single amino acid variants (SAAVs) and implications for disease development. The role of Proteogenomics in identifying SAAVs is briefly discussed, offering insights into the RBP landscape. RNA Editing within RBPs emerges as a promising target for precision medicine, reshaping our understanding of genetic and epigenetic variations in health and disease.
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Tang H, Zhu D, Li W, Zhang G, Zhang H, Peng Q. Exosomal AFAP1-AS1 Promotes the Growth, Metastasis, and Glycolysis of Pituitary Adenoma by Inhibiting HuR Degradation. Mol Neurobiol 2024:10.1007/s12035-024-04387-y. [PMID: 39090353 DOI: 10.1007/s12035-024-04387-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 07/19/2024] [Indexed: 08/04/2024]
Abstract
Exosomal long noncoding RNAs (lncRNAs), which are highly expressed in tumor-derived exosomes, regulate various cellular behaviors such as cell proliferation, metastasis, and glycolysis by facilitating intercellular communication. Here, we explored the role and regulatory mechanism of tumor-derived exosomal lncRNAs in pituitary adenomas (PA). We isolated exosomes from PA cells, and performed in vitro and in vivo assays to examine their effect on the proliferation, metastasis, and glycolysis of PA cells. In addition, we conducted RNA pull-down, RNA immunoprecipitation, co-immunoprecipitation, and ubiquitination assays to investigate the downstream mechanism of exosomal AFAP1-AS1. Exosomes from PA cells augmented the proliferation, mobility, and glycolysis of PA cells. Moreover, AFAP1-AS1 was significantly enriched in these exosomes and stimulated the growth, migration, invasion, and glycolysis of PA cells in vitro, as well as tumor metastasis in vivo. It also enhanced the binding affinity between Hu antigen R (HuR) and SMAD-specific E3 ubiquitin protein ligase 1 (SMURF1), resulting in HuR ubiquitination and degradation accompanied by enhanced expression of hexokinase 2 (HK2) and pyruvate kinase M2 (PKM2). Moreover, HuR overexpression alleviated the exosomal AFAP1-AS1-mediated promotion of growth, metastasis, and glycolysis effects. These findings indicate that tumor-derived exosomal AFAP1-AS1 modulated SMURF1-mediated HuR ubiquitination and degradation to upregulate HK2 and PKM2 expression, thereby enhancing PA cell growth, metastasis, and glucose metabolism. This suggests targeting exosomal AFAP1-AS1 may be a potential strategy for the treatment of PA.
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Affiliation(s)
- Hengxin Tang
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China.
| | - Delong Zhu
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Wenxiang Li
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Guozhi Zhang
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Heng Zhang
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
| | - Qiujiao Peng
- Department of Neurosurgery, Guangzhou First People's Hospital, South China University of Technology, 105 Fengze East Road, Nansha District, Guangzhou, 511457, Guangdong, China
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Zhen Y, Li X, Huang S, Wang R, Yang L, Huang Y, Yan J, Ju J, Wen H, Sun Q. LncRNA lnc-SPRR2G-2 contributes to keratinocyte hyperproliferation and inflammation in psoriasis by activating the STAT3 pathway and downregulating KHSRP. Mol Cell Probes 2024; 76:101967. [PMID: 38942130 DOI: 10.1016/j.mcp.2024.101967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/17/2024] [Accepted: 06/21/2024] [Indexed: 06/30/2024]
Abstract
Psoriasis is a chronic inflammatory disease characterized by increased keratinocyte proliferation and local inflammation. Long noncoding RNAs (lncRNAs) play important regulatory roles in many immune-mediated diseases, including psoriasis. In this study, we aimed to investigate the role and mechanism of lnc-SPRR2G-2 (SPRR2G) in M5-treated psoriatic keratinocytes. Fluorescence in situ hybridization and quantitative real-time polymerase chain reaction (qRT-PCR) showed that lnc-SPRR2G-2 was significantly upregulated in psoriasis tissues and psoriatic keratinocytes. In psoriatic keratinocytes, functional and molecular experiment analyses demonstrated that SPRR2G regulated proliferation, cell cycle and apoptosis, and induced the expression of S100 calcium binding protein A7 (S100A7), interleukin (IL)-1β, IL-8 and C-X-C motif chemokine ligand 10 (CXCL10). The function of SPRR2G in psoriasis is related to the STAT3 signaling pathway and can be inhibited by a STAT3 inhibitor. Moreover, KH-type splicing regulatory protein (KHSRP) was proved to be regulated by lnc-SPRR2G-2 and to control the mRNA decay of psoriasis-related cytokines (p < 0.05). In summary, we reported the functions of lnc-SPRR2G-2 and KHSRP in psoriasis. Our findings provide new insights for the further exploration of the pathogenesis and treatment of psoriasis.
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Affiliation(s)
- Yunyue Zhen
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China; Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Xueqing Li
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China; Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Shan Huang
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China; Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Ruijie Wang
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China; Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Luan Yang
- Department of Dermatology, The Second Affiliated Hospital of Shandong First Medical University, Taian, 271000, Shandong, China
| | - Yingjian Huang
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China; Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - Jianjun Yan
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China
| | - Jiaoying Ju
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China; Laboratory of Basic Medical Science, Qilu Hospital of Shandong University, Jinan, 250012, Shandong, China
| | - He Wen
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China.
| | - Qing Sun
- Department of Dermatology, Qilu Hospital, Shandong University, Jinan, 250012, Shandong, China.
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Wassmer E, Koppány G, Hermes M, Diederichs S, Caudron-Herger M. Refining the pool of RNA-binding domains advances the classification and prediction of RNA-binding proteins. Nucleic Acids Res 2024; 52:7504-7522. [PMID: 38917322 PMCID: PMC11260472 DOI: 10.1093/nar/gkae536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
From transcription to decay, RNA-binding proteins (RBPs) influence RNA metabolism. Using the RBP2GO database that combines proteome-wide RBP screens from 13 species, we investigated the RNA-binding features of 176 896 proteins. By compiling published lists of RNA-binding domains (RBDs) and RNA-related protein family (Rfam) IDs with lists from the InterPro database, we analyzed the distribution of the RBDs and Rfam IDs in RBPs and non-RBPs to select RBDs and Rfam IDs that were enriched in RBPs. We also explored proteins for their content in intrinsically disordered regions (IDRs) and low complexity regions (LCRs). We found a strong positive correlation between IDRs and RBDs and a co-occurrence of specific LCRs. Our bioinformatic analysis indicated that RBDs/Rfam IDs were strong indicators of the RNA-binding potential of proteins and helped predicting new RBP candidates, especially in less investigated species. By further analyzing RBPs without RBD, we predicted new RBDs that were validated by RNA-bound peptides. Finally, we created the RBP2GO composite score by combining the RBP2GO score with new quality factors linked to RBDs and Rfam IDs. Based on the RBP2GO composite score, we compiled a list of 2018 high-confidence human RBPs. The knowledge collected here was integrated into the RBP2GO database at https://RBP2GO-2-Beta.dkfz.de.
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Affiliation(s)
- Elsa Wassmer
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Gergely Koppány
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Malte Hermes
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, and German Cancer Consortium (DKTK), partner site Freiburg, a partnership between DKFZ and University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Maïwen Caudron-Herger
- Research Group “RNA-Protein Complexes & Cell Proliferation”, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
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11
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Li Q, Liu J, Su R, Zhen J, Liu X, Liu G. Small extracellular vesicles-shuttled miR-23a-3p from mesenchymal stem cells alleviate renal fibrosis and inflammation by inhibiting KLF3/STAT3 axis in diabetic kidney disease. Int Immunopharmacol 2024; 139:112667. [PMID: 39018690 DOI: 10.1016/j.intimp.2024.112667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/04/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024]
Abstract
Human umbilical cord mesenchymal stem cells-derived small extracellular vesicles (MSC-sEV) provide a pragmatic solution as a cell-free therapy for patients with diabetic kidney disease (DKD). However, the underlying protective mechanisms of MSC-sEV remain largely unknown in DKD. Invivo and in vitro analyses demonstrated that MSC-sEV attenuated renal fibrosis and inflammation of DKD. The underlying mechanism of the MSC-sEV-induced therapeutic effect was explored by high-throughput sequencing, which identified the unique enrichment of a set of miRNAs in MSC-sEV compared with human skin fibroblasts-sEV (HSF-sEV). Vitro experiments demonstrated that the protective potential was primarily attributed to miR-23a-3p, one of the most abundant miRNAs in MSC-sEV. Further, overexpression or knockdown analyses revealed that miR-23a-3p, and its target Krüppel-like factor 3 (KLF3) suppressed the STAT3 signaling pathway in high glucose (HG) induced HK-2 cells were essential for the renal-protective property of MSC-sEV. Moreover, we found that miR-23a-3p was packaged into MSC-sEV by RNA Binding Motif Protein X-Linked (RBMX) and transmitted to HG-induced HK-2 cells. Finally, inhibiting miR-23a-3p could mitigate the protective effects of MSC-sEV in db/db mice. These findings suggest that a systemic administration of sEV derived from MSC, have the capacity to incorporate into kidney where they can exert renal-protective potential against HG-induced injury through delivery of miR-23a-3p.
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Affiliation(s)
- Qianhua Li
- Nephrology Research Institute of Shandong University, Jinan, Shandong, 250033, China; Department of Nephrology, Multidisciplinary Innovation Center for Nephrology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Jiaxi Liu
- Graduate School of Arts and Sciences, Columbia University, USA
| | - Rongyun Su
- Nephrology Research Institute of Shandong University, Jinan, Shandong, 250033, China; Department of Nephrology, Multidisciplinary Innovation Center for Nephrology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Junhui Zhen
- Department of Pathology, School of Basic Medical Sciences, Shandong University, Jinan, 250012, China
| | - Xiangchun Liu
- Nephrology Research Institute of Shandong University, Jinan, Shandong, 250033, China; Department of Nephrology, Multidisciplinary Innovation Center for Nephrology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Gang Liu
- Nephrology Research Institute of Shandong University, Jinan, Shandong, 250033, China; Department of Nephrology, Multidisciplinary Innovation Center for Nephrology, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China; Key laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, Shandong,250012, China.
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12
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Ji Q, Ma F, Zhang X, Liu Y, Wang P, Li M. Hsa_circ_0005320 affects cell proliferation and the cell cycle via the IGF2BP3/CDK2 axis in bladder cancer. Cell Signal 2024; 119:111154. [PMID: 38565412 DOI: 10.1016/j.cellsig.2024.111154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 03/16/2024] [Accepted: 03/29/2024] [Indexed: 04/04/2024]
Abstract
BACKGROUND Circular RNAs (circRNAs), which are covalently closed non-coding RNAs, are frequently dysregulated in cancer. However, their precise role in bladder cancer (BCa) remains largely unknown. METHODS Expression of hsa_circ_0005320 in tissues and cell lines was detected using quantitative real-time PCR. Proliferation and colony forming capacity of BCa cells were assessed using Cell Counting Kit-8, ethynyl-labeled deoxyuridine, and colony formation assays. The cell cycle was analyzed using flow cytometry. Protein expression of insulin-like growth factor II mRNA-binding protein 3 (IGF2BP3) and cyclin dependent kinase 2 (CDK2) was examined using western blots. The binding of RNA and protein was validated using RNA immunoprecipitation. Additionally, xenograft tumor models were established to validate the function of hsa_circ_0005320 in vivo. RESULTS We screened hsa_circ_0005320 from previous high-throughput sequencing and found that it was highly expressed in BCa tissues and associated with tumor differentiation and depth of invasion in BCa patients. Through functional experiments, we demonstrated that hsa_circ_0005320 promoted cell proliferation and regulated the cell cycle. Mechanistically, hsa_circ_0005320 interacted with and upregulated the expression of IGF2BP3, which binds to and enhances the stability of CDK2 mRNA. Furthermore, knockdown of hsa_circ_0005320 resulted in a reduction in tumor burden in vivo. CONCLUSIONS Collectively, these findings highlight the pro-oncogenic role of hsa_circ_0005320 in BCa through the IGF2BP3/CDK2 axis, providing valuable insights into the mechanism of circRNAs in tumor progression.
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Affiliation(s)
- Quansong Ji
- Department of Urology, the Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Feilu Ma
- Teaching Center for Basic Medical Experiment of China Medical University, Shen yang, Liaoning, China
| | - Xiling Zhang
- Department of Urology, the Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yili Liu
- Department of Urology, the Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Ping Wang
- Department of Urology, the Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Mingshan Li
- Department of Urology, the Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.
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13
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Li L, Yu S, Dou N, Wang X, Gao Y, Li Y. A new tandem repeat-enriched lncRNA XLOC_008672 promotes gastric carcinogenesis by regulating G3BP1 expression. Cancer Sci 2024; 115:1851-1865. [PMID: 38581120 PMCID: PMC11145122 DOI: 10.1111/cas.16172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/08/2024] Open
Abstract
Aberrant expression of forkhead box transcription factor 1 (FOXM1) plays critical roles in a variety of human malignancies and predicts poor prognosis. However, little is known about the crosstalk between FOXM1 and long noncoding RNAs (lncRNAs) in tumorigenesis. The present study identifies a previously uncharacterized lncRNA XLOC_008672 in gastric cancer (GC), which is regulated by FOXM1 and possesses multiple copies of tandem repetitive sequences. LncRNA microarrays are used to screen differentially expressed lncRNAs in FOXM1 knockdown GC cells, and then the highest fold downregulation lncRNA XLOC_008672 is screened out. Sequence analysis reveals that the new lncRNA contains 62 copies of 37-bp tandem repeats. It is transcriptionally activated by FOXM1 and functions as a downstream effector of FOXM1 in GC cells through in vitro and in vivo functional assays. Elevated expression of XLOC_008672 is found in GC tissues and indicates worse prognosis. Mechanistically, XLOC_008672 can bind to small nuclear ribonucleoprotein polypeptide A (SNRPA), thereby enhancing mRNA stability of Ras-GTPase-activating protein SH3 domain-binding protein 1 (G3BP1) and, consequently, facilitating GC cell proliferation and migration. Our study discovers a new uncharacterized lncRNA XLOC_008672 involved in GC carcinogenesis and progression. Targeting FOXM1/XLOC_008672/SNRPA/G3BP1 signaling axis might be a promising therapeutic strategy for GC.
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Affiliation(s)
- Li Li
- Department of Oncology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Shijun Yu
- Department of Oncology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Ning Dou
- Department of Oncology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Xiao Wang
- Department of Medical Oncology, Zhongshan HospitalFudan UniversityShanghaiChina
| | - Yong Gao
- Department of Oncology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
| | - Yandong Li
- Department of Oncology, Shanghai East HospitalTongji University School of MedicineShanghaiChina
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14
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Kristofich J, Nicchitta CV. High-throughput quantitation of protein-RNA UV-crosslinking efficiencies as a predictive tool for high-confidence identification of RNA-binding proteins. RNA (NEW YORK, N.Y.) 2024; 30:644-661. [PMID: 38423626 PMCID: PMC11098464 DOI: 10.1261/rna.079848.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
UV-crosslinking has proven to be an invaluable tool for the identification of RNA-protein interactomes. The paucity of methods for distinguishing background from bona fide RNA-protein interactions, however, makes attribution of RNA-binding function on UV-crosslinking alone challenging. To address this need, we previously reported an RNA-binding protein (RBP) confidence scoring metric (RCS), incorporating both signal-to-noise (S:N) and protein abundance determinations to distinguish high- and low-confidence candidate RBPs. Although RCS has utility, we sought a direct metric for quantification and comparative evaluation of protein-RNA interactions. Here we propose the use of protein-specific UV-crosslinking efficiency (%CL), representing the molar fraction of a protein that is crosslinked to RNA, for functional evaluation of candidate RBPs. Application to the HeLa RNA interactome yielded %CL values for 1097 proteins. Remarkably, %CL values span over five orders of magnitude. For the HeLa RNA interactome, %CL values comprise a range from high efficiency, high specificity interactions, e.g., the Elav protein HuR and the Pumilio homolog Pum2, with %CL values of 45.9 and 24.2, respectively, to very low efficiency and specificity interactions, for example, the metabolic enzymes glyceraldehyde-3-phosphate dehydrogenase, fructose-bisphosphate aldolase, and alpha-enolase, with %CL values of 0.0016, 0.006, and 0.008, respectively. We further extend the utility of %CL through prediction of protein domains and classes with known RNA-binding functions, thus establishing it as a useful metric for RNA interactome analysis. We anticipate that this approach will benefit efforts to establish functional RNA interactomes and support the development of more predictive computational approaches for RBP identification.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
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15
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Que X, Ren L, Yang L, Wang L, Li J, Wu R, Chen Q. Long noncoding RNA BMPR1B-AS1 stability regulated by IGF2BP2 affects the decidualization in endometriosis patients through the SMAD1/5/9 pathway. FASEB J 2024; 38:e23622. [PMID: 38703029 DOI: 10.1096/fj.202302195r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 03/19/2024] [Accepted: 04/08/2024] [Indexed: 05/06/2024]
Abstract
Endometriosis (EMs)-related infertility commonly has decreased endometrial receptivity and normal decidualization is the basis for establishing and maintaining endometrial receptivity. However, the potential molecular regulatory mechanisms of impaired endometrial decidualization in patients with EMs have not been fully clarified. We confirmed the existence of reduced endometrial receptivity in patients with EMs by scanning electron microscopy and quantitative real-time PCR. Here we identified an lncRNA, named BMPR1B-AS1, which is significantly downregulated in eutopic endometrium in EMs patients and plays an essential role in decidual formation. Furthermore, RNA pull-down, mass spectrometry, RNA immunoprecipitation, and rescue analyses revealed that BMPR1B-AS1 positively regulates decidual formation through interaction with the RNA-binding protein insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2). Downregulation of IGF2BP2 led to a decreased stability of BMPR1B-AS1 and inhibition of activation of the SMAD1/5/9 pathway, an inhibitory effect which diminished decidualization in human endometrial stromal cells (hESCs) decidualization. In conclusion, our identified a novel regulatory mechanism in which the IGF2BP2-BMPR1B-AS1-SMAD1/5/9 axis plays a key role in the regulation of decidualization, providing insights into the potential link between abnormal decidualization and infertility in patients with EMs, which will be of clinical significance for the management and treatment of infertility in patients with EMs.
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Affiliation(s)
- Xiaohong Que
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
| | - Lulu Ren
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- Reproductive Medical Center, the First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Lin Yang
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
| | - Lemeng Wang
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Junzui Li
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Rongfeng Wu
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- Reproductive Medical Center, the First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Qionghua Chen
- The School of Clinical Medicine, Fujian Medical University, Fuzhou, Fujian, China
- Clinical Medical Research Center for Gynecology and Reproductive Health of Fujian Province, Laboratory of Research and Diagnosis of Gynecological Diseases of Xiamen City, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, China
- The Graduate School of Fujian Medical University, Fuzhou, Fujian, China
- School of Medicine, Xiamen University, Xiamen, Fujian, China
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16
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Wan X, Shi W, Ma L, Wang L, Zheng R, He J, Wang Y, Li X, Zha X, Wang J, Xu L. A 3'-pre-tRNA-derived small RNA tRF-1-Ser regulated by 25(OH)D promotes proliferation and stemness by inhibiting the function of MBNL1 in breast cancer. Clin Transl Med 2024; 14:e1681. [PMID: 38725048 PMCID: PMC11082093 DOI: 10.1002/ctm2.1681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/28/2024] [Accepted: 04/19/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND We explored the potential novel anticancer mechanisms of 25-hydroxyvitamin D (25(OH)D), a vitamin D metabolite with antitumour effects in breast cancer. It is stable in serum and is used to assess vitamin D levels in clinical practice. Transfer RNA-derived small RNAs are small noncoding RNAs that generate various distinct biological functions, but more research is needed on their role in breast cancer. METHODS Small RNA microarrays were used to explore the novel regulatory mechanism of 25(OH)D. High-throughput RNA-sequencing technology was used to detect transcriptome changes after 25(OH)D treatment and tRF-1-Ser knockdown. RNA pull-down and high-performance liquid chromatography-mass spectrometry/mass spectrometry were used to explore the proteins bound to tRF-1-Ser. In vitro and in vivo functional experiments were conducted to assess the influence of 25(OH)D and tRF-1-Ser on breast cancer. Semi-quantitative PCR was performed to detect alternative splicing events. Western blot assay and qPCR were used to assess protein and mRNA expression. RESULTS The expression of tRF-1-Ser is negatively regulated by 25(OH)D. In our breast cancer (BRCA) clinical samples, we found that the expression of tRF-1-Ser was higher in cancer tissues than in paired normal tissues, and was significantly associated with tumour invasion. Moreover, tRF-1-Ser inhibits the function of MBNL1 by hindering its nuclear translocation. Functional experiments and transcriptome data revealed that the downregulation of tRF-1-Ser plays a vital role in the anticancer effect of 25(OH)D. CONCLUSIONS In brief, our research revealed a novel anticancer mechanism of 25(OH)D, unveiled the vital function of tRF-1-Ser in BRCA progression, and suggested that tRF-1-Ser could emerge as a new therapeutic target for BRCA.
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Affiliation(s)
- Xinyu Wan
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Wenjie Shi
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lingjun Ma
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lexin Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ran Zheng
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jinzhi He
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Ye Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xuan Li
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Xiaoming Zha
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Jue Wang
- Department of Breast DiseaseThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
| | - Lu Xu
- Department of NutritionThe First Affiliated Hospital of Nanjing Medical UniversityNanjingChina
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17
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Xiang T, Li Y, Liu G, Li X. NR1D1-transactivated lncRNA NUTM2A-AS1 promotes chemoresistance and immune evasion in neuroblastoma via inhibiting B7-H3 degradation. J Cell Mol Med 2024; 28:e18360. [PMID: 38785199 PMCID: PMC11117458 DOI: 10.1111/jcmm.18360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/04/2024] [Accepted: 04/13/2024] [Indexed: 05/25/2024] Open
Abstract
Neuroblastoma (NB), a common solid tumour in young children originating from the sympathetic nervous system during embryonic development, poses challenges despite therapeutic advances like high-dose chemotherapy and immunotherapy. Some survivors still grapple with severe side effects and drug resistance. The role of lncRNA NUTM2A-AS1 has been explored in various cancers, but its function in drug-resistant NB progression is unclear. Our study found that NUTM2A-AS1 expression in cisplatin-resistant NB cells increased in a time- and dose-dependent manner. Knockdown of NUTM2A-AS1 significantly improved NB cell sensitivity to cisplatin and inhibited metastatic abilities. Additionally, we identified B7-H3, an immune checkpoint-related protein, as a NUTM2A-AS1-associated protein in NB cells. NUTM2A-AS1 was shown to inhibit the protein degradation of B7-H3. Moreover, NUTM2A-AS1 modulated immune evasion in cisplatin-resistant NB cells through B7-H3. Furthermore, NUTM2A-AS1 expression in cisplatin-resistant NB cells was transactivated by NR1D1. In summary, our results unveil the molecular or biological relationship within the NR1D1/NUTM2A-AS1/B7-H3 axis in NB cells under cisplatin treatment, providing an intriguing avenue for fundamental research into cisplatin-resistant NB.
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Affiliation(s)
- Tian Xiang
- Department of Clinical Laboratory CenterCentral Hospital of Enshi Tujia and Miao Autonomous PrefectureEnshiChina
| | - Yejing Li
- Department of Clinical Laboratory CenterCentral Hospital of Enshi Tujia and Miao Autonomous PrefectureEnshiChina
| | - Gao Liu
- Department of Gastrointestinal SurgeryCentral Hospital of Enshi Tujia and Miao Autonomous PrefectureEnshiChina
| | - Xianyun Li
- Department of Clinical Laboratory CenterCentral Hospital of Enshi Tujia and Miao Autonomous PrefectureEnshiChina
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18
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Magg V, Manetto A, Kopp K, Wu CC, Naghizadeh M, Lindner D, Eke L, Welsch J, Kallenberger SM, Schott J, Haucke V, Locker N, Stoecklin G, Ruggieri A. Turnover of PPP1R15A mRNA encoding GADD34 controls responsiveness and adaptation to cellular stress. Cell Rep 2024; 43:114069. [PMID: 38602876 DOI: 10.1016/j.celrep.2024.114069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 01/25/2024] [Accepted: 03/21/2024] [Indexed: 04/13/2024] Open
Abstract
The integrated stress response (ISR) is a key cellular signaling pathway activated by environmental alterations that represses protein synthesis to restore homeostasis. To prevent sustained damage, the ISR is counteracted by the upregulation of growth arrest and DNA damage-inducible 34 (GADD34), a stress-induced regulatory subunit of protein phosphatase 1 that mediates translation reactivation and stress recovery. Here, we uncover a novel ISR regulatory mechanism that post-transcriptionally controls the stability of PPP1R15A mRNA encoding GADD34. We establish that the 3' untranslated region of PPP1R15A mRNA contains an active AU-rich element (ARE) recognized by proteins of the ZFP36 family, promoting its rapid decay under normal conditions and stabilization for efficient expression of GADD34 in response to stress. We identify the tight temporal control of PPP1R15A mRNA turnover as a component of the transient ISR memory, which sets the threshold for cellular responsiveness and mediates adaptation to repeated stress conditions.
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Affiliation(s)
- Vera Magg
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Alessandro Manetto
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Katja Kopp
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Chia Ching Wu
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Mohsen Naghizadeh
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Doris Lindner
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Lucy Eke
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Julia Welsch
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany
| | - Stefan M Kallenberger
- Digital Health Center, Berlin Institute of Health (BIH) and Charité, 10178 Berlin, Germany; Medical Oncology, National Center for Tumor Diseases, Heidelberg University, 69120 Heidelberg, Germany
| | - Johanna Schott
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany
| | - Volker Haucke
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, 13125 Berlin, Germany; Freie Universität Berlin, Faculty of Biology, Chemistry, and Pharmacy, 14195 Berlin, Germany
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK; The Pirbright Institute, GU24 0NF Pirbright, UK
| | - Georg Stoecklin
- Heidelberg University, Medical Faculty Mannheim, Division of Biochemistry, Mannheim Institute for Innate Immunoscience (MI3) and Mannheim Cancer Center (MCC), 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Alessia Ruggieri
- Heidelberg University, Medical Faculty Heidelberg, Department of Infectious Diseases, Molecular Virology, Center for Integrative Infectious Disease Research, 69120 Heidelberg, Germany.
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19
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Niu R, Guo Y, Shang X. GLIMS: A two-stage gradual-learning method for cancer genes prediction using multi-omics data and co-splicing network. iScience 2024; 27:109387. [PMID: 38510118 PMCID: PMC10951990 DOI: 10.1016/j.isci.2024.109387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/30/2023] [Accepted: 02/27/2024] [Indexed: 03/22/2024] Open
Abstract
Identifying cancer genes is vital for cancer diagnosis and treatment. However, because of the complexity of cancer occurrence and limited cancer genes knowledge, it is hard to identify cancer genes accurately using only a few omics data, and the overall performance of existing methods is being called for further improvement. Here, we introduce a two-stage gradual-learning strategy GLIMS to predict cancer genes using integrative features from multi-omics data. Firstly, it uses a semi-supervised hierarchical graph neural network to predict the initial candidate cancer genes by integrating multi-omics data and protein-protein interaction (PPI) network. Then, it uses an unsupervised approach to further optimize the initial prediction by integrating the co-splicing network in post-transcriptional regulation, which plays an important role in cancer development. Systematic experiments on multi-omics cancer data demonstrated that GLIMS outperforms the state-of-the-art methods for the identification of cancer genes and it could be a useful tool to help advance cancer analysis.
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Affiliation(s)
- Rui Niu
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710129, China
| | - Yang Guo
- School of Information Science and Engineering, Lanzhou University, Lanzhou 730000, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi’an 710129, China
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20
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Feichtner A, Enzler F, Kugler V, Hoppe K, Mair S, Kremser L, Lindner H, Huber RG, Stelzl U, Stefan E, Torres-Quesada O. Phosphorylation of the compartmentalized PKA substrate TAF15 regulates RNA-protein interactions. Cell Mol Life Sci 2024; 81:162. [PMID: 38568213 PMCID: PMC10991009 DOI: 10.1007/s00018-024-05204-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024]
Abstract
Spatiotemporal-controlled second messengers alter molecular interactions of central signaling nodes for ensuring physiological signal transmission. One prototypical second messenger molecule which modulates kinase signal transmission is the cyclic-adenosine monophosphate (cAMP). The main proteinogenic cellular effectors of cAMP are compartmentalized protein kinase A (PKA) complexes. Their cell-type specific compositions precisely coordinate substrate phosphorylation and proper signal propagation which is indispensable for numerous cell-type specific functions. Here we present evidence that TAF15, which is implicated in the etiology of amyotrophic lateral sclerosis, represents a novel nuclear PKA substrate. In cross-linking and immunoprecipitation experiments (iCLIP) we showed that TAF15 phosphorylation alters the binding to target transcripts related to mRNA maturation, splicing and protein-binding related functions. TAF15 appears to be one of multiple PKA substrates that undergo RNA-binding dynamics upon phosphorylation. We observed that the activation of the cAMP-PKA signaling axis caused a change in the composition of a collection of RNA species that interact with TAF15. This observation appears to be a broader principle in the regulation of molecular interactions, as we identified a significant enrichment of RNA-binding proteins within endogenous PKA complexes. We assume that phosphorylation of RNA-binding domains adds another layer of regulation to binary protein-RNAs interactions with consequences to RNA features including binding specificities, localization, abundance and composition.
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Affiliation(s)
- Andreas Feichtner
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Florian Enzler
- Daniel Swarovski Research Laboratory, Department of Visceral, Transplant and Thoracic Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
| | - Valentina Kugler
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria
| | - Katharina Hoppe
- Institute of Developmental Immunology, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Sophia Mair
- Department of Cardiac Surgery, Medical University of Innsbruck, Innrain 66/66a, 6020, Innsbruck, Austria
- Vascage, Center of Clinical Stroke Research, 6020, Innsbruck, Austria
| | - Leopold Kremser
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Herbert Lindner
- Division of Clinical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria
| | - Roland G Huber
- Bioinformatics Institute, Agency for Science Technology and Research, Singapore, 138671, Singapore
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, University of Graz, Schubertstrasse 1, 8010, Graz, Austria
| | - Eduard Stefan
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Institute of Molecular Biology and Center for Molecular Biosciences, University of Innsbruck, Technikerstrasse 25, 6020, Innsbruck, Austria.
| | - Omar Torres-Quesada
- Tyrolean Cancer Research Institute (TKFI), Innrain 66, 6020, Innsbruck, Austria.
- Division of Medical Biochemistry, Biocenter, Medical University of Innsbruck, Innrain 80/82, 6020, Innsbruck, Austria.
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21
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Okwori M, Eslami A. Feature engineering from meta-data for prediction of differentially expressed genes: An investigation of Mus musculus exposed to space-conditions. Comput Biol Chem 2024; 109:108026. [PMID: 38335853 DOI: 10.1016/j.compbiolchem.2024.108026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/29/2023] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
Transcription profiling is a key process that can reveal those biological mechanisms driving the response to various exposure conditions or gene perturbations. In this work, we investigate the prediction of differentially expressed genes (DEGs) when exposed to conditions in space from a set of diverse engineered features. To do this, we collected DEGs and non-differentially expressed genes (NDEGs) of Mus musculus-based experiments on the GeneLab database. We engineered a diverse set of features from factors reported in the literature to affect gene expression. An extreme gradient boosting (XGBoost) model was trained to predict if a given gene would be differentially expressed at various levels of differential expression. The test results on a separate holdout dataset showed an area under the receiver operating characteristics curves (AUCs) of 0.90±0.07, averaged across the five selected percentages of the most and least differentially expressed genes. Subsequently, we investigated the impact of selection of features, both individually with a correlation-based feature-selection procedure and in groups with a combination procedure, on the prediction performance. The feature selection confirmed some known drivers of adaptation to radiation and highlighted some new transcription factors and micro RNAs (miRNAs). Finally, gene ontology (GO) analysis revealed biological processes that tend to have expression patterns most suitable for this approach. This work highlights the potential of detection of differentially expressed genes using a machine learning (ML) approach, and provides some evidence of gene expression changes being captured by a diverse feature set not related to the condition under study.
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Affiliation(s)
- Michael Okwori
- Department of Electrical, Computer and Biomedical Engineering, Union College, Schenectady, 12308, NY, United States of America.
| | - Ali Eslami
- Department of Electrical and Computer Engineering, Wichita State University, Wichita, 67260, KS, United States of America
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22
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Chen Q, Zhao FQ, Han B, Jiang C, Liu H. Methionyl-Methionine Dipeptide Enhances Mammogenesis and Lactogenesis by Suppressing the Expression of a Novel Long Noncoding RNA MGPNCR to Inhibit eIF4B Dephosphorylation. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:6414-6423. [PMID: 38501560 DOI: 10.1021/acs.jafc.4c00580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Previous research has demonstrated that in pregnant mice deficient in l-methionine (Met), the mixture of the dipeptide l-methionyl-l-methionine (Met-Met) with Met was more effective than Met alone in promoting mammogenesis and lactogenesis. This study aimed to investigate the role of a novel long noncoding RNA (lncRNA), named mammary gland proliferation-associated lncRNA (MGPNCR), in these processes. Transcriptomic analysis of mammary tissues from Met-deficient mice, supplemented either with a Met-Met/Met mixture or with Met alone, revealed significantly higher MGPNCR expression in the Met group compared to the mixture group, a finding recapitulated in a mammary epithelial cell model. Our findings suggested that MGPNCR hindered mammogenesis and milk protein synthesis by binding to eukaryotic initiation factor 4B (eIF4B). This interaction promoted the dephosphorylation of eIF4B at serine-422 by enhancing its association with protein phosphatase 2A (PP2A). Our study sheds light on the regulatory mechanisms of lncRNA-mediated dipeptide effects on mammary cell proliferation and milk protein synthesis. These insights underscore the potential benefits of utilizing dipeptides to improve milk protein in animals and potentially in humans.
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Affiliation(s)
- Qiong Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Feng-Qi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, Vermont 05405, United States
| | - Bingqing Han
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
| | - Chao Jiang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310030, China
| | - Hongyun Liu
- College of Animal Sciences, Zhejiang University, Hangzhou, Zhejiang 310030, P. R. China
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23
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Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
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Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
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24
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Xu Q, Bao X, Lin Z, Tang L, He LN, Ren J, Zuo Z, Hu K. AStruct: detection of allele-specific RNA secondary structure in structuromic probing data. BMC Bioinformatics 2024; 25:91. [PMID: 38429654 PMCID: PMC11264973 DOI: 10.1186/s12859-024-05704-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024] Open
Abstract
BACKGROUND Uncovering functional genetic variants from an allele-specific perspective is of paramount importance in advancing our understanding of gene regulation and genetic diseases. Recently, various allele-specific events, such as allele-specific gene expression, allele-specific methylation, and allele-specific binding, have been explored on a genome-wide scale due to the development of high-throughput sequencing methods. RNA secondary structure, which plays a crucial role in multiple RNA-associated processes like RNA modification, translation and splicing, has emerged as an essential focus of relevant research. However, tools to identify genetic variants associated with allele-specific RNA secondary structures are still lacking. RESULTS Here, we develop a computational tool called 'AStruct' that enables us to detect allele-specific RNA secondary structure (ASRS) from RT-stop based structuromic probing data. AStruct shows robust performance in both simulated datasets and public icSHAPE datasets. We reveal that single nucleotide polymorphisms (SNPs) with higher AStruct scores are enriched in coding regions and tend to be functional. These SNPs are highly conservative, have the potential to disrupt sites involved in m6A modification or protein binding, and are frequently associated with disease. CONCLUSIONS AStruct is a tool dedicated to invoke allele-specific RNA secondary structure events at heterozygous SNPs in RT-stop based structuromic probing data. It utilizes allelic variants, base pairing and RT-stop information under different cell conditions to detect dynamic and functional ASRS. Compared to sequence-based tools, AStruct considers dynamic cell conditions and outperforms in detecting functional variants. AStruct is implemented in JAVA and is freely accessible at: https://github.com/canceromics/AStruct .
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Affiliation(s)
- Qingru Xu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Xiaoqiong Bao
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Zhuobin Lin
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Lin Tang
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Li-Na He
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China
| | - Zhixiang Zuo
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510060, China.
| | - Kunhua Hu
- Guangdong Key Laboratory of Liver Disease Research, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
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25
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Wang Y, He J, Ma H, Liu J, Du L, Chai C, Liu Y, Wang X. NR_103776.1 as a novel diagnostic biomarker for systemic lupus erythematosus. Ir J Med Sci 2024; 193:211-221. [PMID: 37369931 DOI: 10.1007/s11845-023-03420-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
BACKGROUND With the development of sequencing technologies, there is increasing evidence that long noncoding RNAs (lncRNAs) are involved in systemic lupus erythematosus (SLE). The level of NR_103776.1 expression in SLE and its clinical associations are still not well defined. OBJECTIVE To identify differentially expressed lncRNAs and explore their functional roles in SLE. METHODS Transcriptome sequencing was used to screen differentially expressed lncRNAs and mRNAs. Expression validation of clinical samples was performed by QRT-PCR. Bioinformatics was used to analyze its prognostic value and potential function. RESULTS Of the 231 significantly differentially expressed lncRNAs, NR_103776.1 could be used to distinguish not only SLE patients and rheumatoid arthritis patients but also active SLE patients, stable SLE patients, and healthy controls. NR_103776.1 was significantly and negatively correlated with inflammatory indexes (CRP and ESR). NR_103776.1 dysregulation might contribute to the metabolism of RNA and proteins in SLE patients. CONCLUSIONS This study not only provided a transcriptome profile of lncRNAs aberrantly expressed in individual nucleated cells of SLE patients but also suggested NR_103776.1 as a novel potential diagnostic biomarker.
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Affiliation(s)
- Yuqun Wang
- Department of Rheumatology and Immunology, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, China
| | - Jia He
- Department of Rheumatology and Immunology, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, China
| | - Honglei Ma
- Department of Rheumatology and Immunology, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, China
| | - Junhong Liu
- Department of Rheumatology and Immunology, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, China
| | - Linping Du
- Department of Rheumatology and Immunology, School of Clinical Medicine, Affiliated Hospital of Weifang Medical University, Weifang Medical University, Weifang, Shandong Province, China
| | - Chunxiang Chai
- Department of Rheumatology and Immunology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, China
| | - Yajing Liu
- Department of Rheumatology and Immunology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, China
| | - Xiaodong Wang
- Department of Rheumatology and Immunology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong Province, China.
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26
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Guan Y, Zhang Y, Zhao X, Wang Y. Comprehensive analysis revealed the immunoinflammatory targets of rheumatoid arthritis based on intestinal flora, miRNA, transcription factors, and RNA-binding proteins databases, GSEA and GSVA pathway observations, and immunoinfiltration typing. Hereditas 2024; 161:6. [PMID: 38273392 PMCID: PMC10809458 DOI: 10.1186/s41065-024-00310-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVE Rheumatoid arthritis (RA) is a chronic inflammatory arthritis. This study aimed to identify potential biomarkers and possible pathogenesis of RA using various bioinformatics analysis tools. METHODS The GMrepo database provided a visual representation of the analysis of intestinal flora. We selected the GSE55235 and GSE55457 datasets from the Gene Expression Omnibus database to identify differentially expressed genes (DEGs) separately. With the intersection of these DEGs with the target genes associated with RA found in the GeneCards database, we obtained the DEGs targeted by RA (DERATGs). Subsequently, Disease Ontology, Gene Ontology, and the Kyoto Encyclopedia of Genes and Genomes were used to analyze DERATGs functionally. Gene Set Enrichment Analysis (GSEA) and Gene Set Variation Analysis (GSVA) were performed on the data from the gene expression matrix. Additionally, the protein-protein interaction network, transcription factor (TF)-targets, target-drug, microRNA (miRNA)-mRNA networks, and RNA-binding proteins (RBPs)-DERATGs correlation analyses were built. The CIBERSORT was used to evaluate the inflammatory immune state. The single-sample GSEA (ssGSEA) algorithm and differential analysis of DERATGs were used among the infiltration degree subtypes. RESULTS There were some correlations between the abundance of gut flora and the prevalence of RA. A total of 54 DERATGs were identified, mainly related to immune and inflammatory responses and immunodeficiency diseases. Through GSEA and GSVA analysis, we found pathway alterations related to metabolic regulations, autoimmune diseases, and immunodeficiency-related disorders. We obtained 20 hub genes and 2 subnetworks. Additionally, we found that 39 TFs, 174 drugs, 2310 miRNAs, and several RBPs were related to DERATGs. Mast, plasma, and naive B cells differed during immune infiltration. We discovered DERATGs' differences among subtypes using the ssGSEA algorithm and subtype grouping. CONCLUSIONS The findings of this study could help with RA diagnosis, prognosis, and targeted molecular treatment.
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Affiliation(s)
- Yin Guan
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Yue Zhang
- Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Xiaoqian Zhao
- Department of Ethics Committee, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, Jiangsu, China
| | - Yue Wang
- Department of Rheumatism Immunity Branch, Affiliated Hospital of Nanjing University of Chinese Medicine, No. 155 Hanzhong Road, Nanjing, 210029, Jiangsu, China.
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27
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Li YJ, Guo Q, Ye MS, Cai G, Xiao WF, Deng S, Xiao Y. YBX1 promotes type H vessel-dependent bone formation in an m5C-dependent manner. JCI Insight 2024; 9:e172345. [PMID: 38385749 PMCID: PMC11143935 DOI: 10.1172/jci.insight.172345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 01/09/2024] [Indexed: 02/23/2024] Open
Abstract
RNA-binding proteins (RBPs) interact with RNA and ubiquitously regulate RNA transcripts during their life cycle, playing a fundamental role in the progression of angiogenesis-related diseases. In the skeletal system, endothelium-dependent angiogenesis is indispensable for bone formation. However, the role of RBPs in endothelium-dependent bone formation is unclear. Here, we show that RBP-Y-box-binding protein 1 (YBX1) was strongly reduced in the bone vasculature of ovariectomy (OVX) mice. Endothelial cell-specific deletion of Ybx1 impaired CD31-high, endomucin-high (CD31hiEMCNhi) endothelium morphology and resulted in low bone mass whereas Ybx1 overexpression promoted angiogenesis-dependent osteogenesis and ameliorated bone loss. Mechanistically, YBX1 deletion disrupted CD31, EMCN, and bone morphogenetic protein 4 (BMP4) stability in an m5C-dependent manner and blocked endothelium-derived BMP4 release, thereby inhibiting osteogenic differentiation of bone mesenchymal stromal cells. Administration of recombinant BMP4 protein restored impaired bone formation in Ybx1 deletion mice. Tail vein injection of CD31-modified polyethylene glycol-poly (lactic-co-glycolic acid) carrying sciadopitysin, a natural YBX1 agonist, pharmacologically partially reversed CD31hiEMCNhi vessels' decline and improved bone mass in both OVX and aging animals. These findings demonstrated the role of RBP-YBX1 in angiogenesis-dependent bone formation and provided a therapeutic approach for ameliorating osteoporosis.
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Affiliation(s)
- Yu-Jue Li
- Department of Endocrinology, Endocrinology Research Center
| | - Qi Guo
- Department of Endocrinology, Endocrinology Research Center
| | - Ming-Sheng Ye
- Department of Endocrinology, Endocrinology Research Center
| | - GuangPing Cai
- Department of Endocrinology, Endocrinology Research Center
| | | | - Sheng Deng
- Department of Pharmacy, Xiangya Hospital of Central South University, Changsha, China
| | - Ye Xiao
- Department of Endocrinology, Endocrinology Research Center
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28
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Ma H, Yang Y, Nie T, Yan R, Si Y, Wei J, Li M, Liu H, Ye W, Zhang H, Cheng L, Zhang L, Lv X, Luo L, Xu Z, Zhang X, Lei Y, Zhang F. Disparate macrophage responses are linked to infection outcome of Hantan virus in humans or rodents. Nat Commun 2024; 15:438. [PMID: 38200007 PMCID: PMC10781751 DOI: 10.1038/s41467-024-44687-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
Hantaan virus (HTNV) is asymptomatically carried by rodents, yet causes lethal hemorrhagic fever with renal syndrome in humans, the underlying mechanisms of which remain to be elucidated. Here, we show that differential macrophage responses may determine disparate infection outcomes. In mice, late-phase inactivation of inflammatory macrophage prevents cytokine storm syndrome that usually occurs in HTNV-infected patients. This is attained by elaborate crosstalk between Notch and NF-κB pathways. Mechanistically, Notch receptors activated by HTNV enhance NF-κB signaling by recruiting IKKβ and p65, promoting inflammatory macrophage polarization in both species. However, in mice rather than humans, Notch-mediated inflammation is timely restrained by a series of murine-specific long noncoding RNAs transcribed by the Notch pathway in a negative feedback manner. Among them, the lnc-ip65 detaches p65 from the Notch receptor and inhibits p65 phosphorylation, rewiring macrophages from the pro-inflammation to the pro-resolution phenotype. Genetic ablation of lnc-ip65 leads to destructive HTNV infection in mice. Thus, our findings reveal an immune-braking function of murine noncoding RNAs, offering a special therapeutic strategy for HTNV infection.
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Affiliation(s)
- Hongwei Ma
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
- Department of Anaesthesiology & Critical Care Medicine, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Yongheng Yang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Tiejian Nie
- Department of Experimental Surgery, Tangdu Hospital, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710038, China
| | - Rong Yan
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Yue Si
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Jing Wei
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
- Shaanxi Provincial Centre for Disease Control and Prevention, Xi'an, Shaanxi, 710054, China
| | - Mengyun Li
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - He Liu
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Wei Ye
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Hui Zhang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Linfeng Cheng
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Liang Zhang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Xin Lv
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China
| | - Limin Luo
- Department of Infectious Disease, Air Force Hospital of Southern Theatre Command, Guangzhou, Guangdong, 510602, China
| | - Zhikai Xu
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
| | - Xijing Zhang
- Department of Anaesthesiology & Critical Care Medicine, Xijing Hospital, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
| | - Yingfeng Lei
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
| | - Fanglin Zhang
- Department of Microbiology & Pathogen Biology, School of Basic Medical Sciences, Air Force Medical University (the Fourth Military Medical University), Xi'an, Shaanxi, 710032, China.
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Sun N, Teyssier N, Wang B, Drake S, Seyler M, Zaltsman Y, Everitt A, Teerikorpi N, Willsey HR, Goodarzi H, Tian R, Kampmann M, Willsey AJ. Autism genes converge on microtubule biology and RNA-binding proteins during excitatory neurogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.22.573108. [PMID: 38187634 PMCID: PMC10769323 DOI: 10.1101/2023.12.22.573108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Recent studies have identified over one hundred high-confidence (hc) autism spectrum disorder (ASD) genes. Systems biological and functional analyses on smaller subsets of these genes have consistently implicated excitatory neurogenesis. However, the extent to which the broader set of hcASD genes are involved in this process has not been explored systematically nor have the biological pathways underlying this convergence been identified. Here, we leveraged CROP-Seq to repress 87 hcASD genes in a human in vitro model of cortical neurogenesis. We identified 17 hcASD genes whose repression significantly alters developmental trajectory and results in a common cellular state characterized by disruptions in proliferation, differentiation, cell cycle, microtubule biology, and RNA-binding proteins (RBPs). We also characterized over 3,000 differentially expressed genes, 286 of which had expression profiles correlated with changes in developmental trajectory. Overall, we uncovered transcriptional disruptions downstream of hcASD gene perturbations, correlated these disruptions with distinct differentiation phenotypes, and reinforced neurogenesis, microtubule biology, and RBPs as convergent points of disruption in ASD.
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30
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Huang W, Xiong T, Zhao Y, Heng J, Han G, Wang P, Zhao Z, Shi M, Li J, Wang J, Wu Y, Liu F, Xi JJ, Wang Y, Zhang QC. Computational prediction and experimental validation identify functionally conserved lncRNAs from zebrafish to human. Nat Genet 2024; 56:124-135. [PMID: 38195860 PMCID: PMC10786727 DOI: 10.1038/s41588-023-01620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/21/2023] [Indexed: 01/11/2024]
Abstract
Functional studies of long noncoding RNAs (lncRNAs) have been hindered by the lack of methods to assess their evolution. Here we present lncRNA Homology Explorer (lncHOME), a computational pipeline that identifies a unique class of long noncoding RNAs (lncRNAs) with conserved genomic locations and patterns of RNA-binding protein (RBP) binding sites (coPARSE-lncRNAs). Remarkably, several hundred human coPARSE-lncRNAs can be evolutionarily traced to zebrafish. Using CRISPR-Cas12a knockout and rescue assays, we found that knocking out many human coPARSE-lncRNAs led to cell proliferation defects, which were subsequently rescued by predicted zebrafish homologs. Knocking down coPARSE-lncRNAs in zebrafish embryos caused severe developmental delays that were rescued by human homologs. Furthermore, we verified that human, mouse and zebrafish coPARSE-lncRNA homologs tend to bind similar RBPs with their conserved functions relying on specific RBP-binding sites. Overall, our study demonstrates a comprehensive approach for studying the functional conservation of lncRNAs and implicates numerous lncRNAs in regulating vertebrate physiology.
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Affiliation(s)
- Wenze Huang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Tuanlin Xiong
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Yuting Zhao
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jian Heng
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
| | - Ge Han
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Pengfei Wang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
- Tsinghua-Peking Center for Life Sciences, Beijing, China
| | - Zhihua Zhao
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Ming Shi
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Juan Li
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China
| | - Jiazhen Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Yixia Wu
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
| | - Feng Liu
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Sciences, Shandong University, Qingdao, China
| | - Jianzhong Jeff Xi
- Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing, China.
| | - Yangming Wang
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China.
| | - Qiangfeng Cliff Zhang
- MOE Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, School of Life Sciences, Tsinghua University, Beijing, China.
- Beijing Advanced Innovation Center for Structural Biology & Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, China.
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Zhu WS, Litterman AJ, Sekhon HS, Kageyama R, Arce MM, Taylor KE, Zhao W, Criswell LA, Zaitlen N, Erle DJ, Ansel KM. GCLiPP: global crosslinking and protein purification method for constructing high-resolution occupancy maps for RNA binding proteins. Genome Biol 2023; 24:281. [PMID: 38062486 PMCID: PMC10701951 DOI: 10.1186/s13059-023-03125-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
GCLiPP is a global RNA interactome capture method that detects RNA-binding protein (RBP) occupancy transcriptome-wide. GCLiPP maps RBP-occupied sites at a higher resolution than phase separation-based techniques. GCLiPP sequence tags correspond with known RBP binding sites and are enriched for sites detected by RBP-specific crosslinking immunoprecipitation (CLIP) for abundant cytosolic RBPs. Comparison of human Jurkat T cells and mouse primary T cells uncovers shared peaks of GCLiPP signal across homologous regions of human and mouse 3' UTRs, including a conserved mRNA-destabilizing cis-regulatory element. GCLiPP signal overlapping with immune-related SNPs uncovers stabilizing cis-regulatory regions in CD5, STAT6, and IKZF1.
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Affiliation(s)
- Wandi S Zhu
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam J Litterman
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Harshaan S Sekhon
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
- University of California Berkeley, Berkeley, CA, USA
| | - Robin Kageyama
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Maya M Arce
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Kimberly E Taylor
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Wenxue Zhao
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
- School of Medicine, Sun Yat-Sen University, Guangzhou, 510080, People's Republic of China
| | - Lindsey A Criswell
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, USA
| | - Noah Zaitlen
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - David J Erle
- Department of Medicine, University of California San Francisco, San Francisco, USA
- Lung Biology Center, University of California San Francisco, San Francisco, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology and Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA.
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32
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Kikuta H, Aramaki T, Mabu S, Akada R, Hoshida H. The presence of an intron relieves gene repression caused by promoter-proximal four-bp specific sequences in yeast. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194982. [PMID: 37659722 DOI: 10.1016/j.bbagrm.2023.194982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Introns can enhance gene expression in eukaryotic cells in a process called intron-mediated enhancement (IME). The levels of enhancement are affected not only by the intron sequence but also by coding sequences (CDSs). However, the parts of CDSs responsible for mediating IME have not yet been identified. In this study, we identified an IME-mediating sequence by analyzing three pairs of IME-sensitive and -insensitive CDSs in Saccharomyces cerevisiae. Expression of the CDSs yCLuc, yRoGLU1, and KmBGA1 was enhanced by the presence of an intron (i.e., they were IME sensitive), but the expression of each corresponding codon-changed CDS, which encoded the identical amino acid sequence, was not enhanced (i.e., they were IME insensitive). Interestingly, the IME-insensitive CDSs showed higher expression levels that were like intron-enhanced expression of IME-sensitive CDSs, suggesting that expression of IME-sensitive CDSs was repressed. A four-nucleotide sequence (TCTT) located in the promoter-proximal position of either the untranslated or coding region was found to be responsible for repression in IME-sensitive CDSs, and repression caused by the TCTT sequence was relieved by the presence of an intron. Further, it was found that the expression of intron-containing yeast-native genes, UBC4 and MPT5, was repressed by TCTT in the CDS but relieved by the introns. These results indicate that TCTT sequences in promoter-proximal positions repress gene expression and that introns play a role in relieving gene repression caused by sequences such as TCTT.
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Affiliation(s)
- Hiroki Kikuta
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Takahiro Aramaki
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Shingo Mabu
- Division of Electrical, Electronic and Information Engineering, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Rinji Akada
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8315, Japan; Yamaguchi University Biomedical Engineering Center, 2-16-1 Tokiwadai, Ube 755-8611, Japan
| | - Hisashi Hoshida
- Division of Applied Chemistry, Graduate School of Sciences and Technology for Innovation, Yamaguchi University, 2-16-1 Tokiwadai, Ube 755-8611, Japan; Research Center for Thermotolerant Microbial Resources, Yamaguchi University, 1677-1 Yoshida, Yamaguchi 753-8315, Japan; Yamaguchi University Biomedical Engineering Center, 2-16-1 Tokiwadai, Ube 755-8611, Japan.
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33
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Singh M, Kumar S. Effect of single nucleotide polymorphisms on the structure of long noncoding RNAs and their interaction with RNA binding proteins. Biosystems 2023; 233:105021. [PMID: 37703988 DOI: 10.1016/j.biosystems.2023.105021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
Long non-coding RNAs (lncRNA) are emerging as a new class of regulatory RNAs with remarkable potential to be utilized as therapeutic targets against many human diseases. Several genome-wide association studies (GWAS) have catalogued Single Nucleotide Polymorphisms (SNPs) present in the noncoding regions of the genome from where lncRNAs originate. In this study, we have selected 67 lncRNAs with GWAS-tagged SNPs and have also investigated their role in affecting the local secondary structures. Majority of the SNPs lead to changes in the secondary structure of lncRNAs to a different extent by altering the base pairing patterns. These structural changes in lncRNA are also manifested in form of alteration in the binding site for RNA binding proteins (RBPs) along with affecting their binding efficacies. Ultimately, these structural modifications may influence the transcriptional and post-transcriptional pathways of these RNAs, leading to the causation of diseases. Hence, it is important to understand the possible underlying mechanism of RBPs in association with GWAS-tagged SNPs in human diseases.
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Affiliation(s)
- Mandakini Singh
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
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34
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Yu J, Li W, Hou GJ, Sun DP, Yang Y, Yuan SX, Dai ZH, Yin HZ, Sun SH, Huang G, Zhou WP, Yang F. Circular RNA cFAM210A, degradable by HBx, inhibits HCC tumorigenesis by suppressing YBX1 transactivation. Exp Mol Med 2023; 55:2390-2401. [PMID: 37907737 PMCID: PMC10689457 DOI: 10.1038/s12276-023-01108-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 07/21/2023] [Accepted: 08/03/2023] [Indexed: 11/02/2023] Open
Abstract
Hepatitis B protein x (HBx) has been reported to promote tumorigenesis in hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC), but the mechanism awaits further investigation. In this study, we found that cFAM210A (a circular RNA derived from the third exon of transcript NM_001098801 of the FAM210A gene; CircBase ID: hsa_circ_0003979) can be silenced by HBx. cFAM210A expression was downregulated and negatively correlated with tumorigenesis in patients with HBV-related HCC. Furthermore, cFAM210A reduced the proliferation, stemness, and tumorigenicity of HCC cells. Mechanistically, HBx increased the N6-methyladenosine (m6A) level of cFAM210A by promoting the expression of RBM15 (an m6A methyltransferase), thus inducing the degradation of cFAM210A via the YTHDF2-HRSP12-RNase P/MRP pathway. cFAM210A bound to YBX1 and inhibited its phosphorylation, suppressing its transactivation function toward MET. These findings suggest the important role of circular RNAs in HBx-induced hepatocarcinogenesis and identify cFAM210A a potential target in the prevention and treatment of HBV-related HCC.
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Affiliation(s)
- Jian Yu
- The Department of General Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Wen Li
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Guo-Jun Hou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Da-Peng Sun
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Yuan Yang
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Sheng-Xian Yuan
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China
| | - Zhi-Hui Dai
- The Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Hao-Zan Yin
- The Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Shu-Han Sun
- The Department of Medical Genetics, Naval Medical University, Shanghai, China
| | - Gang Huang
- The Department of General Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China.
| | - Wei-Ping Zhou
- The Third Department of Hepatic Surgery, Eastern Hepatobiliary Surgery Hospital, Naval Medical University, Shanghai, China.
| | - Fu Yang
- The Department of Medical Genetics, Naval Medical University, Shanghai, China.
- Shanghai Key Laboratory of Medical Bioprotection, Shanghai, 200433, China.
- Key Laboratory of Biological Defense, Ministry of Education, Shanghai, 200433, China.
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35
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Weber AI, Parthasarathy S, Borisova E, Epifanova E, Preußner M, Rusanova A, Ambrozkiewicz MC, Bessa P, Newman A, Müller L, Schaal H, Heyd F, Tarabykin V. Srsf1 and Elavl1 act antagonistically on neuronal fate choice in the developing neocortex by controlling TrkC receptor isoform expression. Nucleic Acids Res 2023; 51:10218-10237. [PMID: 37697438 PMCID: PMC10602877 DOI: 10.1093/nar/gkad703] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 07/24/2023] [Accepted: 08/15/2023] [Indexed: 09/13/2023] Open
Abstract
The seat of higher-order cognitive abilities in mammals, the neocortex, is a complex structure, organized in several layers. The different subtypes of principal neurons are distributed in precise ratios and at specific positions in these layers and are generated by the same neural progenitor cells (NPCs), steered by a spatially and temporally specified combination of molecular cues that are incompletely understood. Recently, we discovered that an alternatively spliced isoform of the TrkC receptor lacking the kinase domain, TrkC-T1, is a determinant of the corticofugal projection neuron (CFuPN) fate. Here, we show that the finely tuned balance between TrkC-T1 and the better known, kinase domain-containing isoform, TrkC-TK+, is cell type-specific in the developing cortex and established through the antagonistic actions of two RNA-binding proteins, Srsf1 and Elavl1. Moreover, our data show that Srsf1 promotes the CFuPN fate and Elavl1 promotes the callosal projection neuron (CPN) fate in vivo via regulating the distinct ratios of TrkC-T1 to TrkC-TK+. Taken together, we connect spatio-temporal expression of Srsf1 and Elavl1 in the developing neocortex with the regulation of TrkC alternative splicing and transcript stability and neuronal fate choice, thus adding to the mechanistic and functional understanding of alternative splicing in vivo.
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Affiliation(s)
- A Ioana Weber
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Srinivas Parthasarathy
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Ekaterina Borisova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Ekaterina Epifanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Alexandra Rusanova
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, 634009, Tomsk, Russia
| | - Mateusz C Ambrozkiewicz
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Paraskevi Bessa
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Andrew G Newman
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
| | - Lisa Müller
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Heiner Schaal
- Heinrich Heine Universität Düsseldorf, Institute of Virology, Medical Faculty, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, 14195, Berlin, Germany
| | - Victor Tarabykin
- Charité Universitätsmedizin Berlin, Institute of Cell Biology and Neurobiology, Charitéplatz 1, 10117 Berlin, Germany
- Institute of Neuroscience, Lobachevsky State University of Nizhny Novgorod, 603950, Nizhny Novgorod Oblast, Russia
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36
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Šimková K, Naraine R, Vintr J, Soukup V, Šindelka R. RNA localization during early development of the axolotl. Front Cell Dev Biol 2023; 11:1260795. [PMID: 37928901 PMCID: PMC10620976 DOI: 10.3389/fcell.2023.1260795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/26/2023] [Indexed: 11/07/2023] Open
Abstract
The asymmetric localization of biomolecules is critical for body plan development. One of the most popular model organisms for early embryogenesis studies is Xenopus laevis but there is a lack of information in other animal species. Here, we compared the early development of two amphibian species-the frog X. laevis and the axolotl Ambystoma mexicanum. This study aimed to identify asymmetrically localized RNAs along the animal-vegetal axis during the early development of A. mexicanum. For that purpose, we performed spatial transcriptome-wide analysis at low resolution, which revealed dynamic changes along the animal-vegetal axis classified into the following categories: profile alteration, de novo synthesis and degradation. Surprisingly, our results showed that many of the vegetally localized genes, which are important for germ cell development, are degraded during early development. Furthermore, we assessed the motif presence in UTRs of degraded mRNAs and revealed the enrichment of several motifs in RNAs of germ cell markers. Our results suggest novel reorganization of the transcriptome during embryogenesis of A. mexicanum to converge to the similar developmental pattern as the X. laevis.
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Affiliation(s)
- Kateřina Šimková
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Ravindra Naraine
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
| | - Jan Vintr
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Vladimír Soukup
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Radek Šindelka
- Laboratory of Gene Expression, Institute of Biotechnology of the Czech Academy of Sciences, Vestec, Czechia
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37
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Karlebach G, Steinhaus R, Danis D, Devoucoux M, Anczuków O, Sheynkman G, Seelow D, Robinson PN. Alternative splicing is coupled to gene expression in a subset of variably expressed genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544742. [PMID: 37398049 PMCID: PMC10312658 DOI: 10.1101/2023.06.13.544742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Numerous factors regulate alternative splicing of human genes at a co-transcriptional level. However, how alternative splicing depends on the regulation of gene expression is poorly understood. We leveraged data from the Genotype-Tissue Expression (GTEx) project to show a significant association of gene expression and splicing for 6874 (4.9%) of 141,043 exons in 1106 (13.3%) of 8314 genes with substantially variable expression in ten GTEx tissues. About half of these exons demonstrate higher inclusion with higher gene expression, and half demonstrate higher exclusion, with the observed direction of coupling being highly consistent across different tissues and in external datasets. The exons differ with respect to sequence characteristics, enriched sequence motifs, RNA polymerase II binding, and inferred transcription rate of downstream introns. The exons were enriched for hundreds of isoform-specific Gene Ontology annotations, suggesting that the coupling of expression and alternative splicing described here may provide an important gene regulatory mechanism that might be used in a variety of biological contexts. In particular, higher inclusion exons could play an important role during cell division.
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Affiliation(s)
- Guy Karlebach
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Robin Steinhaus
- Exploratory Diagnostic Sciences, Berlin Institute of Health, 10117 Berlin, Germany
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt-Universität zu Berlin, 13353 10117 Berlin, Germany
| | - Daniel Danis
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Maeva Devoucoux
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT 06032, USA
- Institute for Systems Genomics, University of Connecticut, Farmington, CT 06032, USA
| | - Gloria Sheynkman
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Dominik Seelow
- Exploratory Diagnostic Sciences, Berlin Institute of Health, 10117 Berlin, Germany
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, corporate member of Freie Universitat Berlin and Humboldt-Universität zu Berlin, 13353 10117 Berlin, Germany
| | - Peter N Robinson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
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38
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Ziff OJ, Harley J, Wang Y, Neeves J, Tyzack G, Ibrahim F, Skehel M, Chakrabarti AM, Kelly G, Patani R. Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition. Neuron 2023; 111:3011-3027.e7. [PMID: 37480846 DOI: 10.1016/j.neuron.2023.06.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 05/09/2023] [Accepted: 06/22/2023] [Indexed: 07/24/2023]
Abstract
Amyotrophic lateral sclerosis (ALS) is characterized by nucleocytoplasmic mislocalization of the RNA-binding protein (RBP) TDP-43. However, emerging evidence suggests more widespread mRNA and protein mislocalization. Here, we employed nucleocytoplasmic fractionation, RNA sequencing, and mass spectrometry to investigate the localization of mRNA and protein in induced pluripotent stem cell-derived motor neurons (iPSMNs) from ALS patients with TARDBP and VCP mutations. ALS mutant iPSMNs exhibited extensive nucleocytoplasmic mRNA redistribution, RBP mislocalization, and splicing alterations. Mislocalized proteins exhibited a greater affinity for redistributed transcripts, suggesting a link between RBP mislocalization and mRNA redistribution. Notably, treatment with ML240, a VCP ATPase inhibitor, partially restored mRNA and protein localization in ALS mutant iPSMNs. ML240 induced changes in the VCP interactome and lysosomal localization and reduced oxidative stress and DNA damage. These findings emphasize the link between RBP mislocalization and mRNA redistribution in ALS motor neurons and highlight the therapeutic potential of VCP inhibition.
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Affiliation(s)
- Oliver J Ziff
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
| | - Jasmine Harley
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; Institute of Molecular and Cell Biology, A(∗)STAR Research Entities, Singapore 138673, Singapore
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Jacob Neeves
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Giulia Tyzack
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Fairouz Ibrahim
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | - Mark Skehel
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK
| | | | - Gavin Kelly
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK; Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, WC1N 3BG London, UK; National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, WC1N 3BG London, UK.
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Paré L, Bideau L, Baduel L, Dalle C, Benchouaia M, Schneider SQ, Laplane L, Clément Y, Vervoort M, Gazave E. Transcriptomic landscape of posterior regeneration in the annelid Platynereis dumerilii. BMC Genomics 2023; 24:583. [PMID: 37784028 PMCID: PMC10546743 DOI: 10.1186/s12864-023-09602-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/18/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididae Platynereis dumerilii (re)emerged recently as a front-line regeneration model. Following amputation of its posterior part, Platynereis worms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered. RESULTS We generated a high-quality de novo Reference transcriptome for the annelid Platynereis dumerilii. We produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included two of these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific gene expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process. CONCLUSIONS In this study, we provided a high-quality de novo Reference transcriptome for the annelid Platynereis that is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration sheds light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.
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Affiliation(s)
- Louis Paré
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loïc Bideau
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Loeiza Baduel
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Caroline Dalle
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Médine Benchouaia
- Département de biologie, GenomiqueENS, Institut de Biologie de l'ENS (IBENS), École normale supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Stephan Q Schneider
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Lucie Laplane
- Université Paris I Panthéon-Sorbonne, CNRS UMR 8590 Institut d'Histoire et de Philosophie des Sciences et des Techniques (IHPST), Paris, France
- Gustave Roussy, UMR 1287, Villejuif, France
| | - Yves Clément
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Michel Vervoort
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France
| | - Eve Gazave
- Université Paris Cité, CNRS, Institut Jacques Monod, Paris, F-75013, France.
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40
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Wang J, Horlacher M, Cheng L, Winther O. RNA trafficking and subcellular localization-a review of mechanisms, experimental and predictive methodologies. Brief Bioinform 2023; 24:bbad249. [PMID: 37466130 PMCID: PMC10516376 DOI: 10.1093/bib/bbad249] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/30/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
RNA localization is essential for regulating spatial translation, where RNAs are trafficked to their target locations via various biological mechanisms. In this review, we discuss RNA localization in the context of molecular mechanisms, experimental techniques and machine learning-based prediction tools. Three main types of molecular mechanisms that control the localization of RNA to distinct cellular compartments are reviewed, including directed transport, protection from mRNA degradation, as well as diffusion and local entrapment. Advances in experimental methods, both image and sequence based, provide substantial data resources, which allow for the design of powerful machine learning models to predict RNA localizations. We review the publicly available predictive tools to serve as a guide for users and inspire developers to build more effective prediction models. Finally, we provide an overview of multimodal learning, which may provide a new avenue for the prediction of RNA localization.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center, Munich, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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41
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Ramakrishnaiah Y, Morris AP, Dhaliwal J, Philip M, Kuhlmann L, Tyagi S. Linc2function: A Comprehensive Pipeline and Webserver for Long Non-Coding RNA (lncRNA) Identification and Functional Predictions Using Deep Learning Approaches. EPIGENOMES 2023; 7:22. [PMID: 37754274 PMCID: PMC10528440 DOI: 10.3390/epigenomes7030022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/02/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Long non-coding RNAs (lncRNAs), comprising a significant portion of the human transcriptome, serve as vital regulators of cellular processes and potential disease biomarkers. However, the function of most lncRNAs remains unknown, and furthermore, existing approaches have focused on gene-level investigation. Our work emphasizes the importance of transcript-level annotation to uncover the roles of specific transcript isoforms. We propose that understanding the mechanisms of lncRNA in pathological processes requires solving their structural motifs and interactomes. A complete lncRNA annotation first involves discriminating them from their coding counterparts and then predicting their functional motifs and target bio-molecules. Current in silico methods mainly perform primary-sequence-based discrimination using a reference model, limiting their comprehensiveness and generalizability. We demonstrate that integrating secondary structure and interactome information, in addition to using transcript sequence, enables a comprehensive functional annotation. Annotating lncRNA for newly sequenced species is challenging due to inconsistencies in functional annotations, specialized computational techniques, limited accessibility to source code, and the shortcomings of reference-based methods for cross-species predictions. To address these challenges, we developed a pipeline for identifying and annotating transcript sequences at the isoform level. We demonstrate the effectiveness of the pipeline by comprehensively annotating the lncRNA associated with two specific disease groups. The source code of our pipeline is available under the MIT licensefor local use by researchers to make new predictions using the pre-trained models or to re-train models on new sequence datasets. Non-technical users can access the pipeline through a web server setup.
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Affiliation(s)
- Yashpal Ramakrishnaiah
- Central Clinical School, Monash University, Melbourne, VIC 3000, Australia
- School of Computing Technologies, Royal Melbourne Institute of Technology University, Melbourne, VIC 3000, Australia
| | - Adam P. Morris
- Monash Data Futures Institute, Monash University, Clayton, VIC 3800, Australia
| | - Jasbir Dhaliwal
- School of Computing Technologies, Royal Melbourne Institute of Technology University, Melbourne, VIC 3000, Australia
| | - Melcy Philip
- Central Clinical School, Monash University, Melbourne, VIC 3000, Australia
| | - Levin Kuhlmann
- Faculty of Information Technology, Monash University, Clayton, VIC 3800, Australia
| | - Sonika Tyagi
- Central Clinical School, Monash University, Melbourne, VIC 3000, Australia
- School of Computing Technologies, Royal Melbourne Institute of Technology University, Melbourne, VIC 3000, Australia
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Zhang M, Wang Y, Yu L, Zhang Y, Wang Y, Shang Z, Xin Y, Li X, Ning N, Zhang Y, Zhang X. Fusobacterium nucleatum promotes colorectal cancer metastasis by excretion of miR-122-5p from cells via exosomes. iScience 2023; 26:107686. [PMID: 37694140 PMCID: PMC10485600 DOI: 10.1016/j.isci.2023.107686] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/23/2023] [Accepted: 08/17/2023] [Indexed: 09/12/2023] Open
Abstract
Fusobacterium nucleatum (Fn) infection and microRNAs (miRNAs) are closely associated with colorectal cancer (CRC) development, but the mechanism by which Fn regulates tumor-suppressive miRNAs via exosomes and facilitates CRC metastasis remains unclear. Here, we identified that Fn infection significantly increased exosomal miR-122-5p levels in the serum of CRC patients and CRC cell culture supernatants through two miRNA panels of high-throughput sequencing and RT-qPCR analysis. In Fn-infected patients, the serum exosomal levels of miR-122-5p were negatively associated with their expression levels of tissues. Downregulated miR-122-5p was demonstrated to enhance the migration, invasion, and metastasis abilities of CRC cells in vivo and in vitro. Secretion of miR-122-5p into exosomes is mediated by hnRNPA2B1. Mechanistically, Fn activated the TGF-β1/Smads signaling pathway to promote EMT by regulation of the miR-122-5p/FUT8 axis. In conclusion, Fn infection may stimulate CRC cells to excrete exosome-wrapped miR-122-5p, and activate the FUT8/TGF-β1/Smads axis to promote metastasis.
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Affiliation(s)
- Mengjiao Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Yifeng Wang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Longchen Yu
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Yanli Zhang
- Department of Clinical Laboratory, Shandong Provincial Third Hospital, Jinan 250031, China
| | - Yanlei Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Ziqi Shang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Yiwei Xin
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Xinyang Li
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Nannan Ning
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Yi Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
| | - Xin Zhang
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan 250012, China
- Shandong Engineering Research Center of Biomarker and Artificial Intelligence Application, Jinan 250012, China
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Marín-Palma D, Fernandez GJ, Ruiz-Saenz J, Taborda NA, Rugeles MT, Hernandez JC. Particulate matter impairs immune system function by up-regulating inflammatory pathways and decreasing pathogen response gene expression. Sci Rep 2023; 13:12773. [PMID: 37550362 PMCID: PMC10406897 DOI: 10.1038/s41598-023-39921-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023] Open
Abstract
Airborne particulate matter produced by industrial sources and automobiles has been linked to increased susceptibility to infectious diseases and it is known to be recognized by cells of the immune system. The molecular mechanisms and changes in gene expression profiles induced in immune cells by PM have not been fully mapped out or systematically integrated. Here, we use RNA-seq to analyze mRNA profiles of human peripheral blood mononuclear cells after exposure to coarse particulate matter (PM10). Our analyses showed that PM10 was able to reprogram the expression of 1,196 genes in immune cells, including activation of a proinflammatory state with an increase in cytokines and chemokines. Activation of the IL-36 signaling pathway and upregulation of chemokines involved in neutrophil and monocyte recruitment suggest mechanisms for inflammation upon PM exposure, while NK cell-recruiting chemokines are repressed. PM exposure also increases transcription factors associated with inflammatory pathways (e.g., JUN, RELB, NFKB2, etc.) and reduces expression of RNases and pathogen response genes CAMP, DEFAs, AZU1, APOBEC3A and LYZ. Our analysis across gene regulatory and signaling pathways suggests that PM plays a role in the dysregulation of immune cell functions, relevant for antiviral responses and general host defense against pathogens.
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Affiliation(s)
- Damariz Marín-Palma
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Geysson Javier Fernandez
- Grupo Biología y Control de Enfermedades Infecciosas BCEI, Universidad de Antioquia-UdeA, Medellín, Colombia
| | - Julian Ruiz-Saenz
- Grupo de Investigación en Ciencias Animales GRICA, Universidad Cooperativa de Colombia, Bucaramanga, Colombia
| | - Natalia A Taborda
- Grupo de Investigaciones Biomédicas Uniremington, Programa de Medicina, Facultad de Ciencias de La Salud, Corporación Universitaria Remington, Medellín, Colombia
- Universidad Cooperativa de Colombia, Campus Medellín-Envigado, Medellín, Colombia
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia UdeA, Medellín, Colombia
| | - Juan C Hernandez
- Infettare, Facultad de Medicina, Universidad Cooperativa de Colombia, Medellín, Colombia.
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Horlacher M, Wagner N, Moyon L, Kuret K, Goedert N, Salvatore M, Ule J, Gagneur J, Winther O, Marsico A. Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning. Genome Biol 2023; 24:180. [PMID: 37542318 PMCID: PMC10403857 DOI: 10.1186/s13059-023-03015-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 07/17/2023] [Indexed: 08/06/2023] Open
Abstract
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves high generalization on eCLIP, iCLIP and miCLIP assays, outperforming state-of-the-art classifiers. RBPNet performs bias correction by modeling the raw signal as a mixture of the protein-specific and background signal. Through model interrogation via Integrated Gradients, RBPNet identifies predictive sub-sequences that correspond to known and novel binding motifs and enables variant-impact scoring via in silico mutagenesis. Together, RBPNet improves imputation of protein-RNA interactions, as well as mechanistic interpretation of predictions.
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Affiliation(s)
- Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Munich, Germany.
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- Department of Informatics, Technical University of Munich, Garching, Germany.
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany.
| | - Nils Wagner
- Department of Informatics, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Lambert Moyon
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Klara Kuret
- National Institute of Chemistry, Ljubljana, Slovenia
- The Francis Crick Institute, London, UK
- Jozef Stefan International Postgraduate School, Jamova cesta 39, 1000, Ljubljana, Slovenia
| | - Nicolas Goedert
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
| | - Marco Salvatore
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jernej Ule
- National Institute of Chemistry, Ljubljana, Slovenia
- The Francis Crick Institute, London, UK
| | - Julien Gagneur
- Computational Health Center, Helmholtz Center Munich, Munich, Germany
- Department of Informatics, Technical University of Munich, Garching, Germany
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany
| | - Ole Winther
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Annalisa Marsico
- Computational Health Center, Helmholtz Center Munich, Munich, Germany.
- Helmholtz Association - Munich School for Data Science (MUDS), Munich, Germany.
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45
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Swahn H, Olmer M, Lotz MK. RNA-binding proteins that are highly expressed and enriched in healthy cartilage but suppressed in osteoarthritis. Front Cell Dev Biol 2023; 11:1208315. [PMID: 37457300 PMCID: PMC10349536 DOI: 10.3389/fcell.2023.1208315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Objectives: RNA-binding proteins (RBPs) have diverse and essential biological functions, but their role in cartilage health and disease is largely unknown. The objectives of this study were (i) map the global landscape of RBPs expressed and enriched in healthy cartilage and dysregulated in osteoarthritis (OA); (ii) prioritize RBPs for their potential role in cartilage and in OA pathogenesis and as therapeutic targets. Methods: Our published bulk RNA-sequencing (RNA-seq) data of healthy and OA human cartilage, and a census of 1,542 RBPs were utilized to identify RBPs that are expressed in healthy cartilage and differentially expressed (DE) in OA. Next, our comparison of healthy cartilage RNA-seq data to 37 transcriptomes in the Genotype-Tissue Expression (GTEx) database was used to determine RBPs that are enriched in cartilage. Finally, expression of RBPs was analyzed in our single cell RNA-sequencing (scRNA-seq) data from healthy and OA human cartilage. Results: Expression of RBPs was higher than nonRBPs in healthy cartilage. In OA cartilage, 188 RBPs were differentially expressed, with a greater proportion downregulated. Ribosome biogenesis was enriched in the upregulated RBPs, while splicing and transport were enriched in the downregulated. To further prioritize RBPs, we selected the top 10% expressed RBPs in healthy cartilage and those that were cartilage-enriched according to GTEx. Intersecting these criteria, we identified Tetrachlorodibenzodioxin (TCDD) Inducible Poly (ADP-Ribose) Polymerase (TIPARP) as a candidate RBP. TIPARP was downregulated in OA. scRNA-seq data revealed TIPARP was most significantly downregulated in the "pathogenic cluster". Conclusion: Our global analyses reveal expression patterns of RBPs in healthy and OA cartilage. We also identified TIPARP and other RBPs as novel mediators in OA pathogenesis and as potential therapeutic targets.
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Affiliation(s)
| | | | - Martin K. Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, United States
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Esposito R, Lanzós A, Uroda T, Ramnarayanan S, Büchi I, Polidori T, Guillen-Ramirez H, Mihaljevic A, Merlin BM, Mela L, Zoni E, Hovhannisyan L, McCluggage F, Medo M, Basile G, Meise DF, Zwyssig S, Wenger C, Schwarz K, Vancura A, Bosch-Guiteras N, Andrades Á, Tham AM, Roemmele M, Medina PP, Ochsenbein AF, Riether C, Kruithof-de Julio M, Zimmer Y, Medová M, Stroka D, Fox A, Johnson R. Tumour mutations in long noncoding RNAs enhance cell fitness. Nat Commun 2023; 14:3342. [PMID: 37291246 PMCID: PMC10250536 DOI: 10.1038/s41467-023-39160-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/01/2023] [Indexed: 06/10/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) are linked to cancer via pathogenic changes in their expression levels. Yet, it remains unclear whether lncRNAs can also impact tumour cell fitness via function-altering somatic "driver" mutations. To search for such driver-lncRNAs, we here perform a genome-wide analysis of fitness-altering single nucleotide variants (SNVs) across a cohort of 2583 primary and 3527 metastatic tumours. The resulting 54 mutated and positively-selected lncRNAs are significantly enriched for previously-reported cancer genes and a range of clinical and genomic features. A number of these lncRNAs promote tumour cell proliferation when overexpressed in in vitro models. Our results also highlight a dense SNV hotspot in the widely-studied NEAT1 oncogene. To directly evaluate the functional significance of NEAT1 SNVs, we use in cellulo mutagenesis to introduce tumour-like mutations in the gene and observe a significant and reproducible increase in cell fitness, both in vitro and in a mouse model. Mechanistic studies reveal that SNVs remodel the NEAT1 ribonucleoprotein and boost subnuclear paraspeckles. In summary, this work demonstrates the utility of driver analysis for mapping cancer-promoting lncRNAs, and provides experimental evidence that somatic mutations can act through lncRNAs to enhance pathological cancer cell fitness.
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Affiliation(s)
- Roberta Esposito
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, 80131, Naples, Italy.
| | - Andrés Lanzós
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Tina Uroda
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Sunandini Ramnarayanan
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
- The SFI Centre for Research Training in Genomics Data Science, Dublin, Ireland
| | - Isabel Büchi
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Taisia Polidori
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Hugo Guillen-Ramirez
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Ante Mihaljevic
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Bernard Mefi Merlin
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Lia Mela
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Eugenio Zoni
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Lusine Hovhannisyan
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Finn McCluggage
- School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Matúš Medo
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Giulia Basile
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Dominik F Meise
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Sandra Zwyssig
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Corina Wenger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Kyriakos Schwarz
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Adrienne Vancura
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Núria Bosch-Guiteras
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, 3012, Bern, Switzerland
| | - Álvaro Andrades
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, 18016, Spain
- Instituto de Investigación Biosanitaria, Granada, 18014, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, 18071, Spain
| | - Ai Ming Tham
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland
| | - Michaela Roemmele
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Pedro P Medina
- GENYO, Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, Granada, 18016, Spain
- Instituto de Investigación Biosanitaria, Granada, 18014, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, 18071, Spain
| | - Adrian F Ochsenbein
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Carsten Riether
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
| | - Marianna Kruithof-de Julio
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Urology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Yitzhak Zimmer
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Michaela Medová
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Radiation Oncology, Inselspital, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Deborah Stroka
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland
- Department of Visceral Surgery and Medicine, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Archa Fox
- School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
- School of Human Sciences, University of Western Australia, Crawley, WA, Australia
| | - Rory Johnson
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, 3010, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, 3008, Bern, Switzerland.
- School of Biology and Environmental Science, University College Dublin, Dublin, D04 V1W8, Ireland.
- Conway Institute for Biomolecular and Biomedical Research, University College Dublin, Dublin, D04 V1W8, Ireland.
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47
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Xu X, Ma L, Zhang X, Guo S, Guo W, Wang Y, Qiu S, Tian X, Miao Y, Yu Y, Wang J. A positive feedback circuit between RN7SK snRNA and m 6A readers is essential for tumorigenesis. Mol Ther 2023; 31:1615-1635. [PMID: 36566349 PMCID: PMC10277899 DOI: 10.1016/j.ymthe.2022.12.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 11/29/2022] [Accepted: 12/20/2022] [Indexed: 12/26/2022] Open
Abstract
N6-Methyladenosine (m6A) RNA modification, methylation at the N6 position of adenosine, plays critical roles in tumorigenesis. m6A readers recognize m6A modifications and thus act as key executors for the biological consequences of RNA methylation. However, knowledge about the regulatory mechanism(s) of m6A readers is extremely limited. In this study, RN7SK was identified as a small nuclear RNA that interacts with m6A readers. m6A readers recognized and facilitated secondary structure formation of m6A-modified RN7SK, which in turn prevented m6A reader mRNA degradation from exonucleases. Thus, a positive feedback circuit between RN7SK and m6A readers is established in tumor cells. From findings on the interaction with RN7SK, new m6A readers, such as EWS RNA binding protein 1 (EWSR1) and KH RNA binding domain containing, signal transduction-associated 1 (KHDRBS1), were identified and shown to boost Wnt/β-catenin signaling and tumorigenesis by suppressing translation of Cullin1 (CUL1). Moreover, several Food and Drug Administration-approved small molecules were demonstrated to reduce RN7SK expression and inhibit tumorigenesis. Together, these findings reveal a common regulatory mechanism of m6A readers and indicate that targeting RN7SK has strong potential for tumor treatment.
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Affiliation(s)
- Xin Xu
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Lifang Ma
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Xiao Zhang
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Susu Guo
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Wanxin Guo
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Yikun Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Shiyu Qiu
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Xiaoting Tian
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Yayou Miao
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Yongchun Yu
- Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China
| | - Jiayi Wang
- Department of Clinical Laboratory, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China; Shanghai Institute of Thoracic Oncology, Shanghai Chest Hospital, Shanghai Jiao Tong University School of Medicine, No. 241, West Huaihai Rd, Shanghai 200030, China; College of Medical Technology, Shanghai Jiao Tong University School of Medicine, No. 197, Ruijin ER Rd, Shanghai 200025, China.
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48
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Stitzinger SH, Sohrabi-Jahromi S, Söding J. Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains. NAR Genom Bioinform 2023; 5:lqad057. [PMID: 37305168 PMCID: PMC10251633 DOI: 10.1093/nargab/lqad057] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 04/24/2023] [Accepted: 05/24/2023] [Indexed: 06/13/2023] Open
Abstract
Numerous cellular processes rely on the binding of proteins with high affinity to specific sets of RNAs. Yet most RNA-binding domains display low specificity and affinity in comparison to DNA-binding domains. The best binding motif is typically only enriched by less than a factor 10 in high-throughput RNA SELEX or RNA bind-n-seq measurements. Here, we provide insight into how cooperative binding of multiple domains in RNA-binding proteins (RBPs) can boost their effective affinity and specificity orders of magnitude higher than their individual domains. We present a thermodynamic model to calculate the effective binding affinity (avidity) for idealized, sequence-specific RBPs with any number of RBDs given the affinities of their isolated domains. For seven proteins in which affinities for individual domains have been measured, the model predictions are in good agreement with measurements. The model also explains how a two-fold difference in binding site density on RNA can increase protein occupancy 10-fold. It is therefore rationalized that local clusters of binding motifs are the physiological binding targets of multi-domain RBPs.
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Affiliation(s)
- Simon H Stitzinger
- Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Salma Sohrabi-Jahromi
- Quantitative and Computational Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Johannes Söding
- To whom correspondence should be addressed. Tel: +49 551 201 2890;
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49
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Wang J, Han Y, Huang F, Tang L, Mu J, Liang Y. Diabetic macrophage small extracellular vesicles-associated miR-503/IGF1R axis regulates endothelial cell function and affects wound healing. Front Immunol 2023; 14:1104890. [PMID: 37287964 PMCID: PMC10243549 DOI: 10.3389/fimmu.2023.1104890] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/28/2023] [Indexed: 06/09/2023] Open
Abstract
Diabetic foot ulcer (DFU) is a break in the skin of the foot caused by diabetes. It is one of the most serious and debilitating complications of diabetes. The previous study suggested that dominant M1 polarization during DFU could be the leading reason behind impaired wound healing. This study concluded that macrophage M1 polarization predominates in DFU skin tissue. iNOS was increased in HG-induced M1-polarized macrophages; conversely, Arg-1 was decreased. Macrophage pellets after HG stimulation can impair endothelial cell (EC) function by inhibiting cell viability, tube formation and cell migration, indicating M1 macrophage-derived small extracellular vesicles (sEVs) -mediated HUVEC dysfunction. sEVs miR-503 was significantly upregulated in response to HG stimulation, but inhibition of miR-503 in HG-stimulated macrophages attenuated M1 macrophage-induced HUVEC dysfunction. ACO1 interacted with miR-503 and mediated the miR-503 package into sEVs. Under HG stimulation, sEVs miR-503 taken in by HUVECs targeted IGF1R in HUVECs and inhibited IGF1R expression. In HUVECs, miR-503 inhibition improved HG-caused HUVEC dysfunction, whereas IGF1R knockdown aggravated HUVEC dysfunction; IGF1R knockdown partially attenuated miR-503 inhibition effects on HUVECs. In the skin wound model in control or STZ-induced diabetic mice, miR-503-inhibited sEVs improved, whereas IGF1R knockdown further hindered wound healing. Therefore, it can be inferred from the results that the M1 macrophage-derived sEVs miR-503 targets IGF1R in HUVECs, inhibits IGF1R expression, leads to HUVEC dysfunction, and impedes wound healing in diabetic patients, while packaging miR-503 as an M1 macrophage-derived sEVs may be mediated by ACO1.
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Affiliation(s)
- Jianqiang Wang
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yuanshan Han
- Scientific Research Department, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Fang Huang
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Liuhuan Tang
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Jianfei Mu
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Ying Liang
- Molecular Nutrition Branch, National Engineering Research Center of Rice and By-Product Deep Processing/College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan, China
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50
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Hao C, Sheng Z, Wang W, Feng R, Zheng Y, Xiao Q, Zhang B. Tumor-derived exosomal miR-148b-3p mediates M2 macrophage polarization via TSC2/mTORC1 to promote breast cancer migration and invasion. Thorac Cancer 2023. [PMID: 37144254 DOI: 10.1111/1759-7714.14891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Emerging evidence has revealed that tumor-associated macrophages (TAMs) and exosomes play a crucial role in the microenvironment for tumor growth. However, the mechanisms through which exosomal miRNAs modulate TAMs and tumor development in breast cancer are not fully understood. METHODS We constructed a macrophage model and an indirect coculture system consist of breast cancer cells and macrophages. Exosomes were isolated from BC cells culture supernatant and identified by transmission electron microscopy, Western blot and Nanosight LM10 system. The expression of miR-148b-3p in exosomes was determined by qRT-PCR and the effect of exosomal miR-148b-3p on macrophage polarization was measured using qRT-PCR and ELISA. The proliferation, migration and invasion of BC cells were estimated by EdU, wound healing assay and transwell assay. We employed bioinformatics, luciferase reporter assay and Western blot to identify the target gene of miR-148b-3p. Western blot was used to clarify the mechanism of exosomal miR-148b-3p mediated the crosstalk between BC cells and M2 macrophages. RESULTS Cancer-derived exosomes could induce M2 polarization of macrophages, which promoted the migration and invasion of breast cancer cells. We found that exosomal miR-148b-3p was overexpressed in breast cancer cell-derived exosomes and correlated with lymph node metastasis, late tumor stage and worse prognosis. Upregulated miR-148b-3p expression in exosomes modulated macrophage polarization by targeting TSC2, which promoted the proliferation and might affect migration and invasion of breast cancer cells. Interestingly, we found that exosomal miR-148b-3p could induce M2 macrophage polarization via the TSC2/mTORC1 signaling pathway in breast cancer. CONCLUSION Overall, our study elucidated that miR-148b-3p could be transported by exosomes from breast cancer cells to surrounding macrophages and induced M2 polarization by targeting TSC2, providing novel insights for breast cancer therapy.
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Affiliation(s)
- Chong Hao
- Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Oncology, Maternal and Child Health Care Hospital of Zibo, Zibo, China
| | - Zhimei Sheng
- Department of Pathology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Wenhao Wang
- Department of Medical Oncology, Affiliated Hospital of Weifang Medical University, Weifang, China
| | - Ruijun Feng
- Department of Pathology, Weifang Medical University, Weifang, China
| | - Yuanhang Zheng
- Department of Pathology, Weifang Medical University, Weifang, China
| | - Qinpei Xiao
- Department of Pathology, Weifang Medical University, Weifang, China
| | - Baogang Zhang
- Department of Pathology, Affiliated Hospital of Weifang Medical University, Weifang, China
- Department of Pathology, Weifang Medical University, Weifang, China
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