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Lee NC, Tilley HH, Acle GA, McGinnis PJ, Wilson GM. Unstructured protein domains stabilize RNA binding and mediate RNA folding by AUF1. J Biol Chem 2025; 301:108442. [PMID: 40147776 DOI: 10.1016/j.jbc.2025.108442] [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: 12/28/2024] [Revised: 03/15/2025] [Accepted: 03/20/2025] [Indexed: 03/29/2025] Open
Abstract
AUF1 is an RNA-binding protein that targets AU-rich elements, cis-acting regulatory sequences commonly enriched in mRNAs encoding inflammatory mediators and oncoproteins. AUF1 post-transcriptionally regulates gene expression by modulating the stability and/or translational efficiency of mRNA targets in a context-specific manner; however, the mechanisms by which AUF1 directly engages RNA substrates and mediates regulatory outcomes remain largely unknown. The purpose of this study was to define the biochemical basis for RNA recognition by AUF1 using the smallest protein isoform (p37AUF1) as a model. AUF1 contains two tandem RNA recognition motifs (RRMs), common RNA-binding domains that stabilize the formation of many ribonucleoprotein complexes. Using quantitative fluorescence anisotropy-based assays, we observed that p37AUF1's tandem RRM domain only weakly binds AU-rich element substrates. Testing a panel of protein mutants revealed that the N- and C-terminal flanking domains each make modest but similar contributions to stabilization of both the initial RNA:protein complex and a subsequent protein-binding event. However, focused protein truncations showed that residues immediately N-terminal of the RRMs were vital for high affinity binding, but only in the context of the C-terminal domain. The C-terminal domain was also required for protein-induced RNA remodeling; both this function and its ribonucleoprotein-stabilizing role involve nonbase-specific contacts with RNA upstream of the AU-rich motif. Finally, our data suggest that the C-terminal domain is intrinsically disordered but may undergo a conformational change upon interaction with RNA ligands. Together, these findings reveal distinct roles for flanking protein domains in RNA binding and remodeling by AUF1.
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Affiliation(s)
- Nina C Lee
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Haley H Tilley
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Grace A Acle
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Patrick J McGinnis
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Gerald M Wilson
- Department of Biochemistry and Molecular Biology, Center for Biomolecular Therapeutics, and Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland, USA.
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2
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Balaraman AK, Afzal M, Moglad E, Babu MA, Priya GP, Bansal P, Rajotiya S, Kondapavuluri BK, Kazmi I, Alzarea SI, Goyal K, Ali H. The interplay of p16INK4a and non-coding RNAs: bridging cellular senescence, aging, and cancer. Biogerontology 2025; 26:50. [PMID: 39907830 DOI: 10.1007/s10522-025-10194-2] [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: 12/24/2024] [Accepted: 01/23/2025] [Indexed: 02/06/2025]
Abstract
p16INK4a is a crucial tumor suppressor and regulator of cellular senescence, forming a molecular bridge between aging and cancer. Dysregulated p16INK4a expression is linked to both premature aging and cancer progression, where non-coding RNAs (ncRNAs) such as long non-coding RNAs (lncRNAs), microRNAs (miRNAs), and small interfering RNAs (siRNAs) play key roles in modulating its function. These ncRNAs interact with p16INK4a through complex post-transcriptional and epigenetic mechanisms, influencing pathways critical to senescence and tumor suppression. In this review, we explore ncRNAs, including ANRIL, MIR31HG, UCA1, MALAT1, miR-24, miR-30, and miR-141, which collectively regulate p16INK4a expression, promoting or inhibiting pathways associated with cancer and aging. ANRIL and MIR31HG modulate p16INK4a silencing via interactions with polycomb repressive complexes (PRC), while miRNAs such as miR-24 and miR-30 target p16INK4a to influence cellular proliferation and senescence. This regulatory interplay underscores the therapeutic potential of ncRNA-targeted strategies to restore p16INK4a function. We summarize recent studies supporting that ncRNAs that control p16INK4a may be diagnostic biomarkers and therapeutic targets for age-related diseases and cancer.
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Affiliation(s)
- Ashok Kumar Balaraman
- Research and Enterprise, University of Cyberjaya, Persiaran Bestari, Cyber 11, 63000, Cyberjaya, Selangor, Malaysia
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, 21442, Jeddah, Saudi Arabia
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al Kharj, Saudi Arabia
| | - M Arockia Babu
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - G Padma Priya
- Department of Chemistry and Biochemistry, School of Sciences, JAIN (Deemed to Be University), Bangalore, Karnataka, India
| | - Pooja Bansal
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | - Sumit Rajotiya
- NIMS Institute of Pharmacy, NIMS University, Jaipur, Rajasthan, India
| | - Benod Kumar Kondapavuluri
- Department of General Surgery, Consultant Head and Neck Surgical Oncology, Dr.D.Y.Patil Medical College, Hospital and Research Centre, Pimpri, Pune, India
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Al-Jouf, Saudi Arabia
| | - Kavita Goyal
- Department of Biotechnology, Graphic Era (Deemed to Be University), Clement Town, Dehradun, 248002, India.
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, India
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Lin JY, Lin JY, Kuo RL, Huang HI. Heterogeneous nuclear ribonucleoprotein A3 binds to the internal ribosomal entry site of enterovirus A71 and affects virus replication in neural cells. J Cell Biochem 2024; 125:e30575. [PMID: 38720641 DOI: 10.1002/jcb.30575] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 12/18/2024]
Abstract
Enterovirus A71 (EV-A71) belongs to the genus Enterovirus of the Picornaviridae family and often causes outbreaks in Asia. EV-A71 infection usually causes hand, foot, and mouth disease and can even affect the central nervous system, causing neurological complications or death. The 5'-untranslated region (5'-UTR) of EV-A71 contains an internal ribosome entry site (IRES) that is responsible for the translation of viral proteins. IRES-transacting factors can interact with the EV-A71 5'-UTR to regulate IRES activity. Heterogeneous nuclear ribonucleoprotein (hnRNP) A3 is a member of the hnRNP A/B protein family of RNA-binding proteins and is involved in RNA transport and modification. We found that hnRNP A3 knockdown promoted the replication of EV-A71 in neural calls. Conversely, increasing the expression of hnRNP A3 within cells inhibits the growth of EV-A71. HnRNP A3 can bind to the EV-A71 5'-UTR, and knockdown of hnRNP A3 enhances the luciferase activity of the EV-A71 5'-UTR IRES. The localization of hnRNP A3 shifts from the nucleus to the cytoplasm of infected cells during viral infection. Additionally, EV-A71 infection can increase the protein expression of hnRNP A3, and the protein level is correlated with efficient viral growth. Based on these findings, we concluded that hnRNP A3 plays a negative regulatory role in EV-A71 replication within neural cells.
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Affiliation(s)
- Jhao-Yin Lin
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Jing-Yi Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, Taiwan
- Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Rei-Lin Kuo
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Hsing-I Huang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Department of Pediatrics, Chang Gung Memorial Hospital, Linkou, Taiwan
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4
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Sarapata K, Kania A. Revealing miRNAs patterns by employing matrix representations and energy analysis. J Mol Graph Model 2024; 132:108835. [PMID: 39106629 DOI: 10.1016/j.jmgm.2024.108835] [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: 06/24/2023] [Revised: 07/16/2024] [Accepted: 07/29/2024] [Indexed: 08/09/2024]
Abstract
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression. Despite their relatively short length (about 21 nucleotides), they can regulate thousands of transcripts within a cell. Due to their low complementarity to targets, studying their activity and binding region preferences (3'UTR, 5'UTR, or CDS) is challenging. In this paper, we analyzed a set of human miRNAs to uncover their general patterns. We began with a sequence logo to verify conservation at specific positions. To discover long-range correlations, we employed chaos game representation (CGR) and genomatrix, methods that enable both graphical and analytical analysis of sequence sets and are well-established in bioinformatics. Our results showed that miRNAs exhibit strongly non-random and characteristic patterns. To incorporate physicochemical properties into the analysis, we applied the electron-ion interaction potential (EIIP) parameter. An important part of our study was to validate the division of miRNAs into two parts-seed and puzzle. The seed region is responsible for target binding, while the puzzle region likely interacts with the RISC complex. We estimated duplex binding energy within the 3'UTR, 5'UTR, and CDS regions using the miRanda tool. Based on the median energy distribution, we divided the miRNAs into two subsets, reflecting different patterns in chaos game representation. Interestingly, one subset displayed significant similarity to conserved and highly confidential miRNAs. Our results confirm the low complementarity of miRNA/mRNA interactions and support the functional division of miRNA structure. Additionally, we present findings related to the localization of transcript target sites, which form the basis for further analyses.
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Affiliation(s)
- Krzysztof Sarapata
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland
| | - Adrian Kania
- Department of Computational Biophysics and Bioinformatics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Cracow, Poland.
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Fan G, Li D, Liu J, Tao N, Meng C, Cui J, Cai J, Sun T. HNRNPD is a prognostic biomarker in non-small cell lung cancer and affects tumor growth and metastasis via the PI3K-AKT pathway. Biotechnol Genet Eng Rev 2024; 40:1571-1590. [PMID: 36971333 DOI: 10.1080/02648725.2023.2196155] [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: 02/10/2023] [Accepted: 03/20/2023] [Indexed: 03/29/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein D (HNRNPD) can regulate expression of key proteins in various cancers. However, the prognostic predictive value and biology function of HNRNPD in non-small cell lung cancer (NSCLC) is unknown. First, we used the TCGA and GEO datasets to determine that HNRNPD predicts the prognosis of NSCLC patients. Following that, we knocked down HNRNPD in NSCLC cell lines in vitro and validated its biological function using CCK-8, transwell assays, wound healing tests, and Western blotting. Finally, we constructed tissue microarrays (TMAs) from 174 NSCLC patients and verified our findings using immunohistochemistry staining for HNRNPD from public databases. In both the public datasets, NSCLC tissues with elevated HNRNPD expression had shorter overall survival (OS). In addition, HNRNPD knockdown NSCLC cell lines showed significantly reduced proliferation, invasion, and metastatic capacity via the PI3K-AKT pathway. Finally, elevated HNRNPD expression in NSCLC TMAs was linked to a poorer prognosis and decreased PD-L1 expression levels. HNRNPD is associated with a poorer prognosis in NSCLC and affects tumor growth and metastasis via the PI3K-AKT pathway.
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Affiliation(s)
- Guoqing Fan
- Department of Respiratory Medicine and Critical Care, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Danni Li
- Department of Laboratory Medicine, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, People's Republic of China
| | - Jingjing Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Ningning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Chao Meng
- Department of Respiratory Medicine and Critical Care, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China
| | - Ju Cui
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, People's Republic of China
| | - Jianping Cai
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Science, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, People's Republic of China
| | - Tieying Sun
- Department of Respiratory Medicine and Critical Care, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School of Peking Union Medical College, Beijing, People's Republic of China
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Wang Z, Han H, Zhang C, Wu C, Di J, Xing P, Qiao X, Weng K, Hao H, Yang X, Hou Y, Jiang B, Su X. Copy number amplification-induced overexpression of lncRNA LOC101927668 facilitates colorectal cancer progression by recruiting hnRNPD to disrupt RBM47/p53/p21 signaling. J Exp Clin Cancer Res 2024; 43:274. [PMID: 39350250 PMCID: PMC11440719 DOI: 10.1186/s13046-024-03193-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Somatic copy number alterations (SCNAs) are pivotal in cancer progression and patient prognosis. Dysregulated long non-coding RNAs (lncRNAs), modulated by SCNAs, significantly impact tumorigenesis, including colorectal cancer (CRC). Nonetheless, the functional significance of lncRNAs induced by SCNAs in CRC remains largely unexplored. METHODS The dysregulated lncRNA LOC101927668, induced by copy number amplification, was identified through comprehensive bioinformatic analyses utilizing multidimensional data. Subsequent in situ hybridization was employed to ascertain the subcellular localization of LOC101927668, and gain- and loss-of-function experiments were conducted to elucidate its role in CRC progression. The downstream targets and signaling pathway influenced by LOC101927668 were identified and validated through a comprehensive approach, encompassing RNA sequencing, RT-qPCR, Western blot analysis, dual-luciferase reporter assay, evaluation of mRNA and protein degradation, and rescue experiments. Analysis of AU-rich elements (AREs) within the mRNA 3' untranslated region (UTR) of the downstream target, along with exploration of putative ARE-binding proteins, was conducted. RNA pull-down, mass spectrometry, RNA immunoprecipitation, and dual-luciferase reporter assays were employed to elucidate potential interacting proteins of LOC101927668 and further delineate the regulatory mechanism between LOC101927668 and its downstream target. Moreover, subcutaneous xenograft and orthotopic liver xenograft tumor models were utilized to evaluate the in vivo impact of LOC101927668 on CRC cells and investigate its correlation with downstream targets. RESULTS Significantly overexpressed LOC101927668, driven by chr7p22.3-p14.3 amplification, was markedly correlated with unfavorable clinical outcomes in our CRC patient cohort, as well as in TCGA and GEO datasets. Moreover, we demonstrated that enforced expression of LOC101927668 significantly enhanced cell proliferation, migration, and invasion, while its depletion impeded these processes in a p53-dependent manner. Mechanistically, nucleus-localized LOC101927668 recruited hnRNPD and translocated to the cytoplasm, accelerating the destabilization of RBM47 mRNA, a transcription factor of p53. As a nucleocytoplasmic shuttling protein, hnRNPD mediated RBM47 destabilization by binding to the ARE motif within RBM47 3'UTR, thereby suppressing the p53 signaling pathway and facilitating CRC progression. CONCLUSIONS The overexpression of LOC101927668, driven by SCNAs, facilitates CRC proliferation and metastasis by recruiting hnRNPD, thus perturbing the RBM47/p53/p21 signaling pathway. These findings underscore the pivotal roles of LOC101927668 and highlight its therapeutic potential in anti-CRC interventions.
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Affiliation(s)
- Zaozao Wang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
| | - Haibo Han
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Clinical Laboratory, Peking University Cancer Hospital and Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Chenghai Zhang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Chenxin Wu
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Jiabo Di
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Pu Xing
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xiaowen Qiao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Kai Weng
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Hao Hao
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xinying Yang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Yifan Hou
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Beihai Jiang
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China
| | - Xiangqian Su
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
- State Key Laboratory of Holistic Integrative Management of Gastrointestinal Cancers, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Gastrointestinal Surgery IV, Peking University Cancer Hospital & Institute, No.52 Fucheng Road, Haidian District, 100142, Beijing, China.
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Bakulin A, Teyssier NB, Kampmann M, Khoroshkin M, Goodarzi H. pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease. PLoS Comput Biol 2024; 20:e1012346. [PMID: 39236079 PMCID: PMC11421795 DOI: 10.1371/journal.pcbi.1012346] [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: 08/31/2023] [Revised: 09/24/2024] [Accepted: 07/22/2024] [Indexed: 09/07/2024] Open
Abstract
Inferring the driving regulatory programs from comparative analysis of gene expression data is a cornerstone of systems biology. Many computational frameworks were developed to address this problem, including our iPAGE (information-theoretic Pathway Analysis of Gene Expression) toolset that uses information theory to detect non-random patterns of expression associated with given pathways or regulons. Our recent observations, however, indicate that existing approaches are susceptible to the technical biases that are inherent to most real world annotations. To address this, we have extended our information-theoretic framework to account for specific biases and artifacts in biological networks using the concept of conditional information. To showcase pyPAGE, we performed a comprehensive analysis of regulatory perturbations that underlie the molecular etiology of Alzheimer's disease (AD). pyPAGE successfully recapitulated several known AD-associated gene expression programs. We also discovered several additional regulons whose differential activity is significantly associated with AD. We further explored how these regulators relate to pathological processes in AD through cell-type specific analysis of single cell and spatial gene expression datasets. Our findings showcase the utility of pyPAGE as a precise and reliable biomarker discovery in complex diseases such as Alzheimer's disease.
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Affiliation(s)
- Artemy Bakulin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Noam B. Teyssier
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Arc Institute, Palo Alto, California, United States of America
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8
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Liu H, Deng S, Yao X, Liu Y, Qian L, Wang Y, Zhang T, Shan G, Chen L, Zhou Y. Ascites exosomal lncRNA PLADE enhances platinum sensitivity by inducing R-loops in ovarian cancer. Oncogene 2024; 43:714-728. [PMID: 38225339 DOI: 10.1038/s41388-024-02940-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/17/2024]
Abstract
Cisplatin resistance is a major cause of therapeutic failure in patients with high-grade serous ovarian cancer (HGSOC). Long noncoding RNAs (lncRNAs) have emerged as key regulators of human cancers; however, their modes of action in HGSOC remain largely unknown. Here, we provide evidence to demonstrate that lncRNA Platinum sensitivity-related LncRNA from Ascites-Derived Exosomes (PLADE) transmitted by ascites exosomes enhance platinum sensitivity in HGSOC. PLADE exhibited significantly decreased expression in ascites exosomes and tumor tissues, as well as in the corresponding metastatic tumors from patients with HGSOC cisplatin-resistance. Moreover, HGSOC patients with higher PLADE expression levels exhibited longer progression-free survival. Gain- and loss-of-function studies have revealed that PLADE promotes cisplatin sensitivity by suppressing cell proliferation, migration and invasion, and enhancing apoptosis in vitro and in vivo. Furthermore, the functions of PLADE in increasing cisplatin sensitivity were proven to be transferred by exosomes to the cultured recipient cells and to the adjacent tumor tissues in mouse models. Mechanistically, PLADE binds to and downregulates heterogeneous nuclear ribonucleoprotein D (HNRNPD) by VHL-mediated ubiquitination, thus inducing an increased amount of RNA: DNA hybrids (R-loop) and DNA damage, consequently promoting cisplatin sensitivity in HGSOC. Collectively, these results shed light on the understanding of the vital roles of long noncoding RNAs in cancers.
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Affiliation(s)
- Hanyuan Liu
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Sisi Deng
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Xuelin Yao
- Department of Endocrinology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Lili Qian
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Yingying Wang
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Tianjiao Zhang
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China
| | - Ge Shan
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Liang Chen
- Department of Cardiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Ying Zhou
- Department of Obstetrics and Gynecology, Core Facility Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, 230001, China.
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9
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Weerakoon H, Mohamed A, Wong Y, Chen J, Senadheera B, Haigh O, Watkins TS, Kazakoff S, Mukhopadhyay P, Mulvenna J, Miles JJ, Hill MM, Lepletier A. Integrative temporal multi-omics reveals uncoupling of transcriptome and proteome during human T cell activation. NPJ Syst Biol Appl 2024; 10:21. [PMID: 38418561 PMCID: PMC10901835 DOI: 10.1038/s41540-024-00346-4] [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: 08/03/2023] [Accepted: 01/25/2024] [Indexed: 03/01/2024] Open
Abstract
Engagement of the T cell receptor (TCR) triggers molecular reprogramming leading to the acquisition of specialized effector functions by CD4 helper and CD8 cytotoxic T cells. While transcription factors, chemokines, and cytokines are known drivers in this process, the temporal proteomic and transcriptomic changes that regulate different stages of human primary T cell activation remain to be elucidated. Here, we report an integrative temporal proteomic and transcriptomic analysis of primary human CD4 and CD8 T cells following ex vivo stimulation with anti-CD3/CD28 beads, which revealed major transcriptome-proteome uncoupling. The early activation phase in both CD4 and CD8 T cells was associated with transient downregulation of the mRNA transcripts and protein of the central glucose transport GLUT1. In the proliferation phase, CD4 and CD8 T cells became transcriptionally more divergent while their proteome became more similar. In addition to the kinetics of proteome-transcriptome correlation, this study unveils selective transcriptional and translational metabolic reprogramming governing CD4 and CD8 T cell responses to TCR stimulation. This temporal transcriptome/proteome map of human T cell activation provides a reference map exploitable for future discovery of biomarkers and candidates targeting T cell responses.
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Affiliation(s)
- Harshi Weerakoon
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
- Faculty of Medicine and Allied Sciences, Rajarata University of Sri Lanka, Saliyapura, Sri Lanka
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Yide Wong
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Jinjin Chen
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | | | - Oscar Haigh
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Thomas S Watkins
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Stephen Kazakoff
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - John J Miles
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
- Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Ailin Lepletier
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia.
- Institute for Glycomics, Griffith Univeristy, Gold Coast, QLD, Australia.
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10
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Voulgareli I, Semitekolou M, Morianos I, Blizou M, Sfika M, Hillas G, Bakakos P, Loukides S. Endotyping Eosinophilic Inflammation in COPD with ELAVL1, ZfP36 and HNRNPD mRNA Genes. J Clin Med 2024; 13:854. [PMID: 38337546 PMCID: PMC10856681 DOI: 10.3390/jcm13030854] [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: 12/26/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Background: Chronic obstructive pulmonary disease (COPD) is a common disease characterized by progressive airflow obstruction, influenced by genetic and environmental factors. Eosinophils have been implicated in COPD pathogenesis, prompting the categorization into eosinophilic and non-eosinophilic endotypes. This study explores the association between eosinophilic inflammation and mRNA expression of ELAVL1, ZfP36, and HNRNPD genes, which encode HuR, TTP and AUF-1 proteins, respectively. Additionally, it investigates the expression of IL-9 and IL-33 in COPD patients with distinct eosinophilic profiles. Understanding these molecular associations could offer insights into COPD heterogeneity and provide potential therapeutic targets. Methods: We investigated 50 COPD patients, of whom 21 had eosinophilic inflammation and 29 had non-eosinophilic inflammation. Epidemiological data, comorbidities, and pulmonary function tests were recorded. Peripheral blood mononuclear cells were isolated for mRNA analysis of ELAVL1, ZfP36, and HNRNPD genes and serum cytokines (IL-9, IL-33) were measured using ELISA kits. Results: The study comprised 50 participants, with 66% being male and a mean age of 68 years (SD: 8.9 years). Analysis of ELAVL1 gene expression revealed a 0.45-fold increase in non-eosinophilic and a 3.93-fold increase in eosinophilic inflammation (p = 0.11). For the ZfP36 gene, expression was 6.19-fold higher in non-eosinophilic and 119.4-fold higher in eosinophilic groups (p = 0.07). Similarly, HNRNPD gene expression was 0.23-fold higher in non-eosinophilic and 0.72-fold higher in eosinophilic inflammation (p = 0.06). Furthermore, serum levels of IL-9 showed no statistically significant difference between the eosinophilic and non-eosinophilic group (58.03 pg/mL vs. 52.55 pg/mL, p = 0.98). Additionally, there was no significant difference in IL-33 serum levels between COPD patients with eosinophilic inflammation and those with non-eosinophilic inflammation (39.61 pg/mL vs. 37.94 pg/mL, p = 0.72). Conclusions: The data suggest a notable trend, lacking statistical significance, towards higher mRNA expression for the ZfP36 and HNRNPD genes for COPD patients with eosinophilic inflammation compared to those with non-eosinophilic inflammation.
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Affiliation(s)
- Ilektra Voulgareli
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (I.V.); (M.B.); (M.S.)
| | - Maria Semitekolou
- School of Medicine, Institute of Molecular Biology and Biotechnology, University of Crete, Foundation for Research and Technology—Hellas Voutes, 71110 Heraklion, Crete, Greece; (M.S.); (I.M.)
| | - Ioannis Morianos
- School of Medicine, Institute of Molecular Biology and Biotechnology, University of Crete, Foundation for Research and Technology—Hellas Voutes, 71110 Heraklion, Crete, Greece; (M.S.); (I.M.)
| | - Myrto Blizou
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (I.V.); (M.B.); (M.S.)
| | - Maria Sfika
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (I.V.); (M.B.); (M.S.)
| | - Georgios Hillas
- 5th Respiratory Medicine Department, “Sotiria” Chest Hospital, 11527 Athens, Greece;
| | - Petros Bakakos
- 1st Respiratory Medicine Department, “Sotiria” Chest Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece;
| | - Stelios Loukides
- 2nd Respiratory Medicine Department, “Attikon” University Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (I.V.); (M.B.); (M.S.)
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11
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Zheng H, Zhang T, Zhang J, Ning J, Fu W, Wang Y, Shi Y, Wei G, Zhang J, Chen X, Ding S. AUF1-mediated inhibition of autophagic lysosomal degradation contributes to CagA stability and Helicobacter pylori-induced inflammation. Gut Microbes 2024; 16:2382766. [PMID: 39068523 PMCID: PMC11285221 DOI: 10.1080/19490976.2024.2382766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/01/2024] [Accepted: 07/17/2024] [Indexed: 07/30/2024] Open
Abstract
CagA, a virulence factor of Helicobacter pylori (H. pylori), is known to drive inflammation in gastric epithelial cells and is typically degraded through autophagy. However, the molecular mechanism by which CagA evades autophagy-mediated degradation remains elusive. This study found that H. pylori inhibits autophagic flux by upregulating the expression of AU-rich element RNA-binding factor 1 (AUF1). We confirmed that AUF1 does not affect autophagy initiation but instead hampers lysosomal clearance, as evidenced by treatments with 3-MA, CQ and BafA1. Upregulated AUF1 stabilizes CagA protein levels by inhibiting the autolysosomal degradation of intracellular CagA in H. pylori-infected gastric epithelial cells. Knocking down AUF1 promotes CagA degradation, an effect that can be reversed by the lysosome inhibitor BafA1 and CQ. Transcriptome analysis of AUF1-knockdown gastric epithelial cells infected with H. pylori indicated that AUF1 regulates the expression of lysosomal-associated hydrolase genes, specifically CTSD, to inhibit autolysosomal degradation. Moreover, we observed that knockdown of AUF1 enhanced the stability of CTSD mRNA and identified AUF1 binding to the 3'UTR region of CTSD mRNA. AUF1-mediated downregulation of CTSD expression contributes to CagA stability, and AUF1 overexpression leads to an increase in CagA levels in exosomes, thus promoting extracellular inflammation. In clinical gastric mucosa, the expression of AUF1 and its cytoplasmic translocation are associated with H. pylori-associated gastritis, with CagA being necessary for the translocation of AUF1 into the cytoplasm. Our findings suggest that AUF1 is a novel host-positive regulator of CagA, and dysregulation of AUF1 expression increases the risk of H. pylori-associated gastritis.
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Affiliation(s)
- Huiling Zheng
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases (BZ0371), Beijing, China
| | - Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jing Zhang
- Department of Laboratory Medicine, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Jing Ning
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases (BZ0371), Beijing, China
| | - Weiwei Fu
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases (BZ0371), Beijing, China
| | - Ye Wang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases (BZ0371), Beijing, China
| | - Yanyan Shi
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, P.R. China
| | - Guochao Wei
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jing Zhang
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases (BZ0371), Beijing, China
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Shigang Ding
- Department of Gastroenterology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory for Helicobacter Pylori Infection and Upper Gastrointestinal Diseases (BZ0371), Beijing, China
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12
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Lembo S, Raimondo A, Balestrino A, Ricciardi L, Di Caprio R, Balato A, Stellato C. AUF-1 and skin inflammation: Atopic dermatitis and psoriasis. J Eur Acad Dermatol Venereol 2024; 38:e110-e112. [PMID: 37611276 DOI: 10.1111/jdv.19463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/16/2023] [Indexed: 08/25/2023]
Affiliation(s)
- Serena Lembo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Annunziata Raimondo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Alessia Balestrino
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Luca Ricciardi
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Roberta Di Caprio
- Unit of Dermatology, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Anna Balato
- Unit of Dermatology, University of Campania Luigi Vanvitelli, Naples, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
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13
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Chang S, Wang Y, Wang X, Liu H, Zhang T, Zheng Y, Wang X, Shan G, Chen L. HNRNPD regulates the biogenesis of circRNAs and the ratio of mRNAs to circRNAs for a set of genes. RNA Biol 2024; 21:1-15. [PMID: 39180763 PMCID: PMC11346550 DOI: 10.1080/15476286.2024.2386500] [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] [Revised: 04/18/2024] [Accepted: 07/25/2024] [Indexed: 08/26/2024] Open
Abstract
Exonic circular RNAs (ecircRNAs) in animal cells are generated by backsplicing, and the biogenesis of ecircRNAs is regulated by an array of RNA binding proteins (RBPs). HNRNPD is a heterogeneous nuclear ribonucleoprotein family member with both cytoplasmic and nuclear roles, and whether HNRNPD regulates the biogenesis of circRNAs remains unknown. In this study, we examine the role of HNRNPD in the biogenesis of ecircRNAs. The levels of ecircRNAs are primarily increased upon depletion of HNRNPD. HNRNPD preferentially binds to motifs enriched with A and U nucleotides, and the flanking introns of ecircRNAs tend to have more numbers and higher intensity of HNRNPD binding sites. The levels of mRNAs are generally not significantly altered in HNRNPD knockout cells. For a small set of genes, the circRNA:mRNA ratio is substantially affected, and the mRNA levels of some of these genes demonstrate a significant decrease in HNRNPD knockout cells. CDK1 is identified as a key gene modulated by HNRNPD in the context of circRNA biogenesis. HNRNPD suppresses the biogenesis of circCDK1 and favours the generation of CDK1 mRNA, and the CDK1 protein is a critical regulator of the cell cycle and apoptosis. HNRNPD can participate in cellular physiology, including the cell cycle and apoptosis, and plays roles in clear cell renal cell carcinoma (ccRCC) by modulating circRNA biogenesis and the mRNA levels of key genes, such as CDK1.
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Affiliation(s)
- Shuhui Chang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Yucong Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Xiaolin Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Hanyuan Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, China
| | - Tao Zhang
- Department of Urology, the Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yangge Zheng
- Courant Institute of Mathematical Sciences, New York University, New York, USA
| | - Xueren Wang
- Department of Anesthesiology, Shanxi Bethune Hospital, Taiyuan, China
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ge Shan
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
| | - Liang Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of USTC, The RNA Institute, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
- Department of Cardiology, The First Affiliated Hospital of USTC, The RNA Institute, Division of Life Sciences and Medicine, University of Science and Technology of China (USTC), Hefei, Anhui, China
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14
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Li J, Wang X, Shi L, Liu B, Sheng Z, Chang S, Cai X, Shan G. A Mammalian Conserved Circular RNA CircLARP1B Regulates Hepatocellular Carcinoma Metastasis and Lipid Metabolism. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305902. [PMID: 37953462 PMCID: PMC10787103 DOI: 10.1002/advs.202305902] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/14/2023] [Indexed: 11/14/2023]
Abstract
Circular RNAs (circRNAs) have emerged as crucial regulators in physiology and human diseases. However, evolutionarily conserved circRNAs with potent functions in cancers are rarely reported. In this study, a mammalian conserved circRNA circLARP1B is identified to play critical roles in hepatocellular carcinoma (HCC). Patients with high circLARP1B levels have advanced prognostic stage and poor overall survival. CircLARP1B facilitates cellular metastatic properties and lipid accumulation through promoting fatty acid synthesis in HCC. CircLARP1B deficient mice exhibit reduced metastasis and less lipid accumulation in an induced HCC model. Multiple lines of evidence demonstrate that circLARP1B binds to heterogeneous nuclear ribonucleoprotein D (HNRNPD) in the cytoplasm, and thus affects the binding of HNRNPD to sensitive transcripts including liver kinase B1 (LKB1) mRNA. This regulation causes decreased LKB1 mRNA stability and lower LKB1 protein levels. Antisense oligodeoxynucleotide complementary to theHNRNPD binding sites in circLARP1B increases the HNRNPD binding to LKB1 mRNA. Through the HNRNPD-LKB1-AMPK pathway, circLARP1B promotes HCC metastasis and lipid accumulation. Results from AAV8-mediated hepatocyte-directed knockdown of circLARP1B or Lkb1 in mouse models also demonstrate critical roles of hepatocytic circLARP1B regulatory pathway in HCC metastasis and lipid accumulation, and indicate that circLARP1B may be potential target of HCC treatment.
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Affiliation(s)
- Jingxin Li
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Xiaolin Wang
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Liang Shi
- Department of General SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Boqiang Liu
- Department of General SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Zhiyong Sheng
- School of Life ScienceBengbu Medical CollegeBengbu233030China
| | - Shuhui Chang
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
| | - Xiujun Cai
- Department of General SurgerySir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
| | - Ge Shan
- Department of Laboratory MedicineThe First Affiliated Hospital of USTCThe CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefei230027China
- Department of Pulmonary and Critical Care MedicineRegional Medical Center for National Institute of Respiratory DiseasesSir Run Run Shaw HospitalSchool of MedicineZhejiang UniversityHangzhou310016China
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15
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Soueid DM, Garner AL. Adaptation of RiPCA for the Live-Cell Detection of mRNA-Protein Interactions. Biochemistry 2023; 62:3323-3336. [PMID: 37963240 PMCID: PMC11466511 DOI: 10.1021/acs.biochem.3c00334] [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] [Indexed: 11/16/2023]
Abstract
RNA-binding proteins (RBPs) act as essential regulators of cell fate decisions, through their ability to bind and regulate the activity of cellular RNAs. For protein-coding mRNAs, RBPs control the localization, stability, degradation, and ultimately translation of mRNAs to impact gene expression. Disruption of the vast network of mRNA-protein interactions has been implicated in many human diseases, and accordingly, targeting these interactions has surfaced as a new frontier in RNA-targeted drug discovery. To catalyze this new field, methods are needed to enable the detection and subsequent screening of mRNA-RBP interactions, particularly in live cells. Using our laboratory's RNA-interaction with Protein-mediated Complementation Assay (RiPCA) technology, herein we describe its application to mRNA-protein interactions and present a guide for the development of future RiPCA assays for structurally diverse classes of mRNA-protein interactions.
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Affiliation(s)
- Dalia M. Soueid
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Amanda L. Garner
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109, United States
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16
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Vyavahare S, Kumar S, Smith K, Mendhe B, Zhong R, Cooley MA, Baban B, Isales CM, Hamrick M, Hill WD, Fulzele S. Inhibiting MicroRNA-141-3p Improves Musculoskeletal Health in Aged Mice. Aging Dis 2023; 14:2303-2316. [PMID: 37199586 PMCID: PMC10676793 DOI: 10.14336/ad.2023.0310-1] [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: 11/07/2022] [Accepted: 03/10/2023] [Indexed: 05/19/2023] Open
Abstract
Emerging evidence shows that the microRNA-141-3p is involved in various age-related pathologies. Previously, our group and others reported elevated levels of miR-141-3p in several tissues and organs with age. Here, we inhibited the expression of miR-141-3p using antagomir (Anti-miR-141-3p) in aged mice and explored its role in healthy aging. We analyzed serum (cytokine profiling), spleen (immune profiling), and overall musculoskeletal phenotype. We found decreased levels of pro-inflammatory cytokines (such as TNF-α, IL-1β, IFN-γ) in serum with Anti-miR-141-3p treatment. The flow-cytometry analysis on splenocytes revealed decreased M1 (pro-inflammatory) and increased M2 (anti-inflammatory) populations. We also found improved bone microstructure and muscle fiber size with Anti-miR-141-3p treatment. Molecular analysis revealed that miR-141-3p regulates the expression of AU-rich RNA-binding factor 1 (AUF1) and promotes senescence (p21, p16) and pro-inflammatory (TNF-α, IL-1β, IFN-γ) environment whereas inhibiting miR-141-3p prevents these effects. Furthermore, we demonstrated that the expression of FOXO-1 transcription factor was reduced with Anti-miR-141-3p and elevated with silencing of AUF1 (siRNA-AUF1), suggesting crosstalk between miR-141-3p and FOXO-1. Overall, our proof-of-concept study demonstrates that inhibiting miR-141-3p could be a potential strategy to improve immune, bone, and muscle health with age.
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Affiliation(s)
- Sagar Vyavahare
- Department of Cell biology and Anatomy, Augusta University, Augusta, GA, USA.
| | - Sandeep Kumar
- Department of Cell biology and Anatomy, Augusta University, Augusta, GA, USA.
| | - Kathryn Smith
- Department of Physiology & Cell Biology, University of Arkansas for Medical Sciences, Arkansas, USA.
| | - Bharati Mendhe
- Department of Cell biology and Anatomy, Augusta University, Augusta, GA, USA.
| | - Roger Zhong
- Department of Neuroscience and Regenerative Medicine, Augusta, GA, USA.
| | - Marion A. Cooley
- Department of Oral Biology and Diagnostic Sciences, Augusta University, Augusta, GA, USA.
| | - Babak Baban
- Department of Oral Biology and Diagnostic Sciences, Augusta University, Augusta, GA, USA.
| | - Carlos M. Isales
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
- Department of Neuroscience and Regenerative Medicine, Augusta, GA, USA.
| | - Mark Hamrick
- Department of Cell biology and Anatomy, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
| | - William D Hill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, SC 29403, USA.
| | - Sadanand Fulzele
- Department of Cell biology and Anatomy, Augusta University, Augusta, GA, USA.
- Department of Medicine, Augusta University, Augusta, GA, USA.
- Center for Healthy Aging, Augusta University, Augusta, GA, USA.
- Department of Neuroscience and Regenerative Medicine, Augusta, GA, USA.
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17
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Jena MK, Khan FB, Ali SA, Abdullah A, Sharma AK, Yadav V, Kancharla S, Kolli P, Mandadapu G, Sahoo AK, Rath PK, Taneera J, Kumar S, Mohanty AK, Goh KW, Ming LC, Ardianto C. Molecular complexity of mammary glands development: a review of lactogenic differentiation in epithelial cells. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2023; 51:491-508. [PMID: 37694522 DOI: 10.1080/21691401.2023.2252872] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 07/31/2023] [Accepted: 08/07/2023] [Indexed: 09/12/2023]
Abstract
The mammary gland is a dynamic organ with various physiological processes like cellular proliferation, differentiation, and apoptosis during the pregnancy-lactation-involution cycle. It is essential to understand the molecular changes during the lactogenic differentiation of mammary epithelial cells (MECs, the milk-synthesizing cells). The MECs are organized as luminal milk-secreting cells and basal myoepithelial cells (responsible for milk ejection by contraction) that form the alveoli. The branching morphogenesis and lactogenic differentiation of the MECs prepare the gland for lactation. This process is governed by many molecular mediators including hormones, growth factors, cytokines, miRNAs, regulatory proteins, etc. Interestingly, various signalling pathways guide lactation and understanding these molecular transitions from pregnancy to lactation will help researchers design further research. Manipulation of genes responsible for milk synthesis and secretion will promote augmentation of milk yield in dairy animals. Identifying protein signatures of lactation will help develop strategies for persistent lactation and shortening the dry period in farm animals. The present review article discusses in details the physiological and molecular changes occurring during lactogenic differentiation of MECs and the associated hormones, regulatory proteins, miRNAs, and signalling pathways. An in-depth knowledge of the molecular events will aid in developing engineered cellular models for studies related to mammary gland diseases of humans and animals.
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Affiliation(s)
- Manoj Kumar Jena
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Farheen Badrealam Khan
- Department of Biology, College of Arts and Science, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Syed Azmal Ali
- Division of Proteomics of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Abdullah Abdullah
- Department of Pharmacy, University of Malakand, Chakdara, Dir Lower, Pakistan
| | - Amarish Kumar Sharma
- Department of Biotechnology, School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Vikas Yadav
- Department of Translational Medicine, Clinical Research Centre, Skane University Hospital, Lund University, Malmo, Sweden
| | | | | | | | - Anjan Kumar Sahoo
- Department of Veterinary Surgery and Radiology, College of Veterinary Science and AH, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Prasana Kumar Rath
- Department of Veterinary Pathology, College of Veterinary Science and AH, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, India
| | - Jalal Taneera
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
- Department of Basic Sciences, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Sudarshan Kumar
- Proteomics and Structural Biology Lab, Animal Biotechnology Centre, National Dairy Research Institute, Karnal, Haryana, India
| | | | - Khang Wen Goh
- Faculty Data Science and Information Technology, INTI International University, Nilai, Malaysia
| | - Long Chiau Ming
- School of Medical and Life Sciences, Sunway University, Sunway City, Malaysia
- PAPRSB Institute of Health Sciences, Universiti Brunei Darussalam, Gadong, Brunei
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
| | - Chrismawan Ardianto
- Department of Pharmacy Practice, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
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18
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Goswami B, Nag S, Ray PS. Fates and functions of RNA-binding proteins under stress. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023:e1825. [PMID: 38014833 DOI: 10.1002/wrna.1825] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 10/03/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
Exposure to stress activates a well-orchestrated set of changes in gene expression programs that allow the cell to cope with and adapt to the stress, or undergo programmed cell death. RNA-protein interactions, mediating all aspects of post-transcriptional regulation of gene expression, play crucial roles in cellular stress responses. RNA-binding proteins (RBPs), which interact with sequence/structural elements in RNAs to control the steps of RNA metabolism, have therefore emerged as central regulators of post-transcriptional responses to stress. Following exposure to a variety of stresses, the dynamic alterations in the RNA-protein interactome enable cells to respond to intracellular or extracellular perturbations by causing changes in mRNA splicing, polyadenylation, stability, translation, and localization. As RBPs play a central role in determining the cellular proteome both qualitatively and quantitatively, it has become increasingly evident that their abundance, availability, and functions are also highly regulated in response to stress. Exposure to stress initiates a series of signaling cascades that converge on post-translational modifications (PTMs) of RBPs, resulting in changes in their subcellular localization, association with stress granules, extracellular export, proteasomal degradation, and RNA-binding activities. These alterations in the fate and function of RBPs directly impact their post-transcriptional regulatory roles in cells under stress. Adopting the ubiquitous RBP HuR as a prototype, three scenarios illustrating the changes in nuclear-cytoplasmic localization, RNA-binding activity, export and degradation of HuR in response to inflammation, genotoxic stress, and heat shock depict the complex and interlinked regulatory mechanisms that control the fate and functions of RBPs under stress. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohanpur, West Bengal, India
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19
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Lu J, Ru J, Chen Y, Ling Z, Liu H, Ding B, Jiang Y, Ma J, Zhang D, Ge J, Li Y, Sun F, Chen D, Zheng S, Wu J. N 6 -methyladenosine-modified circSTX6 promotes hepatocellular carcinoma progression by regulating the HNRNPD/ATF3 axis and encoding a 144 amino acid polypeptide. Clin Transl Med 2023; 13:e1451. [PMID: 37877357 PMCID: PMC10599281 DOI: 10.1002/ctm2.1451] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 09/24/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) play a significant role in the initiation and progression of various cancers, including hepatocellular carcinoma (HCC). Circular syntaxin 6 (circSTX6, also known as hsa_circ_0007905) has been identified as a microRNA (miRNA) sponge in pancreatic adenocarcinoma. However, its full range of functions in terms of protein scaffold and translation remain largely unexplored in the context of HCC. METHODS The expression of circSTX6 and its encoded protein was examined in HCC tumour tissues. N6 -methyladenosine (m6 A) on circSTX6 was verified and quantified by methylated RNA immunoprecipitation (Me-RIP), RIP and dual luciferase reporter assays. The biological functions of circSTX6 and its encoded protein in HCC were clarified by in vitro and in vivo experiments. Mechanistically, the interaction between circSTX6 and heterogeneous nuclear ribonucleoprotein D (HNRNPD) was investigated by RNA pull-down, RIP and fluorescence in situ hybridization (FISH)/IF. The regulatory effects of circSTX6 and HNRNPD on activating transcription factor 3 (ATF3) mRNA were determined by mRNA stability and RIP assays. Furthermore, the presence of circSTX6-encoded protein was verified by mass spectrometry. RESULTS CircSTX6 and its encoded 144 amino acid polypeptide, circSTX6-144aa, were highly expressed in HCC tumour tissues and served as independent risk factors for overall survival in HCC patients. The expression of circSTX6 was regulated by METTL14 in an m6 A-dependent manner. Functionally, circSTX6 accelerated HCC proliferation and tumourigenicity and reinforced tumour metastasis in vitro and in vivo. Mechanistically, circSTX6 acted as a sponge for HNRNPD protein, facilitating its binding to ATF3 mRNA, consequently promoting ATF3 mRNA decay. Meanwhile, circSTX6-144aa promoted HCC proliferation, migration and invasion independent of circSTX6 itself. CONCLUSION Collectively, our study reveals that m6 A-modified circSTX6 drives malignancy in HCC through the HNRNPD/ATF3 axis, while its encoded circSTX6-144aa contributes to HCC progression independent of circSTX6. CirSTX6 and its encoded protein hold promise as potential biomarkers and therapeutic targets in HCC.
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20
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Li Z, Wei H, Hu D, Li X, Guo Y, Ding X, Guo H, Zhang L. Research Progress on the Structural and Functional Roles of hnRNPs in Muscle Development. Biomolecules 2023; 13:1434. [PMID: 37892116 PMCID: PMC10604023 DOI: 10.3390/biom13101434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are a superfamily of RNA-binding proteins consisting of more than 20 members. These proteins play a crucial role in various biological processes by regulating RNA splicing, transcription, and translation through their binding to RNA. In the context of muscle development and regeneration, hnRNPs are involved in a wide range of regulatory mechanisms, including alternative splicing, transcription regulation, miRNA regulation, and mRNA stability regulation. Recent studies have also suggested a potential association between hnRNPs and muscle-related diseases. In this report, we provide an overview of our current understanding of how hnRNPs regulate RNA metabolism and emphasize the significance of the key members of the hnRNP family in muscle development. Furthermore, we explore the relationship between the hnRNP family and muscle-related diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Linlin Zhang
- Key Laboratory of Animal Breeding and Healthy Livestock Farming, College of Animal Science and Veterinary Medicine, Tianjin Agricultural University, Tianjin 300392, China; (Z.L.); (H.W.); (D.H.); (X.L.); (Y.G.); (X.D.); (H.G.)
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21
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Liu Q, Zhu D, Li N, Chen S, Hu L, Yu J, Xiong Y. Regulation of LRRK2 mRNA stability by ATIC and its substrate AICAR through ARE-mediated mRNA decay in Parkinson's disease. EMBO J 2023; 42:e113410. [PMID: 37366237 PMCID: PMC10390876 DOI: 10.15252/embj.2022113410] [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: 12/28/2022] [Revised: 05/08/2023] [Accepted: 05/15/2023] [Indexed: 06/28/2023] Open
Abstract
Mutations in LRRK2 are the most common genetic causes of Parkinson's disease (PD). While the enzymatic activity of LRRK2 has been linked to PD, previous work has also provided support for an important role of elevated LRRK2 protein levels, independent of enzymatic activity, in PD pathogenesis. However, the mechanisms underlying the regulation of LRRK2 protein levels remain unclear. Here, we identify a role for the purine biosynthesis pathway enzyme ATIC in the regulation of LRRK2 levels and toxicity. AICAr, the precursor of ATIC substrate, regulates LRRK2 levels in a cell-type-specific manner in vitro and in mouse tissue. AICAr regulates LRRK2 levels through AUF1-mediated mRNA decay. Upon AICAr treatment, the RNA binding protein AUF1 is recruited to the AU-rich elements (ARE) of LRRK2 mRNA leading to the recruitment of the decapping enzyme complex DCP1/2 and decay of LRRK2 mRNA. AICAr suppresses LRRK2 expression and rescues LRRK2-induced dopaminergic neurodegeneration and neuroinflammation in PD Drosophila and mouse models. Together, this study provides insight into a novel regulatory mechanism of LRRK2 protein levels and function via LRRK2 mRNA decay that is distinct from LRRK2 enzymatic functions.
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Affiliation(s)
- Qinfang Liu
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
| | - Dong Zhu
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
| | - Naren Li
- Department of Physiology & NeurobiologyUniversity of ConnecticutStorrsCTUSA
| | - Shifan Chen
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
| | - Liang Hu
- Department of Physiology & NeurobiologyUniversity of ConnecticutStorrsCTUSA
| | - Jianzhong Yu
- Department of Physiology & NeurobiologyUniversity of ConnecticutStorrsCTUSA
| | - Yulan Xiong
- Department of NeuroscienceUniversity of Connecticut School of MedicineFarmingtonCTUSA
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22
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Udupa P, Shrikondawar AN, Nayak SS, Shah H, Ranjan A, Girisha KM, Bhavani GS, Ghosh DK. Deep intronic mutation in CRTAP results in unstable isoforms of the protein to induce type I collagen aggregation in a lethal type of osteogenesis imperfecta type VII. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166741. [PMID: 37146916 PMCID: PMC7616376 DOI: 10.1016/j.bbadis.2023.166741] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023]
Abstract
Genetic mutations are involved in Mendelian disorders. Unbuffered intronic mutations in gene variants can generate aberrant splice sites in mutant transcripts, resulting in mutant isoforms of proteins with modulated expression, stability, and function in diseased cells. Here, we identify a deep intronic variant, c.794_1403A>G, in CRTAP by genome sequencing of a male fetus with osteogenesis imperfecta (OI) type VII. The mutation introduces cryptic splice sites in intron-3 of CRTAP, resulting in two mature mutant transcripts with cryptic exons. While transcript-1 translates to a truncated isoform (277 amino acids) with thirteen C-terminal non-wild-type amino acids, transcript-2 translates to a wild-type protein sequence, except that this isoform contains an in-frame fusion of non-wild-type twenty-five amino acids in a tetratricopeptide repeat sequence. Both mutant isoforms of CRTAP are unstable due to the presence of a unique 'GWxxI' degron, which finally leads to loss of proline hydroxylation and aggregation of type I collagen. Although type I collagen aggregates undergo autophagy, the overall proteotoxicity resulted in death of the proband cells by senescence. In summary, we present a genetic disease pathomechanism by linking a novel deep intronic mutation in CRTAP to unstable mutant isoforms of the protein in lethal OI type VII.
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Affiliation(s)
- Prajna Udupa
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Akshaykumar Nanaji Shrikondawar
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India
| | - Shalini S Nayak
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Hitesh Shah
- Department of Pediatric Orthopedics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India
| | - Akash Ranjan
- Computational and Functional Genomics Group, Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, Telangana, India
| | - Katta M Girisha
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India; Department of Genetics, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat, Sultanate of Oman
| | - Gandham SriLakshmi Bhavani
- Department of Medical Genetics, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
| | - Debasish Kumar Ghosh
- Enteric Disease Division, Department of Microbiology, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, Karnataka 576104, India.
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23
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Cao J, Kuyumcu-Martinez MN. Alternative polyadenylation regulation in cardiac development and cardiovascular disease. Cardiovasc Res 2023; 119:1324-1335. [PMID: 36657944 PMCID: PMC10262186 DOI: 10.1093/cvr/cvad014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/01/2022] [Accepted: 11/28/2022] [Indexed: 01/21/2023] Open
Abstract
Cleavage and polyadenylation of pre-mRNAs is a necessary step for gene expression and function. Majority of human genes exhibit multiple polyadenylation sites, which can be alternatively used to generate different mRNA isoforms from a single gene. Alternative polyadenylation (APA) of pre-mRNAs is important for the proteome and transcriptome landscape. APA is tightly regulated during development and contributes to tissue-specific gene regulation. Mis-regulation of APA is linked to a wide range of pathological conditions. APA-mediated gene regulation in the heart is emerging as a new area of research. Here, we will discuss the impact of APA on gene regulation during heart development and in cardiovascular diseases. First, we will briefly review how APA impacts gene regulation and discuss molecular mechanisms that control APA. Then, we will address APA regulation during heart development and its dysregulation in cardiovascular diseases. Finally, we will discuss pre-mRNA targeting strategies to correct aberrant APA patterns of essential genes for the treatment or prevention of cardiovascular diseases. The RNA field is blooming due to advancements in RNA-based technologies. RNA-based vaccines and therapies are becoming the new line of effective and safe approaches for the treatment and prevention of human diseases. Overall, this review will be influential for understanding gene regulation at the RNA level via APA in the heart and will help design RNA-based tools for the treatment of cardiovascular diseases in the future.
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Affiliation(s)
- Jun Cao
- Faculty of Environment and Life, Beijing University of Technology, Xueyuan Road, Haidian District, Beijing 100124, PR China
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
- Department of Neurobiology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Institute for Translational Sciences, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77573, USA
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24
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Deng S, Qian L, Liu L, Liu H, Xu Z, Liu Y, Wang Y, Chen L, Zhou Y. Circular RNA ARHGAP5 inhibits cisplatin resistance in cervical squamous cell carcinoma by interacting with AUF1. Cancer Sci 2023; 114:1582-1595. [PMID: 36632741 PMCID: PMC10067438 DOI: 10.1111/cas.15723] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Cervical squamous cell carcinoma (CSCC) is one of the leading causes of cancer death in women worldwide. Patients with advanced cervical carcinoma always have a poor prognosis once resistant to cisplatin due to the lack of effective treatment. It is urgent to investigate the molecular mechanisms of cisplatin resistance. Circular RNAs (circRNAs) are known to exert their regulatory functions in a series of malignancies. However, their effects on CSCC remain to be elucidated. Here, we found that cytoplasmic circARHGAP5, derived from second and third exons of the ARHGAP5 gene, was downregulated in cisplatin-resistant tissues compared with normal cervix tissues and untreated cervical cancer tissues. In addition, experiments from overexpression/knockdown cell lines revealed that circARHGAP5 could inhibit cisplatin-mediated cell apoptosis in CSCC cells both in vitro and in vivo. Mechanistically, circARHGAP5 interacted with AU-rich element RNA-binding protein (AUF1) directly. Overexpression of AUF1 could also inhibit cell apoptosis mediated by cisplatin. Furthermore, we detected the potential targets of AUF1 related to the apoptotic pathway and found that bcl-2-like protein 11 (BIM) was not only negatively regulated by AUF1 but positively regulated by circARHGAP5, which indicated that BIM mRNA might be degraded by AUF1 and thereby inhibited tumor cell apoptosis. Collectively, our data indicated that circARHGAP5 directly bound to AUF1 and prevented AUF1 from interacting with BIM mRNA, thereby playing a pivotal role in cisplatin resistance in CSCC. Our study provides insights into overcoming cancer resistance to cisplatin treatment.
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Affiliation(s)
- Sisi Deng
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Lili Qian
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Luwen Liu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Hanyuan Liu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Zhihao Xu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Yujie Liu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Yingying Wang
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Liang Chen
- Department of Clinical LaboratoryThe First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Ying Zhou
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
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25
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Blatnik MC, Gallagher TL, Amacher SL. Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1751. [PMID: 35851751 PMCID: PMC9840655 DOI: 10.1002/wrna.1751] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 01/31/2023]
Abstract
Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.
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Affiliation(s)
- Monica C. Blatnik
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Thomas L. Gallagher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Sharon L. Amacher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
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26
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Das O, Kundu J, Ghosh A, Gautam A, Ghosh S, Chakraborty M, Masid A, Gauri SS, Mitra D, Dutta M, Mukherjee B, Sinha S, Bhaumik M. AUF-1 knockdown in mice undermines gut microbial butyrate-driven hypocholesterolemia through AUF-1-Dicer-1-mir-122 hierarchy. Front Cell Infect Microbiol 2022; 12:1011386. [PMID: 36601302 PMCID: PMC9806232 DOI: 10.3389/fcimb.2022.1011386] [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: 08/04/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022] Open
Abstract
Introduction and objective Cholesterol homeostasis is a culmination of cellular synthesis, efflux, and catabolism to important physiological entities where short chain fatty acid, butyrate embodied as a key player. This discourse probes the mechanistic molecular details of butyrate action in maintaining host-cholesterol balance. Methods Hepatic mir-122 being the most indispensable regulator of cholesterol metabolic enzymes, we studied upstream players of mir-122 biogenesis in the presence and absence of butyrate in Huh7 cells and mice model. We synthesized unique self-transfecting GMO (guanidinium-morpholino-oligo) linked PMO (Phosphorodiamidate-Morpholino Oligo)-based antisense cell-penetrating reagent to selectively knock down the key player in butyrate mediated cholesterol regulation. Results We showed that butyrate treatment caused upregulation of RNA-binding protein, AUF1 resulting in RNase-III nuclease, Dicer1 instability, and significant diminution of mir-122. We proved the importance of AUF1 and sequential downstream players in AUF1-knock-down mice. Injection of GMO-PMO of AUF1 in mouse caused near absence of AUF1 coupled with increased Dicer1 and mir-122, and reduced serum cholesterol regardless of butyrate treatment indicating that butyrate acts through AUF1. Conclusion The roster of intracellular players was as follows: AUF1-Dicer1-mir-122 for triggering butyrate driven hypocholesterolemia. To our knowledge this is the first report linking AUF-1 with cholesterol biogenesis.
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Affiliation(s)
- Oishika Das
- Department of Immunology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Jayanta Kundu
- School of Applied and Interdisciplinary Sciences, Indian Associations for Cultivation of Science, Kolkata, India
| | - Atanu Ghosh
- School of Applied and Interdisciplinary Sciences, Indian Associations for Cultivation of Science, Kolkata, India
| | - Anupam Gautam
- Department of Algorithms in Bioinformatics, Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany,International Max Planck Research School “From Molecules to Organisms”, Max Planck Institute for Biology Tübingen, Tübingen, Germany,Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, University of Tübingen, Tübingen, Germany
| | - Souradeepa Ghosh
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, India
| | - Mainak Chakraborty
- Department of Immunology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Aaheli Masid
- Department of Immunology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Samiran Sona Gauri
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, India
| | - Debmalya Mitra
- Department of Immunology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Moumita Dutta
- Department of Immunology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Budhaditya Mukherjee
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur, India
| | - Surajit Sinha
- School of Applied and Interdisciplinary Sciences, Indian Associations for Cultivation of Science, Kolkata, India
| | - Moumita Bhaumik
- Department of Immunology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, India,*Correspondence: Moumita Bhaumik,
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Li W, Deng X, Chen J. RNA-binding proteins in regulating mRNA stability and translation: roles and mechanisms in cancer. Semin Cancer Biol 2022; 86:664-677. [PMID: 35381329 PMCID: PMC9526761 DOI: 10.1016/j.semcancer.2022.03.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/25/2022] [Accepted: 03/30/2022] [Indexed: 01/10/2023]
Abstract
RNA-binding proteins (RBPs) are key players in cellular physiology through posttranscriptional regulation of the expression of target RNA transcripts. By modulating the processing, stability and translation of cancer-related messenger RNA (mRNA) transcripts, a large set of RBPs play essential roles in various types of cancers. Perturbations in RBP activity have been causally associated with cancer development, tumor metabolism, drug resistance, cancer stem cell self-renewal, and tumor immune evasion. Here, we summarize the recent advances in cancer pathological roles and mechanisms of RBPs in regulating mRNA stability and translation with an emphasis on the emerging category of RNA modification-associated RBPs. The functional diversity of RBPs in different types of cancers and the therapeutic potential of targeting dysregulated RBPs for cancer treatment are also discussed.
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Affiliation(s)
- Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia 91016, USA; City of Hope Comprehensive Cancer Center, Duarte, CA 91010, USA; Gehr Family Center for Leukemia Research, City of Hope, Duarte, CA 91010, USA.
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28
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Hahm JY, Park J, Jang ES, Chi SW. 8-Oxoguanine: from oxidative damage to epigenetic and epitranscriptional modification. Exp Mol Med 2022; 54:1626-1642. [PMID: 36266447 PMCID: PMC9636213 DOI: 10.1038/s12276-022-00822-z] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/06/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022] Open
Abstract
In pathophysiology, reactive oxygen species control diverse cellular phenotypes by oxidizing biomolecules. Among these, the guanine base in nucleic acids is the most vulnerable to producing 8-oxoguanine, which can pair with adenine. Because of this feature, 8-oxoguanine in DNA (8-oxo-dG) induces a G > T (C > A) mutation in cancers, which can be deleterious and thus actively repaired by DNA repair pathways. 8-Oxoguanine in RNA (o8G) causes problems in aberrant quality and translational fidelity, thereby it is subjected to the RNA decay pathway. In addition to oxidative damage, 8-oxo-dG serves as an epigenetic modification that affects transcriptional regulatory elements and other epigenetic modifications. With the ability of o8G•A in base pairing, o8G alters structural and functional RNA-RNA interactions, enabling redirection of posttranscriptional regulation. Here, we address the production, regulation, and function of 8-oxo-dG and o8G under oxidative stress. Primarily, we focus on the epigenetic and epitranscriptional roles of 8-oxoguanine, which highlights the significance of oxidative modification in redox-mediated control of gene expression.
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Affiliation(s)
- Ja Young Hahm
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Jongyeun Park
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Eun-Sook Jang
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea
| | - Sung Wook Chi
- grid.222754.40000 0001 0840 2678Department of Life Sciences, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678Institute of Life Sciences and Biotechnology, Korea University, Seoul, 02481 Republic of Korea ,grid.222754.40000 0001 0840 2678KU-KIST Graduate School of Converging Science and Technology, Korea University, Seoul, 02481 Republic of Korea
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Cleavage of AUF1 by Coxsackievirus B Affects DDX5 Regulatory on Viral Replication through iTRAQ Proteomics Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:8610467. [PMID: 36246972 PMCID: PMC9560859 DOI: 10.1155/2022/8610467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/09/2022] [Indexed: 11/18/2022]
Abstract
Coxsackievirus B (CVB) 3C protease (3Cpro) plays a specific cleavage role on AU-rich binding factor (AUF1, also called hnRNP D), which consequently disputes the regulation of AUF1 on downstream molecules. In our study, the iTRAQ approach was first used to quantify the differentially expressed cellular proteins in AUF1-overexpressing HeLa cells, which provides straightforward insight into the role of AUF1 during viral infection. A total of 1,290 differentially expressed proteins (DEPs), including 882 upregulated and 408 downregulated proteins, were identified. The DEPs are involved in a variety of cellular processes via GO terms, protein–protein interactions, and a series of further bioinformatics analyses. Among the DEPs, some demonstrated important roles in cellular metabolism. In particular, DDX5 was further verified to be negatively regulated by AUF1 and increased in CVB-infected cells, which in turn promoted CVB replication. These findings provide potential novel ideas for exploring new antiviral therapy targets.
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Wang J, Sun D, Wang M, Cheng A, Zhu Y, Mao S, Ou X, Zhao X, Huang J, Gao Q, Zhang S, Yang Q, Wu Y, Zhu D, Jia R, Chen S, Liu M. Multiple functions of heterogeneous nuclear ribonucleoproteins in the positive single-stranded RNA virus life cycle. Front Immunol 2022; 13:989298. [PMID: 36119073 PMCID: PMC9478383 DOI: 10.3389/fimmu.2022.989298] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/12/2022] [Indexed: 11/13/2022] Open
Abstract
The heterogeneous nuclear ribonucleoproteins (hnRNPs) are a diverse family of RNA binding proteins that are implicated in RNA metabolism, such as alternative splicing, mRNA stabilization and translational regulation. According to their different cellular localization, hnRNPs display multiple functions. Most hnRNPs were predominantly located in the nucleus, but some of them could redistribute to the cytoplasm during virus infection. HnRNPs consist of different domains and motifs that enable these proteins to recognize predetermined nucleotide sequences. In the virus-host interactions, hnRNPs specifically bind to viral RNA or proteins. And some of the viral protein-hnRNP interactions require the viral RNA or other host factors as the intermediate. Through various mechanisms, hnRNPs could regulate viral translation, viral genome replication, the switch of translation to replication and virion release. This review highlights the common features and the distinguish roles of hnRNPs in the life cycle of positive single-stranded RNA viruses.
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Affiliation(s)
- Jingming Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- *Correspondence: Anchun Cheng,
| | - Yukun Zhu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xuming Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Dekang Zhu
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu City, China
- Avian Disease Research Center, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu City, China
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Rajasekaran S, Khan E, Ching SR, Khan M, Siddiqui J, Gradia DF, Lin C, Bouley SJ, Mercadante D, Manning AL, Gerber AP, Walker J, Miles W. PUMILIO competes with AUF1 to control DICER1 RNA levels and miRNA processing. Nucleic Acids Res 2022; 50:7048-7066. [PMID: 35736218 PMCID: PMC9262620 DOI: 10.1093/nar/gkac499] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/27/2022] [Indexed: 12/24/2022] Open
Abstract
DICER1 syndrome is a cancer pre-disposition disorder caused by mutations that disrupt the function of DICER1 in miRNA processing. Studying the molecular, cellular and oncogenic effects of these mutations can reveal novel mechanisms that control cell homeostasis and tumor biology. Here, we conduct the first analysis of pathogenic DICER1 syndrome allele from the DICER1 3'UTR. We find that the DICER1 syndrome allele, rs1252940486, abolishes interaction with the PUMILIO RNA binding protein with the DICER1 3'UTR, resulting in the degradation of the DICER1 mRNA by AUF1. This single mutational event leads to diminished DICER1 mRNA and protein levels, and widespread reprogramming of miRNA networks. The in-depth characterization of the rs1252940486 DICER1 allele, reveals important post-transcriptional regulatory events that control DICER1 levels.
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Affiliation(s)
- Swetha Rajasekaran
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Eshan Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Samuel R Ching
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Misbah Khan
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Jalal K Siddiqui
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Daniela F Gradia
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
- Department of Genetics, Federal University of Parana, Curitiba, Brazil
| | - Chenyu Lin
- Department of Cancer Biology and Genetics, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, 460 West 12th Avenue, Columbus, OH 43210, USA
| | - Stephanie J Bouley
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dayna L Mercadante
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - Amity L Manning
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, 100 Institute Road, Worcester, MA 01609, USA
| | - André P Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, UK
| | - James A Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Wayne O Miles
- To whom correspondence should be addressed. Tel: +1 614 366 2869;
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Evaluation of Heterogeneous Nuclear Ribonucleoprotein D Expression as a Diagnostic Marker for Oral Squamous Cell Carcinoma. Diagnostics (Basel) 2022; 12:diagnostics12061332. [PMID: 35741145 PMCID: PMC9221583 DOI: 10.3390/diagnostics12061332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/13/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
The heterogeneous nuclear ribonucleoprotein D (hnRNPD) serves as a prognostic marker for oral squamous cell carcinoma (OSCC). We evaluated the diagnostic potential of hnRNPD to differentiate between OSCC and normal mucosa. Immunohistochemistry for hnRNPD and a routinely used diagnostic marker deltaNp63 (p40) was performed in 32 normal mucosae and 46 OSCC specimens. Subsequently, receiver-operating characteristic analysis was performed to evaluate the diagnostic potential of hnRNPD in comparison to that of p40. Immunostaining for p40 and hnRNPD was observed in 39 (84.78%) and 38 (82.60%) cases, respectively, in OSCC specimens. The poorly differentiated squamous cell carcinoma displayed 100% (eight cases) immunoreactivity for hnRNPD as compared to 87.5% (seven cases) for p40. Nuclear staining of p40 and hnRNPD was observed in all OSCC specimens. p40 staining was restricted to basal cells, whereas both basal and para-basal cells displayed hnRNPD staining in OSCC specimens. Areas under the curve for p40 and hnRNPD were 0.86 and 0.87, respectively. p40 and hnRNPD showed equal sensitivities (80.95%). However, hnRNPD displayed marginally higher (88.23%) specificity for tumor cells as compared to that of p40 (85.29%). Conclusion: In addition to being a well-established prognostic marker, hnRNPD can serve as a diagnostic marker for OSCC.
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A Novel Strategy for Regulating mRNA's Degradation via Interfering the AUF1's Binding to mRNA. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27103182. [PMID: 35630659 PMCID: PMC9143527 DOI: 10.3390/molecules27103182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/25/2022]
Abstract
The study on the mechanism and kinetics of mRNA degradation provides a new vision for chemical intervention on protein expression. The AU enrichment element (ARE) in mRNA 3′-UTR can be recognized and bound by the ARE binding protein (AU-rich Element factor (AUF1) to recruit RNase for degradation. In the present study, we proposed a novel strategy for expression regulation that interferes with the AUF1-RNA binding. A small-molecule compound, JNJ-7706621, was found to bind AUF1 protein and inhibit mRNA degradation by screening the commercial compound library. We discovered that JNJ-7706621 could inhibit the expression of AUF1 targeted gene IL8, an essential pro-inflammatory factor, by interfering with the mRNA homeostatic state. These studies provide innovative drug design strategies to regulate mRNA homeostasis.
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Kumar V, Kumar A, Kumar M, Lone MR, Mishra D, Chauhan SS. NFκB (RelA) mediates transactivation of hnRNPD in oral cancer cells. Sci Rep 2022; 12:5944. [PMID: 35396527 PMCID: PMC8993925 DOI: 10.1038/s41598-022-09963-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 03/25/2022] [Indexed: 11/09/2022] Open
Abstract
Heterogeneous Ribonucleoprotein D (hnRNPD) is an RNA binding protein involved in post-transcriptional regulation of multiple mediators of carcinogenesis. We previously demonstrated a strong association of hnRNPD over expression with poor outcome in Oral Squamous Cell Carcinoma (OSCC). However, hitherto the precise molecular mechanism of its overexpression in oral cancer was not clear. Therefore, in an attempt to elucidate the transcriptional regulation of hnRNPD expression, we cloned 1406 bp of 5ʹ flanking region of human hnRNPD gene along with 257 bp of its first exon upstream to promoterless luciferase reporter gene in pGL3-Basic. Transfection of the resulting construct in SCC-4 cells yielded 1271 fold higher luciferase activity over parent vector. By promoter deletion analysis, we identified a canonical TATA box containing 126 bp core promoter region that retained ~ 58% activity of the full length promoter. In silico analysis revealed the presence of four putative NFκB binding motifs in the promoter. Sequential deletion of these motifs from the full-length promoter reporter construct coupled with luciferase assays revealed an 82% decrease in promoter activity after deletion of the first (−1358/−1347) motif and 99% reduction after the deletion of second motif (−1052/−1041). In-vivo binding of NFκB (RelA) to these two motifs in SCC-4 cells was confirmed by ChIP assays. Site directed mutagenesis of even one of these two motifs completely abolished promoter activity, while mutagenesis of the remaining two motifs had marginal effect on the same. Consistent with these findings, treatment of SCC-4 cells with PDTC, a known inhibitor of NFκB dramatically reduced the levels hnRNPD mRNA and protein. Finally, the expression of hnRNPD and NFκB in clinical specimen from 37 oral cancer patients was assessed and subjected to Spearmen’s Correlation analysis which revealed a strong positive correlation between the two. Thus, results of the present study for the first time convincingly demonstrate NFκB (RelA) mediated transcriptional upregulation of hnRNPD expression in oral cancer.
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Affiliation(s)
- Vikas Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Anurag Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Manish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences, Bilaspur, India
| | - Moien Rasheed Lone
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Deepika Mishra
- Division of Oral Pathology, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Shyam Singh Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India.
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Cai H, Zheng D, Yao Y, Yang L, Huang X, Wang L. Roles of Embryonic Lethal Abnormal Vision-Like RNA Binding Proteins in Cancer and Beyond. Front Cell Dev Biol 2022; 10:847761. [PMID: 35465324 PMCID: PMC9019298 DOI: 10.3389/fcell.2022.847761] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 03/04/2022] [Indexed: 12/31/2022] Open
Abstract
Embryonic lethal abnormal vision-like (ELAVL) proteins are RNA binding proteins that were originally discovered as indispensable regulators of the development and functioning of the nervous system. Subsequent studies have shown that ELAVL proteins not only exist in the nervous system, but also have regulatory effects in other tissues. ELAVL proteins have attracted attention as potential therapeutic targets because they stabilize multiple mRNAs by binding within the 3′-untranslated region and thus promote the development of tumors, including hepatocellular carcinoma, pancreatic cancer, ovarian cancer, breast cancer, colorectal carcinoma and lung cancer. Previous studies have focused on these important relationships with downstream mRNAs, but emerging studies suggest that ELAVL proteins also interact with non-coding RNAs. In this review, we will summarize the relationship of the ELAVL protein family with mRNA and non-coding RNA and the roles of ELAVL protein family members in a variety of physiological and pathological processes.
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Affiliation(s)
| | | | | | - Lehe Yang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Xiaoying Huang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
| | - Liangxing Wang
- *Correspondence: Lehe Yang, ; Xiaoying Huang, ; Liangxing Wang,
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circDlgap4 Alleviates Cerebral Ischaemic Injury by Binding to AUF1 to Suppress Oxidative Stress and Neuroinflammation. Mol Neurobiol 2022; 59:3218-3232. [PMID: 35294732 DOI: 10.1007/s12035-022-02796-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
Ischaemic stroke is one of the most common causes of mortality and morbidity.circDlgap4 has been implicated in ischemia/reperfusion injury through an unknown mechanism. Here, we studied the function of circDlgap4/AUF1 in ischaemic stroke and its underlying molecular mechanism. N2a cells and primary mouse cortical neurons were subjected to OGD to mimic neuronal injury during ischemia. BV-2 cells were treated with LPS to mimic neuroinflammation. The MTT assay was used to assess cell viability, while flow cytometry was used to measure cell apoptosis. qRT-PCR, western blotting, immunohistochemistry, and immunostaining were employed to determine the levels of circDlgap4, AUF1, NRF2/HO-1, proinflammatory cytokines, NF-κB pathway-related proteins, and IBA-1. RIP and RNA pulldown assays were employed to validate the interactions of circDlgap4/AUF1, AUF1/NRF2, and AUF1/cytokine mRNAs. mRNA degradation was used to determine the effects on mRNA stability. The tMCAO model was used as an in vivo model of ischaemic stroke. TCC staining and neurological scoring were performed to evaluate ischaemic injury. circDlgap4 was decreased following OGD and during tMCAO. circDlgap4 overexpression inhibited OGD-induced cell death and oxidative stress and LPS-induced increases in proinflammatory cytokines by increasing NRF2/HO-1. Knockdown of AUF1 blocked the effects of circDlgap4 overexpression. Mechanistically, RIP, RNA pulldown, and mRNA degradation assay results showed circDlgap4/AUF1/NRF2 mRNA formed a complex to stabilize NRF2 mRNA. Furthermore, AUF1 directly interacted with TNF-α, IL-1β, and COX-2 mRNAs, and circDlgap4/AUF1 binding promoted the degradation of these mRNAs. Finally, circDlgap4 ameliorated ischaemic injury in vivo. circDlgap4 alleviates ischaemic stroke injury by suppressing oxidative stress and neuroinflammation by binding to AUF1.
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Pitolli C, Marini A, Sette C, Pagliarini V. Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer. Int J Mol Sci 2022; 23:ijms23052811. [PMID: 35269953 PMCID: PMC8911335 DOI: 10.3390/ijms23052811] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Alberto Marini
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
- Correspondence:
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Cui X, Hao C, Gong L, Kajitani N, Schwartz S. HnRNP D activates production of HPV16 E1 and E6 mRNAs by promoting intron retention. Nucleic Acids Res 2022; 50:2782-2806. [PMID: 35234917 PMCID: PMC8934624 DOI: 10.1093/nar/gkac132] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/26/2022] [Accepted: 02/11/2022] [Indexed: 12/13/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) E1 and E6 proteins are produced from mRNAs with retained introns, but it has been unclear how these mRNAs are generated. Here, we report that hnRNP D act as a splicing inhibitor of HPV16 E1/E2- and E6/E7-mRNAs thereby generating intron-containing E1- and E6-mRNAs, respectively. N- and C-termini of hnRNP D contributed to HPV16 mRNA splicing control differently. HnRNP D interacted with the components of splicing machinery and with HPV16 RNA to exert its inhibitory function. As a result, the cytoplasmic levels of intron-retained HPV16 mRNAs were increased in the presence of hnRNP D. Association of hnRNP D with HPV16 mRNAs in the cytoplasm was observed, and this may correlate with unexpected inhibition of HPV16 E1- and E6-mRNA translation. Notably, hnRNP D40 interacted with HPV16 mRNAs in an HPV16-driven tonsillar cancer cell line and in HPV16-immortalized human keratinocytes. Furthermore, knockdown of hnRNP D in HPV16-driven cervical cancer cells enhanced production of the HPV16 E7 oncoprotein. Our results suggest that hnRNP D plays significant roles in the regulation of HPV gene expression and HPV-associated cancer development.
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Affiliation(s)
- Xiaoxu Cui
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Chengyu Hao
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden
| | - Lijing Gong
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,China Institute of Sport and Health Sciences, Beijing Sport University, Haidian District, Beijing 100084, China
| | - Naoko Kajitani
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
| | - Stefan Schwartz
- Department of Laboratory Medicine, Lund University, BMC-B13, 221 84 Lund, Sweden.,Department of Medical Biochemistry and Microbiology (IMBIM), Uppsala University, BMC-B9, 751 23 Uppsala, Sweden
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Powell G, Pavlovic Djuranovic S, Djuranovic S. Gene dosage effects of poly(A) track-engineered hypomorphs. MOLECULAR THERAPY-NUCLEIC ACIDS 2021; 26:865-878. [PMID: 34729253 PMCID: PMC8536507 DOI: 10.1016/j.omtn.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/29/2021] [Accepted: 10/01/2021] [Indexed: 11/18/2022]
Abstract
Manipulation of gene activity through creation of hypomorphic mutants has been a long-standing tool in examining gene function. Our previous studies have indicated that hypomorphic mutants could be created by inserting cis-regulatory sequences composed of consecutive adenosine nucleotides called poly(A) tracks. Here we use poly(A) tracks to create hypomorphic mutants and functional characterization of membrane, secretory, and endogenous proteins. Insertion of poly(A) tracks into the sequences of interleukin-2 and membrane protein CD20 results in a programmable reduction of mRNA stability and attenuation of protein expression regardless of the presence of a signaling sequence. Likewise, CRISPR-Cas9 targeted insertion of poly(A) tracks into the coding sequence of the endogenous human genes AUF1 and TP53 results in a programmable reduction of targeted protein and mRNA levels. Functional analyses of AUF1-engineered hypomorphs indicate a direct correlation between AUF1 gene levels and the stability of AUF1-regulated mRNAs. Hypomorphs of TP53 affect expression of the target genes differentially depending on the severity of the hypomorphic mutation. Finally, decreases in TP53 protein affect the same cellular pathways in poly(A) track-engineered cells as in cancer cells, indicating these variants’ biological relevance. These results highlight this technology’s power to create predictable, stable hypomorphs in recombinant or endogenous genes in combination with CRISPR-Cas9 engineering tools.
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Affiliation(s)
- Geralle Powell
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Slavica Pavlovic Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
| | - Sergej Djuranovic
- Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA
- Correspondence: Sergej Djuranovic, Department of Cell Biology and Physiology, Washington University School of Medicine, 600 South Euclid Avenue, Campus Box 8228, St. Louis, MO 63110, USA.
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Aloufi N, Alluli A, Eidelman DH, Baglole CJ. Aberrant Post-Transcriptional Regulation of Protein Expression in the Development of Chronic Obstructive Pulmonary Disease. Int J Mol Sci 2021; 22:ijms222111963. [PMID: 34769392 PMCID: PMC8584689 DOI: 10.3390/ijms222111963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/25/2021] [Accepted: 10/28/2021] [Indexed: 02/07/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is an incurable and prevalent respiratory disorder that is characterized by chronic inflammation and emphysema. COPD is primarily caused by cigarette smoke (CS). CS alters numerous cellular processes, including the post-transcriptional regulation of mRNAs. The identification of RNA-binding proteins (RBPs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs) as main factors engaged in the regulation of RNA biology opens the door to understanding their role in coordinating physiological cellular processes. Dysregulation of post-transcriptional regulation by foreign particles in CS may lead to the development of diseases such as COPD. Here we review current knowledge about post-transcriptional events that may be involved in the pathogenesis of COPD.
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Affiliation(s)
- Noof Aloufi
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
- Department of Medical Laboratory Technology, Applied Medical Science, Taibah University, Universities Road, Medina P.O. Box 344, Saudi Arabia
| | - Aeshah Alluli
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
| | - David H. Eidelman
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada;
| | - Carolyn J. Baglole
- Department of Pathology, McGill University, Montreal, QC H3A 2B4, Canada; (N.A.); (A.A.)
- Department of Medicine, McGill University, Montreal, QC H4A 3J1, Canada;
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC H3G 1Y6, Canada
- Correspondence:
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Li S, Yang P. Relationship between HSPA1A-regulated gene expression and alternative splicing in mouse cardiomyocytes and cardiac hypertrophy. J Thorac Dis 2021; 13:5517-5533. [PMID: 34659818 PMCID: PMC8482330 DOI: 10.21037/jtd-21-1222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 08/30/2021] [Indexed: 11/30/2022]
Abstract
Background Cardiac hypertrophy may be classified as either physiological or pathological. Pathological hypertrophy has a complex etiology and is genetically regulated. In this study, we used a mouse model of cardiac hypertrophy to explore the mechanisms of gene regulation, in particular, modulation of the expression of target genes through transcription factor activity, regulation of immune and inflammation-associated genes and regulation of the alternative splicing of transcription factors. Methods Mouse models of pathological cardiac hypertrophy were established by transverse aortic constriction (TAC). We overexpressed HSPA1A in mouse cardiac HL-1 cells. GO and KEGG pathway annotation database was used to analyze all DEGs. Results The expression of HSPA1A differed significantly between TAC + dantrolene vs. sham + dantrolene (Sham was the non-TAC group, and DMSO was the contrast agent), and TAC + DMSO vs. sham + DMSO. The RNA-binding protein Zfp36 was found to be differentially expressed between both TAC + dantrolene vs. sham + dantrolene and TAC + DMSO vs. sham + DMSO. The expression of mki67 and gm5619 was significantly different between TAC + dantrolene and TAC + DMSO. HSPA1A was found to selectively regulate the expression of non-coding RNAs related to cardiac hypertrophy, including Rn7sk and RMRP. The downregulated genes were mainly related to inflammation and the immune response. HSPA1A negatively regulated alternative splicing of Asxl2 and positively regulated alternative splicing of Runx1. Conclusions HSPA1A was closely related to cardiac hypertrophy. Zfp36 was also related to cardiac hypertrophy. Dantrolene may delay cardiac hypertrophy and ventricular remodeling by regulating the expression of the RNA-binding protein genes mki67 and gm5619. HSPA1A positively regulated the expression of the non-coding RNAs RN7SK and RMRP while negatively regulating the expression of inflammation- and immune response-related genes. HSPA1A can play a role in cardiac hypertrophy by regulating the alternative splicing of asxl2 and runx1.
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Affiliation(s)
- Shuai Li
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Ping Yang
- Jilin Provincial Precision Medicine Key Laboratory for Cardiovascular Genetic Diagnosis, Department of Cardiology, China-Japan Union Hospital of Jilin University, Changchun, China
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English AM, Green KM, Moon SL. A (dis)integrated stress response: Genetic diseases of eIF2α regulators. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1689. [PMID: 34463036 DOI: 10.1002/wrna.1689] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 01/28/2023]
Abstract
The integrated stress response (ISR) is a conserved mechanism by which eukaryotic cells remodel gene expression to adapt to intrinsic and extrinsic stressors rapidly and reversibly. The ISR is initiated when stress-activated protein kinases phosphorylate the major translation initiation factor eukaryotic translation initiation factor 2ɑ (eIF2ɑ), which globally suppresses translation initiation activity and permits the selective translation of stress-induced genes including important transcription factors such as activating transcription factor 4 (ATF4). Translationally repressed messenger RNAs (mRNAs) and noncoding RNAs assemble into cytoplasmic RNA-protein granules and polyadenylated RNAs are concomitantly stabilized. Thus, regulated changes in mRNA translation, stability, and localization to RNA-protein granules contribute to the reprogramming of gene expression that defines the ISR. We discuss fundamental mechanisms of RNA regulation during the ISR and provide an overview of a growing class of genetic disorders associated with mutant alleles of key translation factors in the ISR pathway. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease Translation > Translation Regulation RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Alyssa M English
- Department of Human Genetics, Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Katelyn M Green
- Department of Chemistry, Department of Human Genetics, Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie L Moon
- Department of Human Genetics, Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, USA
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Du X, Wang JM, Zhang DL, Wu T, Zeng XY, Jiang JY, Du ZX. AUF1 Promotes Proliferation and Invasion of Thyroid Cancer via Downregulation of ZBTB2 and Subsequent TRIM58. Front Oncol 2021; 11:681736. [PMID: 34222000 PMCID: PMC8242192 DOI: 10.3389/fonc.2021.681736] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/27/2021] [Indexed: 12/02/2022] Open
Abstract
The pathogenesis of papillary thyroid cancer (PTC), the most common type of thyroid cancer, is not yet fully understood. This limits the therapeutic options for approximately 7% of invasive PTC patients. The critical role of AUF1 in the progression of thyroid cancer was first reported in 2009, however, its molecular mechanism remained unclear. Our study used CRISPR/Cas 9 system to knockdown AUF1 in IHH4 and TPC1 cells. We noticed that the expression of TRIM58 and ZBTB2 were increased in the AUF1 knockdown IHH4 and TPC1 cells. When TRIM58 and ZBTB2 were inhibited by small hairpin RNAs (shRNAs) against TRIM58 (shTRIM58) and ZBTB2 (shZBTB2), respectively, the proliferation, migration, and invasion ability of the AUF1-knockdown IHH4 and TPC1 cells were increased. In addition, two ZBTB2 binding sites (-719~-709 and -677~-668) on TRIM58 promoter and two AUF1 binding sites (1250-1256 and 1258-1265) on ZBTB2 3’-UTR were identified. These results suggested that AUF1 affecting thyroid cancer cells via regulating the expression of ZBTB2 and TRIM58.
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Affiliation(s)
- Xin Du
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jia-Mei Wang
- Department of Laboratory Medicine, The First Affiliated hospital of China Medical University, Shenyang, China
| | - Da-Lin Zhang
- Department of Thyroid Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Tong Wu
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Xiao-Yan Zeng
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of China Medical University, Shenyang, China
| | - Jing-Yi Jiang
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, China
| | - Zhen-Xian Du
- Department of Endocrinology and Metabolism, The First Affiliated Hospital of China Medical University, Shenyang, China
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Tsitsipatis D, Grammatikakis I, Driscoll RK, Yang X, Abdelmohsen K, Harris SC, Yang JH, Herman AB, Chang MW, Munk R, Martindale JL, Mazan-Mamczarz K, De S, Lal A, Gorospe M. AUF1 ligand circPCNX reduces cell proliferation by competing with p21 mRNA to increase p21 production. Nucleic Acids Res 2021; 49:1631-1646. [PMID: 33444453 PMCID: PMC7897478 DOI: 10.1093/nar/gkaa1246] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/28/2020] [Accepted: 12/11/2020] [Indexed: 01/06/2023] Open
Abstract
Mammalian circRNAs can influence different cellular processes by interacting with proteins and other nucleic acids. Here, we used ribonucleoprotein immunoprecipitation (RIP) analysis to identify systematically the circRNAs associated with the cancer-related protein AUF1. Among the circRNAs interacting with AUF1 in HeLa (human cervical carcinoma) cells, we focused on hsa_circ_0032434 (circPCNX), an abundant target of AUF1. Overexpression of circPCNX specifically interfered with the binding of AUF1 to p21 (CDKN1A) mRNA, thereby promoting p21 mRNA stability and elevating the production of p21, a major inhibitor of cell proliferation. Conversely, silencing circPCNX increased AUF1 binding to p21 mRNA, reducing p21 production and promoting cell division. Importantly, eliminating the AUF1-binding region of circPCNX abrogated the rise in p21 levels and rescued proliferation. Therefore, we propose that the interaction of circPCNX with AUF1 selectively prevents AUF1 binding to p21 mRNA, leading to enhanced p21 mRNA stability and p21 protein production, thereby suppressing cell growth.
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Affiliation(s)
- Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Ioannis Grammatikakis
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute IRP, NIH, Bethesda, MD, USA
| | - Riley K Driscoll
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Sophia C Harris
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Allison B Herman
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Ming-Wen Chang
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Supriyo De
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute IRP, NIH, Bethesda, MD, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging (NIA) Intramural Research Program (IRP), National Institutes of Health (NIH), Baltimore, MD, USA
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Oe S, Koike T, Hirahara Y, Tanaka S, Hayashi S, Nakano Y, Kase M, Noda Y, Yamada H, Kitada M. AUF1, an mRNA decay factor, has a discordant role in Cpeb1 expression. Biochem Biophys Res Commun 2020; 534:491-497. [PMID: 33220927 DOI: 10.1016/j.bbrc.2020.11.054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 11/12/2020] [Indexed: 12/19/2022]
Abstract
Cytoplasmic polyadenylation element binding protein 1 (CPEB1) regulates polyadenylation and subsequent translation of CPE-containing mRNAs involved in various physiological and pathological phenomena. Although the significance of CPEB1-mediated translational regulation has recently been reported, the detailed regulatory mechanism of Cpeb1 expression remains unclear. To elucidate the post-transcriptional regulatory mechanisms of Cpeb1 expression, we constructed reporter plasmids containing various deletions or mutations in the Cpeb1 mRNA 3' untranslated region (3'UTR). We investigated their expression levels in Neuro2a neuroblastoma cells. We found that Cpeb1 expression is regulated through an AU-rich element in its 3'UTR. Furthermore, the mRNA decay factor AU-rich binding factor 1 (AUF1) regulates Cpeb1 expression, and knockdown of AUF1 upregulates Cpeb1 mRNA expression but results in a decrease in CPEB1 protein levels. These findings indicate that AUF1 has a discordant role in the expression of Cpeb1.
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Affiliation(s)
- Souichi Oe
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan.
| | - Taro Koike
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Yukie Hirahara
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Susumu Tanaka
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Shinichi Hayashi
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Yosuke Nakano
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Masahiko Kase
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
| | - Yasuko Noda
- Department of Anatomy, Bio-imaging and Neuro-cell Science, Jichi Medical University, Shimotsuke, Tochigi, 329-0498, Japan
| | - Hisao Yamada
- Biwako Professional University of Rehabilitation, Higashi-Ohmi, Shiga, 527-0145, Japan
| | - Masaaki Kitada
- Department of Anatomy, Kansai Medical University, Hirakata, Osaka, 573-1010, Japan
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Qin Y, Li L, Luo E, Hou J, Yan G, Wang D, Qiao Y, Tang C. Role of m6A RNA methylation in cardiovascular disease (Review). Int J Mol Med 2020; 46:1958-1972. [PMID: 33125109 PMCID: PMC7595665 DOI: 10.3892/ijmm.2020.4746] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 09/29/2020] [Indexed: 02/07/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent and abundant type of internal post-transcriptional RNA modification in eukaryotic cells. Multiple types of RNA, including mRNAs, rRNAs, tRNAs, long non-coding RNAs and microRNAs, are involved in m6A methylation. The biological function of m6A modification is dynamically and reversibly mediated by methyltransferases (writers), demethylases (erasers) and m6A binding proteins (readers). The methyltransferase complex is responsible for the catalyzation of m6A modification and is typically made up of methyltransferase-like (METTL)3, METTL14 and Wilms tumor 1-associated protein. Erasers remove methylation by fat mass and obesity-associated protein and ALKB homolog 5. Readers play a role through the recognition of m6A-modified targeted RNA. The YT521-B homology domain family, heterogeneous nuclear ribonucleoprotein and insulin-like growth factor 2 mRNA-binding protein serve as m6A readers. The m6A methylation on transcripts plays a pivotal role in the regulation of downstream molecular events and biological functions, such as RNA splicing, transport, stability and translatability at the post-transcriptional level. The dysregulation of m6A modification is associated with cancer, drug resistance, virus replication and the pluripotency of embryonic stem cells. Recently, a number of studies have identified aberrant m6A methylation in cardiovascular diseases (CVDs), including cardiac hypertrophy, heart failure, arterial aneurysm, vascular calcification and pulmonary hypertension. The aim of the present review article was to summarize the recent research progress on the role of m6A modification in CVD and give a brief perspective on its prospective applications in CVD.
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Affiliation(s)
- Yuhan Qin
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Linqing Li
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Erfei Luo
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Jiantong Hou
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Gaoliang Yan
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Dong Wang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Yong Qiao
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Chengchun Tang
- Department of Cardiology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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Tian XY, Li J, Liu TH, Li DN, Wang JJ, Zhang H, Deng ZL, Chen FJ, Cai JP. The overexpression of AUF1 in colorectal cancer predicts a poor prognosis and promotes cancer progression by activating ERK and AKT pathways. Cancer Med 2020; 9:8612-8623. [PMID: 33016643 PMCID: PMC7666750 DOI: 10.1002/cam4.3464] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 01/09/2023] Open
Abstract
Background AUF1 is one of the AU‐rich binding proteins, which promotes rapid ARE‐mRNA degradation. Recently, it has been reported that AUF1 is involved in regulating the antioxidant system because of its capacity to bind specifically to RNA containing oxidized bases and degrade oxidized RNA. Many antioxidant proteins have been reported to be overexpressed in colorectal cancer (CRC), however, the role of AUF1 in the progression of CRC has not been explored. Methods The expression level of AUF1 protein in human CRC cell lines and CRC tissues was detected by western blotting and immunohistochemistry (IHC. The effects of AUF1 knockdown on CRC cell proliferation, migration, invasion and changes in the signaling pathways were evaluated using a cell counting kit‐8 (CCK‐8), Transwell assays and western blotting. Subcutaneous xenograft tumor model was employed to further substantiate the role of AUF1 in CRC. Results AUF1 protein was upregulated in CRC tissues and CRC cells, and high expression of AUF1 was significantly associated with advanced AJCC stage (P = .001), lymph node metastasis (P = .007), distant metastasis (P = .038) and differentiation (P = .009) of CRC specimens. CRC patients with the high expression of AUF1 had an extremely poor prognosis. The knockdown of AUF1 suppressed CRC cell line proliferation, migration and invasion, inhibited CRC cells tumorigenesis and growth in nude mice, and reduced phosphorylated‐ERK1/2 and phosphorylated AKT in CRC cells. Conclusion Our findings demonstrate that AUF1 is probably involved in the progression of CRC via the activation of the ERK1/2 and AKT pathways. AU‐rich RNA‐binding factor 1 could be used as a novel prognostic biomarker and a potential therapeutic target for CRC.
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Affiliation(s)
- Xin-Yuan Tian
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jin Li
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Teng-Hui Liu
- The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
| | - Dan-Ni Li
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - Jing-Jing Wang
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China
| | - He Zhang
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Zhou-Lu Deng
- Department of General Surgery, China-Japan Friendship Hospital, Beijing, P.R. China
| | - Fu-Jun Chen
- Department of Anorectal Surgery, First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, P.R. China
| | - Jian-Ping Cai
- Peking University Fifth School of Clinical Medicine, Beijing Hospital, Beijing, P.R. China.,The MOH Key Laboratory of Geriatrics, Beijing Hospital, National Center of Gerontology, Beijing, P.R. China
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Davila-Calderon J, Patwardhan NN, Chiu LY, Sugarman A, Cai Z, Penutmutchu SR, Li ML, Brewer G, Hargrove AE, Tolbert BS. IRES-targeting small molecule inhibits enterovirus 71 replication via allosteric stabilization of a ternary complex. Nat Commun 2020; 11:4775. [PMID: 32963221 PMCID: PMC7508794 DOI: 10.1038/s41467-020-18594-3] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
Enterovirus 71 (EV71) poses serious threats to human health, particularly in Southeast Asia, and no drugs or vaccines are available. Previous work identified the stem loop II structure of the EV71 internal ribosomal entry site as vital to viral translation and a potential target. After screening an RNA-biased library using a peptide-displacement assay, we identify DMA-135 as a dose-dependent inhibitor of viral translation and replication with no significant toxicity in cell-based studies. Structural, biophysical, and biochemical characterization support an allosteric mechanism in which DMA-135 induces a conformational change in the RNA structure that stabilizes a ternary complex with the AUF1 protein, thus repressing translation. This mechanism is supported by pull-down experiments in cell culture. These detailed studies establish enterovirus RNA structures as promising drug targets while revealing an approach and mechanism of action that should be broadly applicable to functional RNA targeting. Human enterovirus 71 (EV71) contains an internal ribosome entry site (IRES) that promotes translation of viral RNA. Here the authors show that an antiviral small molecule DMA-135 binds to the EV71 IRES RNA, inducing conformational change and stabilizing a ternary complex to repress translation.
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Affiliation(s)
| | | | - Liang-Yuan Chiu
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Andrew Sugarman
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA
| | - Zhengguo Cai
- Department of Chemistry, Duke University, Durham, NC, USA
| | | | - Mei-Ling Li
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Gary Brewer
- Department of Biochemistry and Molecular Biology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA.
| | | | - Blanton S Tolbert
- Department of Chemistry, Case Western Reserve University, Cleveland, OH, USA.
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mRNA Post-Transcriptional Regulation by AU-Rich Element-Binding Proteins in Liver Inflammation and Cancer. Int J Mol Sci 2020; 21:ijms21186648. [PMID: 32932781 PMCID: PMC7554771 DOI: 10.3390/ijms21186648] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/12/2022] Open
Abstract
AU-rich element-binding proteins (AUBPs) represent important post-transcriptional regulators of gene expression. AUBPs can bind to the AU-rich elements present in the 3'-UTR of more than 8% of all mRNAs and are thereby able to control the stability and/or translation of numerous target mRNAs. The regulation of the stability and the translation of mRNA transcripts by AUBPs are highly complex processes that occur through multiple mechanisms depending on the cell type and the cellular context. While AUBPs have been shown to be involved in inflammatory processes and the development of various cancers, their important role and function in the development of chronic metabolic and inflammatory fatty liver diseases (FLDs), as well as in the progression of these disorders toward cancers such as hepatocellular carcinoma (HCC), has recently started to emerge. Alterations of either the expression or activity of AUBPs are indeed significantly associated with FLDs and HCC, and accumulating evidence indicates that several AUBPs are deeply involved in a significant number of cellular processes governing hepatic metabolic disorders, inflammation, fibrosis, and carcinogenesis. Herein, we discuss our current knowledge of the roles and functions of AUBPs in liver diseases and cancer. The relevance of AUBPs as potential biomarkers for different stages of FLD and HCC, or as therapeutic targets for these diseases, are also highlighted.
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